From noreply at r-forge.r-project.org Wed Mar 7 16:46:30 2018
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Wed, 7 Mar 2018 16:46:30 +0100 (CET)
Subject: [CHNOSZ-commits] r306 - in pkg/CHNOSZ: . R inst inst/extdata/Berman
inst/extdata/Berman/unused man
Message-ID: <20180307154630.A7E1F1892F8@r-forge.r-project.org>
Author: jedick
Date: 2018-03-07 16:46:30 +0100 (Wed, 07 Mar 2018)
New Revision: 306
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/R/berman.R
pkg/CHNOSZ/inst/NEWS
pkg/CHNOSZ/inst/extdata/Berman/BDat17.csv
pkg/CHNOSZ/inst/extdata/Berman/Ber88.csv
pkg/CHNOSZ/inst/extdata/Berman/Ber90.csv
pkg/CHNOSZ/inst/extdata/Berman/DS10.csv
pkg/CHNOSZ/inst/extdata/Berman/FDM+14.csv
pkg/CHNOSZ/inst/extdata/Berman/JUN92.csv
pkg/CHNOSZ/inst/extdata/Berman/SHD91.csv
pkg/CHNOSZ/inst/extdata/Berman/ZS92.csv
pkg/CHNOSZ/inst/extdata/Berman/unused/BA96.csv
pkg/CHNOSZ/man/extdata.Rd
Log:
extdata/Berman/*.csv: remove/change value multipliers
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2018-02-27 01:20:37 UTC (rev 305)
+++ pkg/CHNOSZ/DESCRIPTION 2018-03-07 15:46:30 UTC (rev 306)
@@ -1,6 +1,6 @@
-Date: 2018-02-27
+Date: 2018-03-07
Package: CHNOSZ
-Version: 1.1.3-13
+Version: 1.1.3-14
Title: Thermodynamic Calculations for Geobiochemistry
Authors at R: c(
person("Jeffrey", "Dick", , "j3ffdick at gmail.com", role = c("aut", "cre"),
Modified: pkg/CHNOSZ/R/berman.R
===================================================================
--- pkg/CHNOSZ/R/berman.R 2018-02-27 01:20:37 UTC (rev 305)
+++ pkg/CHNOSZ/R/berman.R 2018-03-07 15:46:30 UTC (rev 306)
@@ -28,10 +28,10 @@
dat <- dat[!duplicated(dat$name), ]
# remove the multipliers
multexp <- c(0, 0, 0, 0, # Ber88 Table 2
- 0, -2, -5, -7, # Table 3a
- 6, 12, 6, 10, # Table 4
- 0, 0, 0, 2, 5, 0, # Table 3b
- 0, 0, 0, -3, -5, 2, 6, -4 # Table 5
+ 0, 0, 0, 0, # Table 3a
+ 5, 5, 5, 8, # Table 4
+ 0, 0, 0, 0, 0, 0, # Table 3b
+ 0, 0, 0, 0, 0, 0, 0, 0 # Table 5
)
dat[, 2:27] <- t(t(dat[, 2:27]) / 10^multexp)
# if name is missing, return the entire data frame (used in test-berman.R)
Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS 2018-02-27 01:20:37 UTC (rev 305)
+++ pkg/CHNOSZ/inst/NEWS 2018-03-07 15:46:30 UTC (rev 306)
@@ -1,4 +1,4 @@
-CHANGES IN CHNOSZ 1.1.3-13 (2018-02-27)
+CHANGES IN CHNOSZ 1.1.3-14 (2018-03-07)
---------------------------------------
- Lines in 1-D diagram()s can optionally be drawn as splines using the
@@ -34,6 +34,9 @@
- read.fasta(): add support for file connections created using
archive::archive_read (https://github.com/jimhester/archive).
+- Change files in extdata/Berman to be more like winTWQ format (no
+ value multipliers, except 10^5, 10^5, 10^5, and 10^8 on v1 to v4).
+
CHANGES IN CHNOSZ 1.1.3 (2017-11-13)
------------------------------------
Modified: pkg/CHNOSZ/inst/extdata/Berman/BDat17.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/Berman/BDat17.csv 2018-02-27 01:20:37 UTC (rev 305)
+++ pkg/CHNOSZ/inst/extdata/Berman/BDat17.csv 2018-03-07 15:46:30 UTC (rev 306)
@@ -1,2 +1,2 @@
name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,d5
-antigorite,-66076529,-71364156,3602.996,174.246,7394.51,0,-5483.63,8728.412,-1.485,4,27.2,80,,,,,,,,,,,,,,
+antigorite,-66076529,-71364156,3602.996,174.246,7394.51,0,-548363000,87284120000,-0.1485,4E-07,2.72,0.8,,,,,,,,,,,,,,
Modified: pkg/CHNOSZ/inst/extdata/Berman/Ber88.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/Berman/Ber88.csv 2018-02-27 01:20:37 UTC (rev 305)
+++ pkg/CHNOSZ/inst/extdata/Berman/Ber88.csv 2018-03-07 15:46:30 UTC (rev 306)
@@ -1,68 +1,68 @@
name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,d5
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-"albite,high",-3703293,-3921618,224.412,10.083,393.64,-24.155,-78.928,107.064,-1.945,4.861,26.307,32.407,,,,,,,,,,,,,,
-"albite,low",-3711715,-3935100,207.443,10.043,393.64,-24.155,-78.928,107.064,-1.945,4.861,26.307,32.407,,,,,,,,,,,,,,
-almandine,-4941728,-5265502,339.927,11.511,573.96,-14.831,-292.92,502.208,-0.558,0.321,18.613,74.539,,,,,,,,,,,,,,
-andalusite,-2441806,-2589972,91.434,5.147,236.48,-11.029,-75.268,93.644,-0.77,1.923,23.443,7.189,,,,,,,,,,,,,,
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-antigorite,-66076529,-71364156,3602.996,174.246,7394.51,0,-5483.63,8728.412,-1.978,4.944,24.965,39.444,,,,,,,,,,,,,,
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-Ca-Al-pyroxene,-3122310,-3298767,140.751,6.356,310.7,-16.716,-74.553,94.878,-0.87,2.171,22.25,52.863,,,,,,,,,,,,,,
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-chrysotile,-4035373,-4363356,220.134,10.72,610.02,-55.812,-18.573,19.547,-1.81,4.524,27.151,67.351,,,,,,,,,,,,,,
-clinochlore,-8250546,-8909590,435.154,21.147,1214.28,-112.171,0,-125.625,-1.819,0,26.452,0,,,,,,,,,,,,,,
-coesite,-852585,-907604,39.424,2.064,94.907,-7.673,-5.279,2.627,-1.037,3,7.396,43.605,,,,,,,,,,,,,,
-cordierite,-8651517,-9158727,417.97,23.311,954.39,-79.623,-23.173,-37.021,-1.158,0,3.003,18.017,,,,,,,,,,,,,,
-corundum,-1582199,-1675700,50.82,2.558,155.02,-8.284,-38.614,40.908,-0.385,0.375,21.342,47.18,,,,,,,,,,,,,,
-"cristobalite,alpha",-853918,-907753,43.394,2.587,83.51,-3.747,-24.554,28.007,-2.515,0,20.824,0,535,298,0.048,-14.216,44.142,0,,,,,,,,
-"cristobalite,beta",-853327,-906377,46.029,2.73,83.51,-3.747,-24.554,28.007,-1.1,5.535,3.189,0,,,,,,,,,,,,,,
-diaspore,-920806,-999378,35.308,1.776,143.24,-15.404,-3.231,6.463,-0.599,0,29.718,0,,,,,,,,,,,,,,
-diopside,-3026202,-3200583,142.5,6.62,305.41,-16.049,-71.66,92.184,-0.872,1.707,27.795,83.082,,,,,,,,,,,,,,
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-"enstatite,clino",-1458601,-1545926,66.325,3.131,139.96,-4.97,-44.002,53.571,-0.75,0.448,21.915,74.92,,,,,,,,,,,,,,
-enstatite,-1458181,-1545552,66.17,3.133,166.58,-12.006,-22.706,27.915,-0.749,0.447,24.656,74.67,,,,,,,,,,,,,,
-"enstatite,proto",-1456965,-1543959,67.438,3.242,166.58,-12.006,-22.706,27.915,-0.75,0.448,16.832,116.65,,,,,,,,,,,,,,
-fayalite,-1380154,-1479360,150.93,4.63,248.93,-19.239,0,-13.91,-0.73,0,26.546,79.482,,,,,,,,,,,,,,
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-forsterite,-2055023,-2174420,94.01,4.366,238.64,-20.013,0,-11.624,-0.791,1.351,29.464,88.633,,,,,,,,,,,,,,
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-grossular,-6270974,-6632859,255.15,12.538,573.43,-20.394,-188.872,231.931,-0.654,1.635,18.994,79.756,,,,,,,,,,,,,,
-hematite,-743681,-825627,87.437,3.027,146.86,0,-55.768,52.563,-0.479,0.304,38.31,1.65,955,298,0,-7.403,27.921,1287,,,,,,,,
-ilmenite,-1155320,-1231947,108.628,3.17,150,-4.416,-33.237,34.815,-0.584,1.23,27.248,29.968,,,,,,,,,,,,,,
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-kaolinite,-3799770,-4120327,203.7,9.952,523.23,-44.267,-22.443,9.231,-1.2,0,32,0,,,,,,,,,,,,,,
-kyanite,-2443370,-2594220,82.43,4.412,262.68,-20.014,-19.997,-6.318,-0.646,0,23.973,0,,,,,,,,,,,,,,
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-lime,-603350,-635090,37.75,1.676,58.79,-1.339,-11.471,10.298,-1.022,2.565,34.61,67.406,,,,,,,,,,,,,,
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-meionite,-13105915,-13849723,730,34.036,1511.35,-132.433,0,-75.161,-1.11,0,9.34,0,,,,,,,,,,,,,,
-merwinite,-4309707,-4537497,251.777,9.847,453.62,-32.5,0,-34.423,-0.551,1.381,29.376,87.235,,,,,,,,,,,,,,
-monticellite,-2132222,-2250027,108.3,5.148,226.34,-15.427,-11.797,-2.329,-0.904,2,27.863,76.339,,,,,,,,,,,,,,
-muscovite,-5596723,-5976740,293.157,14.087,651.49,-38.732,-185.232,274.247,-1.717,4.295,33.527,0,,,,,,,,,,,,,,
-paragonite,-5563572,-5944208,277.699,13.216,577.57,-14.728,-322.144,505.008,-1.973,4.933,39.424,59.701,,,,,,,,,,,,,,
-periclase,-569209,-601500,26.951,1.125,61.11,-2.962,-6.212,0.584,-0.622,1.511,37.477,3.556,,,,,,,,,,,,,,
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-K-feldspar,-3745415,-3970791,214.145,10.869,381.37,-19.41,-120.373,183.643,-1.805,5.112,15.145,54.85,,,,,,,1436,298,282.98,-4.83,36.21,-15.733,34.77,41.063
-"K-feldspar,high",-3738804,-3959704,229.157,10.896,381.37,-19.41,-120.373,183.643,-1.805,5.112,15.145,54.85,,,,,,,,,,,,,,
-"K-feldspar,low",-3745415,-3970791,214.145,10.869,381.37,-19.41,-120.373,183.643,-1.805,5.112,15.145,54.85,,,,,,,,,,,,,,
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-pyrope,-5936009,-6286548,266.359,11.316,640.72,-45.421,-47.019,0,-0.576,0.442,22.519,37.044,,,,,,,,,,,,,,
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-"quartz,beta",-855033,-908627,44.207,2.37,80.01,-2.403,-35.467,49.157,-1.238,7.087,0,0,,,,,,,,,,,,,,
-rutile,-889497,-944750,50.46,1.882,77.84,0,-33.678,40.294,-0.454,0.584,25.716,15.409,,,,,,,,,,,,,,
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-pseudowollastonite,-1543085,-1627427,85.279,4.016,141.16,-4.172,-58.576,94.074,-1.245,3.113,28.18,0,,,,,,,,,,,,,,
-zoisite,-6494148,-6889488,297.576,13.588,749.17,-65.093,-23.805,12.486,-0.515,1.288,34.67,0,,,,,,,,,,,,,,
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+"enstatite,clino",-1458601,-1545926,66.325,3.131,139.96,-497,-4400200,535710000,-0.075,4.48E-08,2.1915,0.7492,,,,,,,,,,,,,,
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+"enstatite,proto",-1456965,-1543959,67.438,3.242,166.58,-1200.6,-2270600,279150000,-0.075,4.48E-08,1.6832,1.1665,,,,,,,,,,,,,,
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+grossular,-6270974,-6632859,255.15,12.538,573.43,-2039.4,-18887200,2319310000,-0.0654,1.635E-07,1.8994,0.79756,,,,,,,,,,,,,,
+hematite,-743681,-825627,87.437,3.027,146.86,0,-5576800,525630000,-0.0479,3.04E-08,3.831,0.0165,955,298,0,-0.07403,0.00027921,1287,,,,,,,,
+ilmenite,-1155320,-1231947,108.628,3.17,150,-441.6,-3323700,348150000,-0.0584,1.23E-07,2.7248,0.29968,,,,,,,,,,,,,,
+jadeite,-2846482,-3025118,133.574,6.034,311.29,-2005.1,-5350300,662570000,-0.086,2.149E-07,2.3118,0.25785,,,,,,,,,,,,,,
+kaolinite,-3799770,-4120327,203.7,9.952,523.23,-4426.7,-2244300,92310000,-0.12,0,3.2,0,,,,,,,,,,,,,,
+kyanite,-2443370,-2594220,82.43,4.412,262.68,-2001.4,-1999700,-63180000,-0.0646,0,2.3973,0,,,,,,,,,,,,,,
+lawsonite,-4509709,-4865666,229.176,10.144,728.67,-8248.1,0,850560000,-0.0769,1.922E-07,2.6283,0,,,,,,,,,,,,,,
+lime,-603350,-635090,37.75,1.676,58.79,-133.9,-1147100,102980000,-0.1022,2.565E-07,3.461,0.67406,,,,,,,,,,,,,,
+magnesite,-1029875,-1113636,65.21,2.803,162.3,-1109.3,-4882600,874660000,-0.089,2.212E-07,1.8436,4.15968,,,,,,,,,,,,,,
+magnetite,-1014235,-1117403,146.114,4.452,207.93,0,-7243300,664360000,-0.0582,1.751E-07,3.0291,1.3847,848,298,0,-0.19502,0.00061037,1565,,,,,,,,
+margarite,-5852244,-6236603,265.084,12.958,699.8,-5587.1,-6807700,734320000,-0.1155,2.886E-07,2.1019,1.24556,,,,,,,,,,,,,,
+meionite,-13105915,-13849723,730,34.036,1511.35,-13243.3,0,-751610000,-0.111,0,0.934,0,,,,,,,,,,,,,,
+merwinite,-4309707,-4537497,251.777,9.847,453.62,-3250,0,-344230000,-0.0551,1.381E-07,2.9376,0.87235,,,,,,,,,,,,,,
+monticellite,-2132222,-2250027,108.3,5.148,226.34,-1542.7,-1179700,-23290000,-0.0904,2E-07,2.7863,0.76339,,,,,,,,,,,,,,
+muscovite,-5596723,-5976740,293.157,14.087,651.49,-3873.2,-18523200,2742470000,-0.1717,4.295E-07,3.3527,0,,,,,,,,,,,,,,
+paragonite,-5563572,-5944208,277.699,13.216,577.57,-1472.8,-32214400,5050080000,-0.1973,4.933E-07,3.9424,0.59701,,,,,,,,,,,,,,
+periclase,-569209,-601500,26.951,1.125,61.11,-296.2,-621200,5840000,-0.0622,1.511E-07,3.7477,0.03556,,,,,,,,,,,,,,
+phlogopite,-5827224,-6207342,334.158,14.977,610.38,-2083.8,-21533000,2841040000,-0.1697,0,3.4447,0,,,,,,,,,,,,,,
+K-feldspar,-3745415,-3970791,214.145,10.869,381.37,-1941,-12037300,1836430000,-0.1805,5.112E-07,1.5145,0.5485,,,,,,,1436,298,282.98,-4830,3621000,-0.15733,3.477E-05,410630
+"K-feldspar,high",-3738804,-3959704,229.157,10.896,381.37,-1941,-12037300,1836430000,-0.1805,5.112E-07,1.5145,0.5485,,,,,,,,,,,,,,
+"K-feldspar,low",-3745415,-3970791,214.145,10.869,381.37,-1941,-12037300,1836430000,-0.1805,5.112E-07,1.5145,0.5485,,,,,,,,,,,,,,
+prehnite,-5820154,-6198606,288.634,14.016,716.05,-6404.6,-2182500,268500000,-0.1427,0,0.1468,11.28353,,,,,,,,,,,,,,
+pyrope,-5936009,-6286548,266.359,11.316,640.72,-4542.1,-4701900,0,-0.0576,4.42E-08,2.2519,0.37044,,,,,,,,,,,,,,
+pyrophyllite,-5266865,-5640781,239.4,12.76,665.93,-5897.4,-4979900,661810000,-0.1354,0,1.2637,3.81661,,,,,,,,,,,,,,
+quartz,-856288,-910700,41.46,2.269,80.01,-240.3,-3546700,491570000,-0.2434,1.0137E-06,2.3895,0,848,373,0.0237,-0.09187,0.00024607,0,,,,,,,,
+"quartz,beta",-855033,-908627,44.207,2.37,80.01,-240.3,-3546700,491570000,-0.1238,7.087E-07,0,0,,,,,,,,,,,,,,
+rutile,-889497,-944750,50.46,1.882,77.84,0,-3367800,402940000,-0.0454,5.84E-08,2.5716,0.15409,,,,,,,,,,,,,,
+sillimanite,-2439265,-2586091,95.93,4.983,256.73,-1887.2,-2977400,250960000,-0.0753,0,1.3431,0,,,,,,,,,,,,,,
+sphene,-2455134,-2596652,129.29,5.565,234.62,-1040.3,-5118300,591460000,-0.059,0,2.52,0,,,,,,,,,,,,,,
+spinel,-2176537,-2300313,84.535,3.977,235.9,-1766.6,-1710400,40620000,-0.0489,0,2.1691,0.50528,,,,,,,,,,,,,,
+talc,-5517657,-5897387,261.24,13.61,664.11,-5187.2,-2147200,-327370000,-0.1699,5.665E-07,2.9447,0,,,,,,,,,,,,,,
+tremolite,-11578548,-12305578,551.15,27.268,1229.36,-6401.9,-32089900,4208810000,-0.1392,3.481E-07,2.4374,0.98338,,,,,,,,,,,,,,
+"tridymite,low",-854026,-907750,43.77,2.675,75.37,0,-5958100,958250000,-0.2508,0,1.9339,0,383,298,0,0.4267,-0.00144575,130,,,,,,,,
+"tridymite,high",-853844,-907045,45.524,2.737,75.37,0,-5958100,958250000,-0.074,3.735E-07,0.4829,0,,,,,,,,,,,,,,
+wollastonite,-1546123,-1631500,81.81,3.983,149.07,-690.3,-3659300,484350000,-0.1245,3.113E-07,2.818,0,,,,,,,,,,,,,,
+pseudowollastonite,-1543085,-1627427,85.279,4.016,141.16,-417.2,-5857600,940740000,-0.1245,3.113E-07,2.818,0,,,,,,,,,,,,,,
+zoisite,-6494148,-6889488,297.576,13.588,749.17,-6509.3,-2380500,124860000,-0.0515,1.288E-07,3.467,0,,,,,,,,,,,,,,
+clinozoisite,-6496497,-6894968,287.076,13.673,749.17,-6509.3,-2380500,124860000,-0.0515,1.288E-07,3.467,0,,,,,,,,,,,,,,
Modified: pkg/CHNOSZ/inst/extdata/Berman/Ber90.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/Berman/Ber90.csv 2018-02-27 01:20:37 UTC (rev 305)
+++ pkg/CHNOSZ/inst/extdata/Berman/Ber90.csv 2018-03-07 15:46:30 UTC (rev 306)
@@ -1,5 +1,5 @@
name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,d5
-almandine,-4943492,-5267216,340.007,11.511,573.96,-14.831,-292.92,502.208,-0.558,0.321,18.613,74.539,,,,,,,,,,,,,,
-annite,-4793115,-5142800,420,15.408,727.21,-47.7504,-138.319,211.906,-1.697,0,34.447,0,,,,,,,,,,,,,,
-ilmenite,-1155794,-1232448,108.628,3.17,150,-4.416,-33.237,34.815,-0.584,1.23,27.248,29.968,,,,,,,,,,,,,,
-phlogopite,-5830350,-6210391,334.346,14.977,610.38,-20.838,-215.33,284.104,-1.697,0,34.447,0,,,,,,,,,,,,,,
+almandine,-4943492,-5267216,340.007,11.511,573.96,-1483.1,-29292000,5022080000,-0.0558,3.21E-08,1.8613,0.74539,,,,,,,,,,,,,,
+annite,-4793115,-5142800,420,15.408,727.21,-4775.04,-13831900,2119060000,-0.1697,0,3.4447,0,,,,,,,,,,,,,,
+ilmenite,-1155794,-1232448,108.628,3.17,150,-441.6,-3323700,348150000,-0.0584,1.23E-07,2.7248,0.29968,,,,,,,,,,,,,,
+phlogopite,-5830350,-6210391,334.346,14.977,610.38,-2083.8,-21533000,2841040000,-0.1697,0,3.4447,0,,,,,,,,,,,,,,
Modified: pkg/CHNOSZ/inst/extdata/Berman/DS10.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/Berman/DS10.csv 2018-02-27 01:20:37 UTC (rev 305)
+++ pkg/CHNOSZ/inst/extdata/Berman/DS10.csv 2018-03-07 15:46:30 UTC (rev 306)
@@ -1,6 +1,6 @@
name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,d5
-hedenbergite,-2674300,-2837802.5,173.59,6.785,353.31148,-31.06646,20.47911742,-56.3018581,-1.7457,15.1,27.96487,0,,,,,,,,,,,,,,
-andradite,-5419000,-5761985.8,316.4,13.167,569.7558,-14.4144,-224.41040802,314.6543781,-0.6539136,1.635,20.72525,56.1,,,,,,,,,,,,,,
-ferro-actinolite,-9839000,-10518042.6,685.1,28.26,1321.15758,-89.66454,-217.05844286,323.6159154,-1.5,0,28.4,0,,,,,,,,,,,,,,
-grunerite,-8964807,-9623000,725,27.8,1347.83,-93.5691,-202.2848,303.919,-1.5,0,28.4,0,,,,,,,,,,,,,,
-ilvaite,-3440000,-3695605.5,291.5,10.016,682.79138,-87.87112,301.8356871,-566.6432624,-0.6838,0.24,18.01543,115.2,,,,,,,,,,,,,,
+hedenbergite,-2674300,-2837802.5,173.59,6.785,353.31148,-3106.646,2047911.742,-563018581,-0.17457,1.51E-06,2.796487,0,,,,,,,,,,,,,,
+andradite,-5419000,-5761985.8,316.4,13.167,569.7558,-1441.44,-22441040.802,3146543781,-0.06539136,1.635E-07,2.072525,0.561,,,,,,,,,,,,,,
+ferro-actinolite,-9839000,-10518042.6,685.1,28.26,1321.15758,-8966.454,-21705844.286,3236159154,-0.15,0,2.84,0,,,,,,,,,,,,,,
+grunerite,-8964807,-9623000,725,27.8,1347.83,-9356.91,-20228480,3039190000,-0.15,0,2.84,0,,,,,,,,,,,,,,
+ilvaite,-3440000,-3695605.5,291.5,10.016,682.79138,-8787.112,30183568.71,-5666432624,-0.06838,2.4E-08,1.801543,1.152,,,,,,,,,,,,,,
Modified: pkg/CHNOSZ/inst/extdata/Berman/FDM+14.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/Berman/FDM+14.csv 2018-02-27 01:20:37 UTC (rev 305)
+++ pkg/CHNOSZ/inst/extdata/Berman/FDM+14.csv 2018-03-07 15:46:30 UTC (rev 306)
@@ -1,2 +1,2 @@
name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,d5
-aragonite,-1128353.67,-1207213.7,88.7,3.42,195,-21,-0.1,22,-1.345,1.7,41.8,0,,,,,,,,,,,,,,
+aragonite,-1128353.67,-1207213.7,88.7,3.42,195,-2100,-10000,220000000,-0.1345,1.7E-07,4.18,0,,,,,,,,,,,,,,
Modified: pkg/CHNOSZ/inst/extdata/Berman/JUN92.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/Berman/JUN92.csv 2018-02-27 01:20:37 UTC (rev 305)
+++ pkg/CHNOSZ/inst/extdata/Berman/JUN92.csv 2018-03-07 15:46:30 UTC (rev 306)
@@ -1,3 +1,3 @@
name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,d5
-glaucophane,-11225858,-11960500,535,26.05,1717.5,-192.72,70.5,0,-1.16,2.9,22,88,,,,,,,,,,,,,,
-pumpellyite,-13448936,-14402300,584,29.55,1576,-106.038,-283.042,383.8351,-0.51516,1.288,34.67,0,,,,,,,,,,,,,,
+glaucophane,-11225858,-11960500,535,26.05,1717.5,-19272,7050000,0,-0.116,2.9E-07,2.2,0.88,,,,,,,,,,,,,,
+pumpellyite,-13448936,-14402300,584,29.55,1576,-10603.8,-28304200,3838351000,-0.051516,1.288E-07,3.467,0,,,,,,,,,,,,,,
Modified: pkg/CHNOSZ/inst/extdata/Berman/SHD91.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/Berman/SHD91.csv 2018-02-27 01:20:37 UTC (rev 305)
+++ pkg/CHNOSZ/inst/extdata/Berman/SHD91.csv 2018-03-07 15:46:30 UTC (rev 306)
@@ -1,12 +1,12 @@
name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,d5
-muscovite,-5603417,-5983434,293.157,14.087,651.49,-38.732,-185.232,274.247,-1.717,4.295,33.527,0,,,,,,,,,,,,,,
-phlogopite,-5837044,-6217085,334.346,14.977,610.38,-20.838,-215.33,284.104,-1.697,0,34.447,0,,,,,,,,,,,,,,
-K-feldspar,-3752109,-3977485,214.145,10.869,381.37,-19.41,-120.373,183.643,-1.805,5.112,15.145,54.85,,,,,,,1436,298,282.98,-4.83,36.21,-15.733,34.77,41.063
-"K-feldspar,high",-3745498,-3966398,229.157,10.896,381.37,-19.41,-120.373,183.643,-1.805,5.112,15.145,54.85,,,,,,,,,,,,,,
-"K-feldspar,low",-3752109,-3977485,214.145,10.869,381.37,-19.41,-120.373,183.643,-1.805,5.112,15.145,54.85,,,,,,,,,,,,,,
-paragonite,-5570375,-5951011,277.699,13.216,577.57,-14.728,-322.144,505.008,-1.973,4.933,39.424,59.701,,,,,,,,,,,,,,
-albite,-3710096,-3928421,224.412,10.083,393.64,-24.155,-78.928,107.064,-1.945,4.861,26.307,32.407,,,,,,,,,,,,,,
-"albite,high",-3710096,-3928421,224.412,10.083,393.64,-24.155,-78.928,107.064,-1.945,4.861,26.307,32.407,,,,,,,,,,,,,,
-"albite,low",-3718518,-3941903,207.443,10.043,393.64,-24.155,-78.928,107.064,-1.945,4.861,26.307,32.407,,,,,,,,,,,,,,
-jadeite,-2853285,-3031921,133.574,6.034,311.29,-20.051,-53.503,66.257,-0.86,2.149,23.118,25.785,,,,,,,,,,,,,,
-annite,-4799809,-5149494,420,15.408,727.21,-47.7504,-138.319,211.906,-1.697,0,34.447,0,,,,,,,,,,,,,,
+muscovite,-5603417,-5983434,293.157,14.087,651.49,-3873.2,-18523200,2742470000,-0.1717,4.295E-07,3.3527,0,,,,,,,,,,,,,,
+phlogopite,-5837044,-6217085,334.346,14.977,610.38,-2083.8,-21533000,2841040000,-0.1697,0,3.4447,0,,,,,,,,,,,,,,
+K-feldspar,-3752109,-3977485,214.145,10.869,381.37,-1941,-12037300,1836430000,-0.1805,5.112E-07,1.5145,0.5485,,,,,,,1436,298,282.98,-4830,3621000,-0.15733,3.477E-05,410630
+"K-feldspar,high",-3745498,-3966398,229.157,10.896,381.37,-1941,-12037300,1836430000,-0.1805,5.112E-07,1.5145,0.5485,,,,,,,,,,,,,,
+"K-feldspar,low",-3752109,-3977485,214.145,10.869,381.37,-1941,-12037300,1836430000,-0.1805,5.112E-07,1.5145,0.5485,,,,,,,,,,,,,,
+paragonite,-5570375,-5951011,277.699,13.216,577.57,-1472.8,-32214400,5050080000,-0.1973,4.933E-07,3.9424,0.59701,,,,,,,,,,,,,,
+albite,-3710096,-3928421,224.412,10.083,393.64,-2415.5,-7892800,1070640000,-0.1945,4.861E-07,2.6307,0.32407,,,,,,,,,,,,,,
+"albite,high",-3710096,-3928421,224.412,10.083,393.64,-2415.5,-7892800,1070640000,-0.1945,4.861E-07,2.6307,0.32407,,,,,,,,,,,,,,
+"albite,low",-3718518,-3941903,207.443,10.043,393.64,-2415.5,-7892800,1070640000,-0.1945,4.861E-07,2.6307,0.32407,,,,,,,,,,,,,,
+jadeite,-2853285,-3031921,133.574,6.034,311.29,-2005.1,-5350300,662570000,-0.086,2.149E-07,2.3118,0.25785,,,,,,,,,,,,,,
+annite,-4799809,-5149494,420,15.408,727.21,-4775.04,-13831900,2119060000,-0.1697,0,3.4447,0,,,,,,,,,,,,,,
Modified: pkg/CHNOSZ/inst/extdata/Berman/ZS92.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/Berman/ZS92.csv 2018-02-27 01:20:37 UTC (rev 305)
+++ pkg/CHNOSZ/inst/extdata/Berman/ZS92.csv 2018-03-07 15:46:30 UTC (rev 306)
@@ -1,11 +1,11 @@
name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,d5
-fluormuscovite,-5772803,-6111401,299.03,14.087,680.36024,-65.15743,0,11.058312,-1.7169021,4.2947,33.5273302,0,NA,NA,NA,NA,NA,NA,NA,NA,,,,,,
-fluorphlogopite,-6063382,-6403168,336.394,14.637,653.70816,-51.7519,0,-32.459472,-1.6969784,0,34.4473262,0,NA,NA,NA,NA,NA,NA,NA,NA,,,,,,
-fluorannite,-4983910,-5293254,422.291,15.075,742.82736,-68.1741,0,41.844184,-1.6969784,0,34.4473262,0,NA,NA,NA,NA,NA,NA,NA,NA,,,,,,
-fluortremolite,-11782144,-12457969,570.279,27.045,1272.64728,-94.93496,0,-1.05177392,-1.3917727,3.4809,24.3738877,98.338,NA,NA,NA,NA,NA,NA,NA,NA,,,,,,
-fluorapatite,-6443050,-6823447,387.857,15.753,668.77056,-45.34201,0,-74.634192,0,0,0,0,NA,NA,NA,NA,NA,NA,NA,NA,,,,,,
-hydroxyapatite,-6297702,-6694689,398.735,15.822,758.81024,-64.80598,0,-44.793904,0,0,0,0,NA,NA,NA,NA,NA,NA,NA,NA,,,,,,
-chlorapatite,-6217424,-6597260,399.907,16.403,663.87528,-44.35877,0,-69.023448,0,0,0,0,NA,NA,NA,NA,NA,NA,NA,NA,,,,,,
-fluortalc,-5717018,-6056244,264.052,13.33,602.74704,-47.66831,0,-29.2588712,-1.6988979,5.665,29.4468112,0,NA,NA,NA,NA,NA,NA,NA,NA,,,,,,
-chlorphlogopite,-5600840,-5939422,360.703,16.59,573.45904,-20.63549,-164.657136,210.576536,-1.6969784,0,34.4473262,0,NA,NA,NA,NA,NA,NA,NA,NA,,,,,,
-chlorannite,-4582036,-4890196,449.529,17.247,690.44368,-47.60137,-87.253136,137.682888,-1.6969784,0,34.4473262,0,NA,NA,NA,NA,NA,NA,NA,NA,,,,,,
+fluormuscovite,-5772803,-6111401,299.03,14.087,680.36024,-6515.743,0,110583120,-0.17169021,4.2947E-07,3.35273302,0,NA,NA,NA,NA,NA,NA,NA,NA,,,,,,
+fluorphlogopite,-6063382,-6403168,336.394,14.637,653.70816,-5175.19,0,-324594720,-0.16969784,0,3.44473262,0,NA,NA,NA,NA,NA,NA,NA,NA,,,,,,
+fluorannite,-4983910,-5293254,422.291,15.075,742.82736,-6817.41,0,418441840,-0.16969784,0,3.44473262,0,NA,NA,NA,NA,NA,NA,NA,NA,,,,,,
+fluortremolite,-11782144,-12457969,570.279,27.045,1272.64728,-9493.496,0,-10517739.2,-0.13917727,3.4809E-07,2.43738877,0.98338,NA,NA,NA,NA,NA,NA,NA,NA,,,,,,
+fluorapatite,-6443050,-6823447,387.857,15.753,668.77056,-4534.201,0,-746341920,0,0,0,0,NA,NA,NA,NA,NA,NA,NA,NA,,,,,,
+hydroxyapatite,-6297702,-6694689,398.735,15.822,758.81024,-6480.598,0,-447939040,0,0,0,0,NA,NA,NA,NA,NA,NA,NA,NA,,,,,,
+chlorapatite,-6217424,-6597260,399.907,16.403,663.87528,-4435.877,0,-690234480,0,0,0,0,NA,NA,NA,NA,NA,NA,NA,NA,,,,,,
+fluortalc,-5717018,-6056244,264.052,13.33,602.74704,-4766.831,0,-292588712,-0.16988979,5.665E-07,2.94468112,0,NA,NA,NA,NA,NA,NA,NA,NA,,,,,,
+chlorphlogopite,-5600840,-5939422,360.703,16.59,573.45904,-2063.549,-16465713.6,2105765360,-0.16969784,0,3.44473262,0,NA,NA,NA,NA,NA,NA,NA,NA,,,,,,
+chlorannite,-4582036,-4890196,449.529,17.247,690.44368,-4760.137,-8725313.6,1376828880,-0.16969784,0,3.44473262,0,NA,NA,NA,NA,NA,NA,NA,NA,,,,,,
Modified: pkg/CHNOSZ/inst/extdata/Berman/unused/BA96.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/Berman/unused/BA96.csv 2018-02-27 01:20:37 UTC (rev 305)
+++ pkg/CHNOSZ/inst/extdata/Berman/unused/BA96.csv 2018-03-07 15:46:30 UTC (rev 306)
@@ -1,21 +1,21 @@
name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,d5
-almandine,,-5265440,341.51,11.529,621.43,-32.879,-150.81,221.187,-0.57,0.434,18.599,74.711,,,,,,,,,,,,,,
-anthophyllite,,-12074470,537.4,26.33,1233.79,-71.34,-221.638,233.394,-1.139,0,28.105,62.894,,,,,,,,,,,,,,
-cordierite,,-9161480,416.23,23.311,954.39,-79.623,-23.173,-37.021,-1.158,0,3.003,18.017,,,,,,,,,,,,,,
-Fe-cordierite,,-8430550,482.18,23.706,983.48,-84.037,-18.703,-8.568,-1.7,0,4.265,0,,,,,,,,,,,,,,
-fayalite,,-1477170,151.73,4.639,252,-20.137,0,-6.219,-0.822,1.944,26.21,84.233,,,,,,,,,,,,,,
-ferrosilite,,-1192910,96.47,3.295,174.2,-13.93,-4.544,-3.771,-0.911,0.303,31.406,80.4,,,,,,,,,,,,,,
-forsterite,,-2174420,94.18,4.36,233.18,-18.016,0,-26.794,-0.791,1.351,29.464,88.633,,,,,,,,,,,,,,
-geikelite,,-1570520,74.41,3.077,146.2,-4.16,-39.998,40.233,-0.529,0,23.314,88.328,,,,,,,,,,,,,,
-hematite,,-826740,87.36,3.027,146.86,0,-55.768,52.563,-0.479,0.304,38.31,1.65,955,298,0,-7.403,27.921,1287,,,,,,,,
-hercynite,,-1945360,123.13,4.08,251.77,-20.444,-13.483,13.15,-0.51,0,15.819,96.276,,,,,,,,,,,,,,
-ilmenite,,-1233320,108.5,3.17,150,-4.416,-33.237,34.815,-0.529,0,23.314,88.328,,,,,,,,,,,,,,
-iron-a,,0,27.45,0.709,51.87,-3.794,-25.43,50.68,-0.602,0,45.071,14.104,1042,298,-0.00057,-22.208,34.823,1000,,,,,,,,
-iron-g,,7720,35.64,0.691,66.24,-12.371,63.733,-106.04,-0.467,-1.445,47.153,14.451,,,,,,,,,,,,,,
-magnetite,,-1116960,146.04,4.452,207.93,0,-72.433,66.436,-0.582,1.751,30.291,138.47,848,298,0,-19.502,61.037,1565,,,,,,,,
-enstatite,,-1546040,66.18,3.133,166.58,-12.006,-22.706,27.915,-0.749,0.447,24.656,74.67,,,,,,,,,,,,,,
-orthocorundum,,-1634950,33.93,3.123,119.38,7.748,-65.091,42.288,-0.749,0.447,24.656,74.67,,,,,,,,,,,,,,
-pyrope,,-6284740,268.8,11.311,590.9,-28.27,-133.208,126.033,-0.576,0.442,22.519,37.044,,,,,,,,,,,,,,
-rutile,,-944750,50.88,1.883,77.84,0,-33.678,40.294,-0.454,0.585,25.716,15.409,,,,,,,,,,,,,,
-spinel,,-2302160,80.37,3.978,244.67,-20.04,,,-0.489,0,21.691,50.528,,,,,,,,,,,,,,
-talc,,-5898960,261.21,13.61,664.11,-51.872,-21.472,-32.737,-1.847,5.878,25.616,0,,,,,,,,,,,,,,
+almandine,,-5265440,341.51,11.529,621.43,-3287.9,-15081000,2211870000,-0.057,4.34E-08,1.8599,0.74711,,,,,,,,,,,,,,
+anthophyllite,,-12074470,537.4,26.33,1233.79,-7134,-22163800,2333940000,-0.1139,0,2.8105,0.62894,,,,,,,,,,,,,,
+cordierite,,-9161480,416.23,23.311,954.39,-7962.3,-2317300,-370210000,-0.1158,0,0.3003,0.18017,,,,,,,,,,,,,,
+Fe-cordierite,,-8430550,482.18,23.706,983.48,-8403.7,-1870300,-85680000,-0.17,0,0.4265,0,,,,,,,,,,,,,,
+fayalite,,-1477170,151.73,4.639,252,-2013.7,0,-62190000,-0.0822,1.944E-07,2.621,0.84233,,,,,,,,,,,,,,
+ferrosilite,,-1192910,96.47,3.295,174.2,-1393,-454400,-37710000,-0.0911,3.03E-08,3.1406,0.804,,,,,,,,,,,,,,
+forsterite,,-2174420,94.18,4.36,233.18,-1801.6,0,-267940000,-0.0791,1.351E-07,2.9464,0.88633,,,,,,,,,,,,,,
+geikelite,,-1570520,74.41,3.077,146.2,-416,-3999800,402330000,-0.0529,0,2.3314,0.88328,,,,,,,,,,,,,,
+hematite,,-826740,87.36,3.027,146.86,0,-5576800,525630000,-0.0479,3.04E-08,3.831,0.0165,955,298,0,-0.07403,0.00027921,1287,,,,,,,,
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/chnosz -r 306
From noreply at r-forge.r-project.org Wed Mar 14 18:54:46 2018
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Wed, 14 Mar 2018 18:54:46 +0100 (CET)
Subject: [CHNOSZ-commits] r307 - in pkg/CHNOSZ: . R demo inst man
tests/testthat vignettes
Message-ID: <20180314175446.E19C11893B8@r-forge.r-project.org>
Author: jedick
Date: 2018-03-14 18:54:46 +0100 (Wed, 14 Mar 2018)
New Revision: 307
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/R/diagram.R
pkg/CHNOSZ/demo/buffer.R
pkg/CHNOSZ/inst/NEWS
pkg/CHNOSZ/man/buffer.Rd
pkg/CHNOSZ/man/diagram.Rd
pkg/CHNOSZ/tests/testthat/test-diagram.R
pkg/CHNOSZ/vignettes/anintro.Rmd
Log:
diagram(): allow 'saturation' to be specified for 'type' of diagram
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2018-03-07 15:46:30 UTC (rev 306)
+++ pkg/CHNOSZ/DESCRIPTION 2018-03-14 17:54:46 UTC (rev 307)
@@ -1,6 +1,6 @@
-Date: 2018-03-07
+Date: 2018-03-15
Package: CHNOSZ
-Version: 1.1.3-14
+Version: 1.1.3-15
Title: Thermodynamic Calculations for Geobiochemistry
Authors at R: c(
person("Jeffrey", "Dick", , "j3ffdick at gmail.com", role = c("aut", "cre"),
Modified: pkg/CHNOSZ/R/diagram.R
===================================================================
--- pkg/CHNOSZ/R/diagram.R 2018-03-07 15:46:30 UTC (rev 306)
+++ pkg/CHNOSZ/R/diagram.R 2018-03-14 17:54:46 UTC (rev 307)
@@ -14,8 +14,8 @@
diagram <- function(
# species affinities or activities
eout,
- # what to plot
- what="loga.equil", alpha=FALSE, normalize=FALSE, as.residue=FALSE, balance=NULL,
+ # type of plot
+ type="auto", alpha=FALSE, normalize=FALSE, as.residue=FALSE, balance=NULL,
groups=as.list(1:length(eout$values)), xrange=NULL,
# figure size and sides for axis tick marks
mar=NULL, yline=par("mgp")[1]+0.3, side=1:4,
@@ -24,7 +24,7 @@
# sizes
cex=par("cex"), cex.names=1, cex.axis=par("cex"),
# line styles
- lty=NULL, lwd=par("lwd"), dotted=NULL, spline.method=NULL,
+ lty=NULL, lwd=par("lwd"), dotted=NULL, spline.method=NULL, contour.method="edge",
# colors
col=par("col"), col.names=par("col"), fill=NULL,
fill.NA="slategray1", limit.water=TRUE,
@@ -41,25 +41,27 @@
## check that eout is valid input
if(!"sout" %in% names(eout)) stop("'eout' does not look like output from equil() or affinity()")
- ## 'what' can be:
- # loga.equil - equilibrium activities of species of interest (eout)
- # basis species - equilibrium activity of a basis species (aout)
- # missing - property from affinity() or predominances of species (aout)
+ ## 'type' can be:
+ # 'auto' - property from affinity() (1D) or maximum affinity (affinity 2D) (aout) or loga.equil (eout)
+ # 'loga.equil' - equilibrium activities of species of interest (eout)
+ # name of basis species - equilibrium activity of a basis species (aout)
+ # 'saturation' - affinity=0 line for each species (2D)
eout.is.aout <- FALSE
plot.loga.basis <- FALSE
- if(missing(what)) {
+ if(type %in% c("auto", "saturation")) {
if(!"loga.equil" %in% names(eout)) {
eout.is.aout <- TRUE
# get the balancing coefficients
- n.balance <- balance(eout, balance)
+ if(type=="auto") n.balance <- balance(eout, balance)
+ else n.balance <- rep(1, length(eout$values))
}
- } else if(what %in% rownames(eout$basis)) {
+ } else if(type %in% rownames(eout$basis)) {
# to calculate the loga of basis species at equilibrium
if(!missing(groups)) stop("can't plot equilibrium activities of basis species for grouped species")
if(isTRUE(alpha) | is.character(alpha)) stop("equilibrium activities of basis species not available with alpha=TRUE")
plot.loga.basis <- TRUE
- } else if(what=="loga.equil" & !"loga.equil" %in% names(eout)) stop("'eout' is not the output from equil()")
- else if(what!="loga.equil") stop(what, " is not a basis species or 'loga.equil'")
+ } else if(type=="loga.equil" & !"loga.equil" %in% names(eout)) stop("'eout' is not the output from equil()")
+ else if(type!="loga.equil") stop(type, " is not a valid diagram type")
## consider a different number of species if we're grouping them together
ngroups <- length(groups)
@@ -69,6 +71,11 @@
plotvals <- eout$loga.equil
plotvar <- "loga.equil"
+ ## number of dimensions (T, P or chemical potentials that are varied)
+ # length(eout$vars) - the number of variables = the maximum number of dimensions
+ # length(dim(eout$values[[1]])) - nd=1 if it was a transect along multiple variables
+ nd <- min(length(eout$vars), length(dim(eout$values[[1]])))
+
## deal with output from affinity()
if(eout.is.aout) {
# plot property from affinity(), divided by balancing coefficients
@@ -83,15 +90,12 @@
# 20171027 use parentheses to avoid ambiguity about order of operations
if(plotvar=="A") {
plotvar <- "A/(2.303RT)"
- message("diagram: plotting A/(2.303RT) / n.balance (maximum affinity method for 2-D diagrams)")
+ if(nd==2 & type=="auto") message("diagram: using maximum affinity method for 2-D diagram")
+ else if(nd==2 & type=="saturation") message("diagram: plotting saturation lines for 2-D diagram")
+ else message("diagram: plotting A/(2.303RT) / n.balance")
} else message(paste("diagram: plotting", plotvar, " / n.balance"))
}
- ## number of dimensions (T, P or chemical potentials that are varied)
- # length(eout$vars) - the number of variables = the maximum number of dimensions
- # length(dim(eout$values[[1]])) - nd=1 if it was a transect along multiple variables
- nd <- min(length(eout$vars), length(dim(eout$values[[1]])))
-
## use molality instead of activity if the affinity calculation include ionic strength 20171101
use.molality <- "IS" %in% names(eout)
@@ -125,10 +129,10 @@
## calculate the equilibrium logarithm of activity of a basis species
## (such that affinities of formation reactions are zero)
if(plot.loga.basis) {
- ibasis <- match(what, rownames(eout$basis))
+ ibasis <- match(type, rownames(eout$basis))
# the logarithm of activity used in the affinity calculation
is.loga.basis <- can.be.numeric(eout$basis$logact[ibasis])
- if(!is.loga.basis) stop(paste("the logarithm of activity for basis species", what, "is not numeric - was a buffer selected?"))
+ if(!is.loga.basis) stop(paste("the logarithm of activity for basis species", type, "is not numeric - was a buffer selected?"))
loga.basis <- as.numeric(eout$basis$logact[ibasis])
# the reaction coefficients for this basis species
nu.basis <- eout$species[, ibasis]
@@ -137,7 +141,7 @@
# eout$values is a strange name for affinity ... should be named something like eout$affinity ...
loga.basis - eout$values[[x]]/nu.basis[x]
})
- plotvar <- what
+ plotvar <- type
}
## alpha: plot fractional degree of formation
@@ -157,7 +161,7 @@
## identify predominant species
predominant <- NA
- if(plotvar %in% c("loga.equil", "alpha", "A/(2.303RT)")) {
+ if(plotvar %in% c("loga.equil", "alpha", "A/(2.303RT)") & type!="saturation") {
pv <- plotvals
# some additional steps for affinity values, but not for equilibrated activities
if(eout.is.aout) {
@@ -197,9 +201,6 @@
}
}
- # a warning about that we can only show properties of the first species on a 2-D diagram
- if(nd==2 & length(plotvals) > 1 & identical(predominant, NA)) warning("showing only first species in 2-D property diagram")
-
## where we'll put extra output for predominance diagrams (lx, ly, is)
out2D <- list()
@@ -534,8 +535,31 @@
}
# colors and curves (predominance), or contours (properties)
if(identical(predominant, NA)) {
- zs <- plotvals[[1]]
- contour(xs, ys, zs, add=TRUE, col=col, lty=lty, lwd=lwd, labcex=cex)
+ if(type=="saturation") {
+ # for saturation plot, contour affinity=0 for all species
+ for(i in 1:length(plotvals)) {
+ zs <- plotvals[[i]]
+ # skip plotting if this species has no possible saturation line, or a line outside the plot range
+ if(length(unique(as.numeric(zs)))==1) {
+ message("diagram: no saturation line possible for ", names[i])
+ next
+ }
+ if(all(zs < 0) | all(zs > 0)) {
+ message("diagram: beyond range for saturation line of ", names[i])
+ next
+ }
+ if(identical(contour.method, NULL) | identical(contour.method, NA) | identical(contour.method, ""))
+ contour(xs, ys, zs, add=TRUE, col=col, lty=lty, lwd=lwd, labcex=cex, levels=0, labels=names[i], drawlabels=FALSE)
+ else contour(xs, ys, zs, add=TRUE, col=col, lty=lty, lwd=lwd, labcex=cex, levels=0, labels=names[i], method=contour.method)
+ }
+ } else {
+ # otherwise, make contours of properties using first species only
+ if(length(plotvals) > 1) warning("showing only first species in 2-D property diagram")
+ print('hello')
+ print(length(plotvals))
+ zs <- plotvals[[1]]
+ contour(xs, ys, zs, add=TRUE, col=col, lty=lty, lwd=lwd, labcex=cex, method=contour.method)
+ }
pn <- list(lx=NULL, ly=NULL, is=NULL)
} else {
# put predominance matrix in the right order for image() etc
@@ -551,6 +575,14 @@
} # end if(nd==2)
} # end if(plot.it)
+ # warn if we have a system with both Berman and Helgeson minerals 20180315
+ ref1 <- get("thermo")$obigt$ref1
+ ref2 <- get("thermo")$obigt$ref2
+ ispecies <- eout$species$ispecies
+ hasHelgeson <- any(grepl("HDNB78", ref1[ispecies])) | any(grepl("HDNB78", ref2[ispecies]))
+ hasBerman <- any(get("thermo")$obigt$state[ispecies]=="cr_Berman")
+ if(hasHelgeson & hasBerman) warning("the system has minerals from both the Helgeson and Berman datasets; data may not be internally consistent")
+
out <- c(eout, list(plotvar=plotvar, plotvals=plotvals, names=names, predominant=predominant), out2D)
return(invisible(out))
}
Modified: pkg/CHNOSZ/demo/buffer.R
===================================================================
--- pkg/CHNOSZ/demo/buffer.R 2018-03-07 15:46:30 UTC (rev 306)
+++ pkg/CHNOSZ/demo/buffer.R 2018-03-14 17:54:46 UTC (rev 307)
@@ -19,12 +19,12 @@
bufferline("QFM", 38)
bufferline("PPM", 102)
bufferline("HM", 51)
-# method 2: in diagram(), use the `what` argument
+# method 2: in diagram(), use the `type` argument
basis("H2", 0)
for(logact in c(-6, -10, -15)) {
species(c("formaldehyde", "HCN"), logact)
a <- affinity(T=xlim, P=300)
- d <- diagram(a, what="H2", lty=c(3, 2), add=TRUE)
+ d <- diagram(a, type="H2", lty=c(3, 2), add=TRUE)
text(a$vals[[1]][13], mean(sapply(d$plotvals, c)[13, ]), logact)
}
# add legends and title
Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS 2018-03-07 15:46:30 UTC (rev 306)
+++ pkg/CHNOSZ/inst/NEWS 2018-03-14 17:54:46 UTC (rev 307)
@@ -1,4 +1,4 @@
-CHANGES IN CHNOSZ 1.1.3-14 (2018-03-07)
+CHANGES IN CHNOSZ 1.1.3-15 (2018-03-15)
---------------------------------------
- Lines in 1-D diagram()s can optionally be drawn as splines using the
@@ -37,6 +37,12 @@
- Change files in extdata/Berman to be more like winTWQ format (no
value multipliers, except 10^5, 10^5, 10^5, and 10^8 on v1 to v4).
+- diagram(): rename 'what' argument to 'type'.
+
+- digram(): add new type of diagram, 'saturation', which is used to
+ plot saturation lines for minerals (where their affinity equals
+ zero).
+
CHANGES IN CHNOSZ 1.1.3 (2017-11-13)
------------------------------------
Modified: pkg/CHNOSZ/man/buffer.Rd
===================================================================
--- pkg/CHNOSZ/man/buffer.Rd 2018-03-07 15:46:30 UTC (rev 306)
+++ pkg/CHNOSZ/man/buffer.Rd 2018-03-14 17:54:46 UTC (rev 307)
@@ -71,7 +71,7 @@
mod.buffer("AC",logact=-10)
affinity(O2=c(-85,-70,4),T=c(25,100,4),return.buffer=TRUE)
# see below for a different strategy using the
-# 'what' argument of diagram
+# 'type' argument of diagram
## buffer made of three species
## Pyrite-Pyrrhotite-Magnetite (PPM)
@@ -133,7 +133,7 @@
affinity(return.buffer=TRUE)
# one can solve for the logarithm of activity of a
-# basis species using the 'what' argument of diagram
+# basis species using the 'type' argument of diagram
basis("CHNOS")
basis("CO2", 999)
species("acetic acid", -3)
@@ -142,16 +142,16 @@
lCO2 <- axis.label("CO2")
main <- substitute(a~~b~~c,list(a=lCO2, b="buffered by",
c="acetic acid"))
-d <- diagram(a, what="CO2", main=main)
+d <- diagram(a, type="CO2", main=main)
species(1, -10)
a <- affinity(O2=c(-85, -70, 4), T=c(25, 100, 4))
-d <- diagram(a, what="CO2", add=TRUE, lty=2)
+d <- diagram(a, type="CO2", add=TRUE, lty=2)
# add a legend
lAC <- expr.species("CH3COOH", log="aq")
ltext <- c(as.expression(lAC), -3, -10)
lty <- c(NA, 1, 2)
legend("topright", legend=ltext, lty=lty, bg="white")
-# do return.buffer and diagram(what) give the same results?
+# do return.buffer and diagram(type=...) give the same results?
and <- as.numeric(d$plotvals[[1]])
basis("CO2", "AC")
mod.buffer("AC", logact=-10)
Modified: pkg/CHNOSZ/man/diagram.Rd
===================================================================
--- pkg/CHNOSZ/man/diagram.Rd 2018-03-07 15:46:30 UTC (rev 306)
+++ pkg/CHNOSZ/man/diagram.Rd 2018-03-14 17:54:46 UTC (rev 307)
@@ -12,8 +12,8 @@
diagram(
# species affinities or activities
eout,
- # what to plot
- what = "loga.equil", alpha = FALSE, normalize = FALSE,
+ # type plot
+ type = "auto", alpha = FALSE, normalize = FALSE,
as.residue = FALSE, balance=NULL, groups=as.list(1:length(eout$values)),
# figure size and sides for axis tick marks
xrange=NULL, mar=NULL, yline=par("mgp")[1]+0.3, side=1:4,
@@ -22,7 +22,7 @@
# character sizes
cex=par("cex"), cex.names=1, cex.axis=par("cex"),
# line styles
- lty=NULL, lwd=par("lwd"), dotted=NULL, spline.method = NULL,
+ lty=NULL, lwd=par("lwd"), dotted=NULL, spline.method = NULL, contour.method = "edge",
# colors
col=par("col"), col.names=par("col"), fill=NULL,
fill.NA="slategray1", limit.water=TRUE,
@@ -39,7 +39,7 @@
\arguments{
\item{eout}{list, object returned by \code{\link{equilibrate}} or \code{\link{affinity}}}
- \item{what}{character, what property to calculate and plot}
+ \item{type}{character, type of plot, or name of basis species whose activity to plot}
\item{alpha}{logical or character (\samp{balance}), for speciation diagrams, plot degree of formation instead of activities?}
\item{normalize}{logical, divide chemical affinities by balance coefficients (rescale to whole formulas)?}
\item{as.residue}{logical, divide chemical affinities by balance coefficients (no rescaling)?}
@@ -61,6 +61,7 @@
\item{lwd}{numeric, line width}
\item{dotted}{numeric, how often to skip plotting points on predominance field boundaries (to gain the effect of dotted or dashed boundary lines)}
\item{spline.method}{character, method used in \code{\link{splinefun}}}
+ \item{contour.method}{character, labelling method used in \code{\link{contour}} (use NULL for no labels).}
\item{col}{character, color of activity lines (1D diagram) or predominance field boundaries (2D diagram), or colors of bars in a strip diagram (\code{strip})}
\item{col.names}{character, colors for labels of species}
\item{fill}{character, colors used to fill predominance fields}
@@ -140,14 +141,16 @@
\section{Affinity Diagrams}{
The function behaves differently when the output from \code{affinity} is being used instead of the equilibrium activities from \code{equilibrate}.
-If \code{what} is missing, and the number of dimensions is 0 or 1, a property of a reaction, such as the equilibrium constant (\samp{logK}), is plotted.
+If \code{type} is \samp{auto}, and the number of dimensions is 0 or 1, the property computed by \code{\link{affinity}} for each species is plotted.
+This is usually the affinity of the formation reaction, but can be set to some other property, such as the equilibrium constant (\samp{logK}).
+If \code{type} is \samp{auto}, and the number of dimensions is 2, then equilibrium predominance (maximum affinity) fields are plotted.
+This algorithm is based on a comparison of the affinities of the formation reactions scaled by the balancing coefficients that are determined by the \code{balance} argument.
-If \code{what} is missing, and the number of dimensions is 2, then highest potential (equilibrium predominance) fields are plotted.
-This algorithm is based on comparing the relative magnitudes of the affinities of the formation reactions, also referred to as the maximum affinity method.
-In this case, the balancing coefficients are determined usingi the \code{balance} argument.
-
-If \code{what} is the name of a basis species, it indicates to plot the equilibrium activity of a selected basis species in all of the formation reactions.
-A contour plot is made in the case of 2-D diagrams of the equilibrium activity of a basis species (see the \CO2-acetic acid example in \code{\link{buffer}}, and only the first species of interest is used in the calculation; a warning is produced if there is more than one.
+If \code{type} is \samp{saturation}, the function plots the line for each species where the affinity of formation equals zero.
+If for a given species no saturation line is possible or the range of the diagram is beyond the saturation line, the function prints a message instead.
+If \code{type} is the name of a basis species, the equilibrium activity of the selected basis species in each of the formation reactions is plotted.
+In the case of 2-D diagrams, both of these options use \code{\link{contour}} to draw the lines (see the \CO2-acetic acid example in \code{\link{buffer}}.
+The \samp{saturation} diagram can handle multiple species, but if \code{type} is the name a basis species, then only the first species of interest is used in the calculation, and a warning is produced if there is more than one.
}
\section{Activity Coefficients}{
@@ -187,7 +190,7 @@
basis("CHNOS")
species(c("ethanol", "lactic acid", "deoxyribose", "ribose"))
a <- affinity(T=c(0, 150))
-diagram(a, what="O2", legend.x="topleft", col=rev(rainbow(4)), lwd=2)
+diagram(a, type="O2", legend.x="topleft", col=rev(rainbow(4)), lwd=2)
title(main="Equilibrium logfO2 for 1e-3 mol/kg of CO2 and ... ")
### 1-D diagrams: logarithms of activities
Modified: pkg/CHNOSZ/tests/testthat/test-diagram.R
===================================================================
--- pkg/CHNOSZ/tests/testthat/test-diagram.R 2018-03-07 15:46:30 UTC (rev 306)
+++ pkg/CHNOSZ/tests/testthat/test-diagram.R 2018-03-14 17:54:46 UTC (rev 307)
@@ -7,7 +7,7 @@
a <- affinity()
expect_message(diagram(a, plot.it=FALSE), "balance: from moles of CO2 in formation reactions")
e <- equilibrate(a)
- expect_error(diagram(e, "Z"), "Z is not a basis species")
+ expect_error(diagram(e, "Z"), "Z is not a valid diagram type")
})
test_that("expected messages, errors and results arise using output from affinity()", {
@@ -81,9 +81,8 @@
basis("CHNOS")
species(c("alanine", "glycine", "serine", "methionine"))
a <- affinity(T=c(0, 200, 6), O2=c(-90, -60, 5))
- # TODO: fix plot.line() function in diagram() so that the plot can be made
- #expect_equal(diagram(a), diagram(a, plot.it=FALSE))
- expect_warning(diagram(a, what="CO2", plot.it=FALSE), "showing only first species in 2-D property diagram")
+ # now the warning is invokes next to the actual plotting, so no warning is produced with plot.it=FALSE 20180315
+ #expect_warning(diagram(a, type="CO2", plot.it=FALSE), "showing only first species in 2-D property diagram")
})
test_that("NaN values from equilibrate() are preserved (as NA in predominance calculation)", {
Modified: pkg/CHNOSZ/vignettes/anintro.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/anintro.Rmd 2018-03-07 15:46:30 UTC (rev 306)
+++ pkg/CHNOSZ/vignettes/anintro.Rmd 2018-03-14 17:54:46 UTC (rev 307)
@@ -807,7 +807,7 @@
* the buffers are active in calculations of affinity of other species;
* use `mod.buffer()` to change or add buffers in `thermo$buffer`;
* [`demo(buffer)`](../demo) uses it for mineral buffers (solid lines).
-2. Use the `what` argument of `diagram()` to solve for the activity of the indicated basis species:
+2. Use the `type` argument of `diagram()` to solve for the activity of the indicated basis species:
* more convenient (the buffers come from the currently defined species of interest), but only a single basis species can be buffered, and it's not used in the calculation of affinity;
* [`demo(buffer)`](../demo) uses it for aqueous organic species as buffers (dotted and dashed lines).
From noreply at r-forge.r-project.org Tue Mar 27 09:57:23 2018
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Tue, 27 Mar 2018 09:57:23 +0200 (CEST)
Subject: [CHNOSZ-commits] r308 - in pkg/CHNOSZ: . R inst man
Message-ID: <20180327075723.CC84A1894C8@r-forge.r-project.org>
Author: jedick
Date: 2018-03-27 09:57:23 +0200 (Tue, 27 Mar 2018)
New Revision: 308
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/R/berman.R
pkg/CHNOSZ/R/util.fasta.R
pkg/CHNOSZ/inst/NEWS
pkg/CHNOSZ/man/berman.Rd
Log:
berman(): read data from berman.csv if present in working directory
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2018-03-14 17:54:46 UTC (rev 307)
+++ pkg/CHNOSZ/DESCRIPTION 2018-03-27 07:57:23 UTC (rev 308)
@@ -1,6 +1,6 @@
-Date: 2018-03-15
+Date: 2018-03-27
Package: CHNOSZ
-Version: 1.1.3-15
+Version: 1.1.3-16
Title: Thermodynamic Calculations for Geobiochemistry
Authors at R: c(
person("Jeffrey", "Dick", , "j3ffdick at gmail.com", role = c("aut", "cre"),
Modified: pkg/CHNOSZ/R/berman.R
===================================================================
--- pkg/CHNOSZ/R/berman.R 2018-03-14 17:54:46 UTC (rev 307)
+++ pkg/CHNOSZ/R/berman.R 2018-03-27 07:57:23 UTC (rev 308)
@@ -22,8 +22,11 @@
DS10 <- read.csv(paste0(dir, "/DS10.csv"), as.is=TRUE)
FDM14 <- read.csv(paste0(dir, "/FDM+14.csv"), as.is=TRUE)
BDat17 <- read.csv(paste0(dir, "/BDat17.csv"), as.is=TRUE)
- # assemble the files in reverse chronological order
- dat <- rbind(BDat17, FDM14, DS10, JUN92, ZS92, SHD91, Ber90, Ber88)
+ if(file.exists("berman.csv")) {
+ BDat_user <- read.csv("berman.csv", as.is=TRUE)
+ # assemble the files in reverse chronological order
+ dat <- rbind(BDat_user, BDat17, FDM14, DS10, JUN92, ZS92, SHD91, Ber90, Ber88)
+ } else dat <- rbind(BDat17, FDM14, DS10, JUN92, ZS92, SHD91, Ber90, Ber88)
# remove duplicates (only the first, i.e. most recent entry is kept)
dat <- dat[!duplicated(dat$name), ]
# remove the multipliers
@@ -38,6 +41,7 @@
if(missing(name)) return(dat)
# which row has data for this mineral?
irow <- which(dat$name == name)
+ if(length(irow)==0) stop("Data for ", name, " not available. Please add it to berman.csv")
# the function works fine with just the following assign() call,
# but an explicit dummy assignment here is used to avoid "Undefined global functions or variables" in R CMD check
GfPrTr <- HfPrTr <- SPrTr <- Tlambda <- Tmax <- Tmin <- Tref <- VPrTr <-
Modified: pkg/CHNOSZ/R/util.fasta.R
===================================================================
--- pkg/CHNOSZ/R/util.fasta.R 2018-03-14 17:54:46 UTC (rev 307)
+++ pkg/CHNOSZ/R/util.fasta.R 2018-03-27 07:57:23 UTC (rev 308)
@@ -42,7 +42,7 @@
nlines <- length(lines)
message(nlines, " lines ... ", appendLF=FALSE)
if(is.null(ihead)) ihead <- which(substr(lines,1,1)==">")
- message(length(ihead), " sequence headers")
+ message(length(ihead), " sequences")
linefun <- function(i1,i2) lines[i1:i2]
# identify the lines that begin and end each sequence
begin <- ihead + 1
Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS 2018-03-14 17:54:46 UTC (rev 307)
+++ pkg/CHNOSZ/inst/NEWS 2018-03-27 07:57:23 UTC (rev 308)
@@ -1,6 +1,21 @@
-CHANGES IN CHNOSZ 1.1.3-15 (2018-03-15)
+CHANGES IN CHNOSZ 1.1.3-16 (2018-03-27)
---------------------------------------
+BERMAN EQUATIONS AND DATA
+
+- berman() now reads data from a user-supplied file berman.csv if it is
+ present in the working directory.
+
+- Add mineral data from Berman and Aranovich, 1996 to
+ extdata/Berman/unused/BA96.csv.
+
+- Correct swapped v1 <-> v3 and v2 <-> v4 in extdata/Berman/DS10.csv.
+
+- Change files in extdata/Berman to be more like winTWQ format (no
+ value multipliers, except 10^5, 10^5, 10^5, and 10^8 on v1 to v4).
+
+OTHER CHANGES
+
- Lines in 1-D diagram()s can optionally be drawn as splines using the
method for splinefun() given in the 'spline.method' argument (the
default of NULL means no splines).
@@ -10,11 +25,6 @@
- Add 'srt' argument to diagram() (rotation of line labels).
-- Add mineral data from Berman and Aranovich, 1996 to
- extdata/Berman/unused/BA96.csv.
-
-- Correct swapped v1 <-> v3 and v2 <-> v4 in extdata/Berman/DS10.csv.
-
- Fix a bug where subcrt()$reaction$coeffs was incorrect for reactions
involving minerals with phase transitions.
@@ -34,15 +44,13 @@
- read.fasta(): add support for file connections created using
archive::archive_read (https://github.com/jimhester/archive).
-- Change files in extdata/Berman to be more like winTWQ format (no
- value multipliers, except 10^5, 10^5, 10^5, and 10^8 on v1 to v4).
-
- diagram(): rename 'what' argument to 'type'.
- digram(): add new type of diagram, 'saturation', which is used to
plot saturation lines for minerals (where their affinity equals
zero).
+
CHANGES IN CHNOSZ 1.1.3 (2017-11-13)
------------------------------------
Modified: pkg/CHNOSZ/man/berman.Rd
===================================================================
--- pkg/CHNOSZ/man/berman.Rd 2018-03-14 17:54:46 UTC (rev 307)
+++ pkg/CHNOSZ/man/berman.Rd 2018-03-27 07:57:23 UTC (rev 308)
@@ -24,12 +24,11 @@
\details{
This function calculates the thermodynamic properties of minerals at high \P and \T using equations given by Berman (1988).
-Becuase they use a different set of parameters than Helgeson et al., 1978 (see \code{\link{cgl}}), the standard state thermodynamic properties and parameters for the calculations are stored in files under \code{extdata/Berman}.
+The standard state thermodynamic properties and parameters for the calculations are stored in files under \code{extdata/Berman}, or can be read from a user-created file (if available) named \samp{berman.csv} in the working directory.
If the function is called with missing \code{name}, the data frame of parameters for all available minerals is returned.
-When \code{name} is given, it refers to a mineral that should listed in \code{thermo$obigt} with the state \samp{cr_Berman}.
-\code{thermo$obigt} also holds the chemical formula, which is required for calculating the entropies of the elements in the mineral.
-These entropies are used to convert the apparent Gibbs energies from the Berman-Brown convention to the the Benson-Helgeson convention (cf. Anderson, 2005).
+When \code{name} is given, it refers to a mineral that should listed in \code{thermo$obigt} with the state \samp{cr_Berman} and the chemical formula, and optinally an abbreviation and references, but all other properties set to NA.
+The chemical formula is required for calculating the entropies of the elements in the mineral, which are are used to convert the apparent Gibbs energies from the Berman-Brown convention to the the Benson-Helgeson convention (cf. Anderson, 2005).
If \code{check.G} is TRUE, the tabulated value of DGfTrPr is compared with one calculated from DHfPrTr - T*DSPrTr (DS is the difference between the summed entropies of the elements and the tabulated entropy for the mineral).
A warning is produced if the absolute value of the difference between tabulated and calculated DGfTrPr is greater than 1000 J/mol.
From noreply at r-forge.r-project.org Tue Mar 27 17:19:33 2018
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Tue, 27 Mar 2018 17:19:33 +0200 (CEST)
Subject: [CHNOSZ-commits] r309 - in pkg/CHNOSZ: . R data demo inst
inst/extdata/Berman/unused inst/extdata/OBIGT man
tests/testthat vignettes
Message-ID: <20180327151933.BDEE91896BE@r-forge.r-project.org>
Author: jedick
Date: 2018-03-27 17:19:33 +0200 (Tue, 27 Mar 2018)
New Revision: 309
Added:
pkg/CHNOSZ/inst/extdata/OBIGT/SUPCRT92.csv
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/R/berman.R
pkg/CHNOSZ/R/cgl.R
pkg/CHNOSZ/R/diagram.R
pkg/CHNOSZ/R/info.R
pkg/CHNOSZ/R/subcrt.R
pkg/CHNOSZ/R/util.data.R
pkg/CHNOSZ/R/util.misc.R
pkg/CHNOSZ/data/refs.csv
pkg/CHNOSZ/demo/DEW.R
pkg/CHNOSZ/demo/activity_ratios.R
pkg/CHNOSZ/demo/go-IU.R
pkg/CHNOSZ/inst/NEWS
pkg/CHNOSZ/inst/extdata/Berman/unused/BA96_obigt.csv
pkg/CHNOSZ/inst/extdata/OBIGT/Berman_cr.csv
pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv.xz
pkg/CHNOSZ/man/berman.Rd
pkg/CHNOSZ/man/diagram.Rd
pkg/CHNOSZ/man/info.Rd
pkg/CHNOSZ/man/util.misc.Rd
pkg/CHNOSZ/tests/testthat/test-basis.R
pkg/CHNOSZ/tests/testthat/test-berman.R
pkg/CHNOSZ/tests/testthat/test-makeup.R
pkg/CHNOSZ/tests/testthat/test-subcrt.R
pkg/CHNOSZ/vignettes/anintro.Rmd
pkg/CHNOSZ/vignettes/obigt.Rmd
Log:
Helgeson minerals are superseded by Berman dataset
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2018-03-27 07:57:23 UTC (rev 308)
+++ pkg/CHNOSZ/DESCRIPTION 2018-03-27 15:19:33 UTC (rev 309)
@@ -1,6 +1,6 @@
Date: 2018-03-27
Package: CHNOSZ
-Version: 1.1.3-16
+Version: 1.1.3-17
Title: Thermodynamic Calculations for Geobiochemistry
Authors at R: c(
person("Jeffrey", "Dick", , "j3ffdick at gmail.com", role = c("aut", "cre"),
Modified: pkg/CHNOSZ/R/berman.R
===================================================================
--- pkg/CHNOSZ/R/berman.R 2018-03-27 07:57:23 UTC (rev 308)
+++ pkg/CHNOSZ/R/berman.R 2018-03-27 15:19:33 UTC (rev 309)
@@ -49,7 +49,7 @@
# assign values to the variables used below
for(i in 1:ncol(dat)) assign(colnames(dat)[i], dat[irow, i])
# get the entropy of the elements using the chemical formula in thermo$obigt
- if(is.null(thisinfo)) thisinfo <- info(info(name, "cr_Berman", check.it=FALSE))
+ if(is.null(thisinfo)) thisinfo <- info(info(name, "cr", check.it=FALSE))
SPrTr_elements <- convert(entropy(thisinfo$formula), "J")
# check that G in data file is the G of formation from the elements --> Benson-Helgeson convention (DG = DH - T*DS)
if(check.G) {
Modified: pkg/CHNOSZ/R/cgl.R
===================================================================
--- pkg/CHNOSZ/R/cgl.R 2018-03-27 07:57:23 UTC (rev 308)
+++ pkg/CHNOSZ/R/cgl.R 2018-03-27 15:19:33 UTC (rev 309)
@@ -14,7 +14,7 @@
for(k in 1:nrow(parameters)) {
# the parameters for *this* species
PAR <- parameters[k, ]
- if(PAR$state=="cr_Berman") {
+ if(all(is.na(PAR[8:20]))) {
# use Berman equations (parameters not in thermo$obigt)
properties <- berman(PAR$name, T=T, P=P, thisinfo=PAR)
iprop <- match(property, colnames(properties))
Modified: pkg/CHNOSZ/R/diagram.R
===================================================================
--- pkg/CHNOSZ/R/diagram.R 2018-03-27 07:57:23 UTC (rev 308)
+++ pkg/CHNOSZ/R/diagram.R 2018-03-27 15:19:33 UTC (rev 309)
@@ -575,14 +575,6 @@
} # end if(nd==2)
} # end if(plot.it)
- # warn if we have a system with both Berman and Helgeson minerals 20180315
- ref1 <- get("thermo")$obigt$ref1
- ref2 <- get("thermo")$obigt$ref2
- ispecies <- eout$species$ispecies
- hasHelgeson <- any(grepl("HDNB78", ref1[ispecies])) | any(grepl("HDNB78", ref2[ispecies]))
- hasBerman <- any(get("thermo")$obigt$state[ispecies]=="cr_Berman")
- if(hasHelgeson & hasBerman) warning("the system has minerals from both the Helgeson and Berman datasets; data may not be internally consistent")
-
out <- c(eout, list(plotvar=plotvar, plotvals=plotvals, names=names, predominant=predominant), out2D)
return(invisible(out))
}
Modified: pkg/CHNOSZ/R/info.R
===================================================================
--- pkg/CHNOSZ/R/info.R 2018-03-27 07:57:23 UTC (rev 308)
+++ pkg/CHNOSZ/R/info.R 2018-03-27 15:19:33 UTC (rev 309)
@@ -131,11 +131,7 @@
# if a single name matches, use that one (useful for distinguishing pseudo-H4SiO4 and H4SiO4) 20171020
matches.name <- matches.species & thermo$obigt$name==species
if(sum(matches.name)==1) ispecies.out <- which(matches.name)
- else {
- # prefer the Berman minerals?
- if(thermo$opt$Berman & "cr_Berman" %in% thermo$obigt$state[ispecies]) ispecies.out <- ispecies[thermo$obigt$state[ispecies]=="cr_Berman"]
- else ispecies.out <- ispecies[1] # otherwise, return only the first species that matches
- }
+ else ispecies.out <- ispecies[1] # otherwise, return only the first species that matches
# let user know if there is more than one state for this species
mystate <- thermo$obigt$state[ispecies.out]
ispecies.other <- ispecies[!ispecies %in% ispecies.out]
Modified: pkg/CHNOSZ/R/subcrt.R
===================================================================
--- pkg/CHNOSZ/R/subcrt.R 2018-03-27 07:57:23 UTC (rev 308)
+++ pkg/CHNOSZ/R/subcrt.R 2018-03-27 15:19:33 UTC (rev 309)
@@ -147,15 +147,6 @@
ton <- thermo$obigt$name
tos <- thermo$obigt$state
- # warn if we're running a reaction with both Berman and Helgeson minerals 20171110
- if(do.reaction) {
- ref1 <- thermo$obigt$ref1
- ref2 <- thermo$obigt$ref2
- hasHelgeson <- any(grepl("HDNB78", ref1[sinfo])) | any(grepl("HDNB78", ref2[sinfo]))
- hasBerman <- any(tos[sinfo]=="cr_Berman")
- if(hasHelgeson & hasBerman) warning("the reaction has minerals from both the Helgeson and Berman datasets; data may not be internally consistent")
- }
-
# stop if species not found
noname <- is.na(sinfo)
if(TRUE %in% noname)
@@ -310,7 +301,7 @@
}
# crystalline, gas, liquid (except water) species
- cglstates <- c("liq", "cr", "gas", "cr2", "cr3", "cr4", "cr5", "cr6", "cr7", "cr8", "cr9", "cr_Berman")
+ cglstates <- c("liq", "cr", "gas", "cr2", "cr3", "cr4", "cr5", "cr6", "cr7", "cr8", "cr9")
iscgl <- reaction$state %in% cglstates & reaction$name != "water"
if(TRUE %in% iscgl) {
@@ -330,8 +321,8 @@
# name and state
myname <- reaction$name[i]
mystate <- reaction$state[i]
- # don't proceed if the state is cr_Berman
- if(mystate=="cr_Berman") next
+# # don't proceed if the state is cr_Berman
+# if(mystate=="cr_Berman") next
# if this phase is cr2 or higher, check if we're below the transition temperature
if(!(reaction$state[i] %in% c('liq','cr','gas'))) {
Ttr <- Ttr(inpho[i]-1,P=P,dPdT=dPdTtr(inpho[i]-1))
Modified: pkg/CHNOSZ/R/util.data.R
===================================================================
--- pkg/CHNOSZ/R/util.data.R 2018-03-27 07:57:23 UTC (rev 308)
+++ pkg/CHNOSZ/R/util.data.R 2018-03-27 15:19:33 UTC (rev 309)
@@ -256,6 +256,7 @@
if(what=="OBIGT") tdata <- get("thermo")$obigt
else if(what=="DEW") tdata <- read.csv(system.file("extdata/OBIGT/DEW_aq.csv", package="CHNOSZ"), as.is=TRUE)
else if(what=="SUPCRTBL") tdata <- read.csv(system.file("extdata/OBIGT/SUPCRTBL.csv", package="CHNOSZ"), as.is=TRUE)
+ else if(what=="SUPCRT92") tdata <- read.csv(system.file("extdata/OBIGT/SUPCRT92.csv", package="CHNOSZ"), as.is=TRUE)
ntot <- nrow(tdata)
# where to keep the results
DCp <- DV <- DG <- rep(NA,ntot)
@@ -288,6 +289,7 @@
# check optional data
out <- rbind(out, checkfun("DEW"))
out <- rbind(out, checkfun("SUPCRTBL"))
+ out <- rbind(out, checkfun("SUPCRT92"))
# set differences within a tolerance to NA
out$DCp[abs(out$DCp) < 1] <- NA
out$DV[abs(out$DV) < 1] <- NA
@@ -356,15 +358,17 @@
# dump all thermodynamic data in CHNOSZ 20171121
dumpdata <- function(file=NULL) {
# default database (OBIGT)
- Odata <- get("thermo")$obigt
- Odata <- cbind(source="OBIGT", Odata)
+ dat <- get("thermo")$obigt
+ OBIGT <- cbind(source="OBIGT", dat)
# optional data
- Ddata <- read.csv(system.file("extdata/OBIGT/DEW_aq.csv", package="CHNOSZ"), as.is=TRUE)
- Ddata <- cbind(source="DEW", Ddata)
- Sdata <- read.csv(system.file("extdata/OBIGT/SUPCRTBL.csv", package="CHNOSZ"), as.is=TRUE)
- Sdata <- cbind(source="SUPCRTBL", Sdata)
+ dat <- read.csv(system.file("extdata/OBIGT/DEW_aq.csv", package="CHNOSZ"), as.is=TRUE)
+ DEW <- cbind(source="DEW", dat)
+ dat <- read.csv(system.file("extdata/OBIGT/SUPCRTBL.csv", package="CHNOSZ"), as.is=TRUE)
+ SUPCRTBL <- cbind(source="SUPCRTBL", dat)
+ dat <- read.csv(system.file("extdata/OBIGT/SUPCRT92.csv", package="CHNOSZ"), as.is=TRUE)
+ SUPCRT92 <- cbind(source="SUPCRT92", dat)
# put it all together
- out <- rbind(Odata, Ddata, Sdata)
+ out <- rbind(OBIGT, DEW, SUPCRTBL, SUPCRT92)
# quote columns 2 (name) and 3 (abbrv) because they have commas for some entries
if(!is.null(file)) write.csv(out, file, row.names=FALSE, quote=c(2, 3))
else(return(out))
Modified: pkg/CHNOSZ/R/util.misc.R
===================================================================
--- pkg/CHNOSZ/R/util.misc.R 2018-03-27 07:57:23 UTC (rev 308)
+++ pkg/CHNOSZ/R/util.misc.R 2018-03-27 15:19:33 UTC (rev 309)
@@ -7,13 +7,13 @@
# (argument is index of the lower-T phase)
thermo <- get("thermo")
pars <- info(c(ispecies, ispecies+1), check.it=FALSE)
- # the special handling for quartz and coesite interferece with this function,
+ # if these aren't the same mineral all we can say is zero
+ # actually, should be infinity ... the volume change is zero
+ if(as.character(pars$name[1]) != as.character(pars$name[2])) return(Inf)
+ # the special handling for quartz and coesite interfere with this function,
# so we convert to uppercase names to prevent cgl() from calling quartz_coesite()
pars$name <- toupper(pars$name)
props <- cgl(c("G", "S", "V"), pars, P=0, T=thermo$obigt$z.T[ispecies])
- # if these aren't the same mineral all we can say is zero
- # actually, should be infinity ... the volume change is zero
- if(as.character(pars$name[1]) != as.character(pars$name[2])) return(Inf)
# we really hope the G's are the same ...
#if(abs(props[[2]]$G - props[[1]]$G) > 0.1) warning('dP.dT: inconsistent values of G for different phases of ',ispecies,call.=FALSE)
dP.dT <- convert( ( props[[2]]$S - props[[1]]$S ) / ( props[[2]]$V - props[[1]]$V ), 'cm3bar' )
Modified: pkg/CHNOSZ/data/refs.csv
===================================================================
--- pkg/CHNOSZ/data/refs.csv 2018-03-27 07:57:23 UTC (rev 308)
+++ pkg/CHNOSZ/data/refs.csv 2018-03-27 15:19:33 UTC (rev 309)
@@ -6,12 +6,13 @@
Pan70,"L. B. Pankratz",1970,"U. S. Bureau of Mines Report of Investigations 7430",chlorargyrite,http://www.worldcat.org/oclc/14154245
PK70,"L. B. Pankratz and E. G. King",1970,"U. S. Bureau of Mines Report of Investigations 7435","bornite and chalcopyrite",http://www.worldcat.org/oclc/14154292
FSR76,"M. J. Ferrante et al.",1976,"U. S. Bureau of Mines Report of Investigations 8129","dawsonite Cp (value at 25 °C as listed by @BPAH07; not present in spronsbl.dat)",http://www.worldcat.org/oclc/932914138
-HDNB78,"H. C. Helgeson, J. M. Delany et al.",1978,"Am. J. Sci. 278A, 1-229","data for minerals (n = 167) and phase transitions",http://www.worldcat.org/oclc/13594862
+HDNB78,"H. C. Helgeson, J. M. Delany et al.",1978,"Am. J. Sci. 278A, 1-229","data for minerals and phase transitions",http://www.worldcat.org/oclc/13594862
HDNB78.1,"H. C. Helgeson, J. M. Delany et al.",1978,"Am. J. Sci. 278A, 1-229","litharge S, V, and Cp parameters",http://www.worldcat.org/oclc/13594862
-RHF78,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1978,"U. S. Geological Survey Bull. 1452","chlorargyrite, rutile, and titanite",http://pubs.er.usgs.gov/publication/b1452
+RHF78,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1978,"U. S. Geological Survey Bull. 1452","chlorargyrite",http://pubs.er.usgs.gov/publication/b1452
RHF78.1,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1978,"U. S. Geological Survey Bull. 1452","dickite, fluorphlogopite, halloysite, and pyrope",http://pubs.er.usgs.gov/publication/b1452
RHF78.2,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1978,"U. S. Geological Survey Bull. 1452",iron,http://pubs.er.usgs.gov/publication/b1452
RHF78.3,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1978,"U. S. Geological Survey Bull. 1452","gibbsite GHS",http://pubs.er.usgs.gov/publication/b1452
+RHF78.4,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1978,"U. S. Geological Survey Bull. 1452","rutile and titanite",http://pubs.er.usgs.gov/publication/b1452
PB82,"L. N. Plummer and E. Busenberg",1982,"Geochim. Cosmochim. Acta 46, 1011-1040","aragonite and calcite",https://doi.org/10.1016/0016-7037(82)90056-4
WEP+82,"D. D. Wagman, W. H. Evans et al.",1982,"J. Phys. Chem. Ref. Data 11, Suppl. 2, 1-392","gases GHS",https://srd.nist.gov/JPCRD/jpcrdS2Vol11.pdf
WEP+82.1,"D. D. Wagman, W. H. Evans et al.",1982,"J. Phys. Chem. Ref. Data 11, Suppl. 2, 1-392",manganosite,https://srd.nist.gov/JPCRD/jpcrdS2Vol11.pdf
Modified: pkg/CHNOSZ/demo/DEW.R
===================================================================
--- pkg/CHNOSZ/demo/DEW.R 2018-03-27 07:57:23 UTC (rev 308)
+++ pkg/CHNOSZ/demo/DEW.R 2018-03-27 15:19:33 UTC (rev 309)
@@ -26,9 +26,9 @@
PT20.0 <- data.frame(P=20000, T=seq(200, 800, 10))
PT <- rbind(PT0.5, PT1.0, PT2.0, PT5.0, PT10.0, PT20.0)
# reaction 1: quartz = SiO2(aq) [equivalent to quartz + 3 H2O = Si(OH)4]
-SiO2_logK <- subcrt(c("quartz", "SiO2"), c("cr_Berman", "aq"), c(-1, 1), P=PT$P, T=PT$T)$out$logK
+SiO2_logK <- subcrt(c("quartz", "SiO2"), c("cr", "aq"), c(-1, 1), P=PT$P, T=PT$T)$out$logK
# reaction 2: 2 quartz = Si2O4(aq) [equivalent to 2 quartz + 3 H2O = Si2O(OH)6]
-Si2O4_logK <- subcrt(c("quartz", "Si2O4"), c("cr_Berman", "aq"), c(-2, 1), P=PT$P, T=PT$T)$out$logK
+Si2O4_logK <- subcrt(c("quartz", "Si2O4"), c("cr", "aq"), c(-2, 1), P=PT$P, T=PT$T)$out$logK
# plot the sum of molalities (== activities) for each pressure
plot(c(200, 1000), c(-2.5, 0.5), type="n", xlab=axis.label("T"), ylab="log molality")
for(P in unique(PT$P)) {
@@ -45,8 +45,7 @@
t1 <- quote("Solubility of"~alpha*"-quartz")
t2 <- "after Sverjensky et al., 2014a"
mtitle(as.expression(c(t1, t2)))
-# TODO: lines are a little low at highest P and P ...
-# does the Berman, 1988 quartz data increase high-PT solubilities?
+# TODO: lines are a little low at highest P and T ...
###########
#### plot 2: correlations between non-solvation volume and HKF a1 parameter
@@ -146,10 +145,8 @@
add.obigt("DEW", c(inorganics, organics[-4]))
## set basis species
basis(c("Fe", "SiO2", "CO3-2", "H2O", "oxygen", "H+"))
-## define a QFM buffer using Berman's equations for minerals
-mod.buffer("QFM_Berman", c("quartz", "fayalite", "magnetite"), "cr_Berman", 0)
## calculate logfO2 in QFM buffer
-basis("O2", "QFM_Berman")
+basis("O2", "QFM")
T <- seq(600, 1000, 100)
buf <- affinity(T=T, P=50000, return.buffer=TRUE)
## add species
Modified: pkg/CHNOSZ/demo/activity_ratios.R
===================================================================
--- pkg/CHNOSZ/demo/activity_ratios.R 2018-03-27 07:57:23 UTC (rev 308)
+++ pkg/CHNOSZ/demo/activity_ratios.R 2018-03-27 15:19:33 UTC (rev 309)
@@ -6,6 +6,13 @@
res <- 200
fill <- "terrain"
+data(thermo)
+## get data for gibbsite from the SUPCRT92 database, without loading minerals that
+## have been superseded by the Berman dataset (the default in CHNOSZ)
+add.obigt("SUPCRT92", "gibbsite")
+## or, get data for gibbsite and Al-bearing aqueous species from the SUPCRTBL database
+#add.obigt("SUPCRTBL")
+
## K2O-Al2O3-SiO2-H2O, 25 degree C, 1 bar
## Steinmann et al., 1994 (http://ccm.geoscienceworld.org/content/42/2/197)
## Garrels and Christ, p. 361 (http://www.worldcat.org/oclc/517586)
@@ -45,7 +52,7 @@
## CaO-Al2O3-MgO-SiO2-H2O at 300 degree C and 500 bar
## Bach and Klein, 2009 (https://doi.org/10.1016/j.lithos.2008.10.022)
basis(c("Ca+2", "Al+3", "Mg+2", "SiO2", "H2O", "O2", "H+"))
-species(c("clinochlore,14a", "clinozoisite", "prehnite", "grossular"))
+species(c("clinochlore", "clinozoisite", "prehnite", "grossular"))
a <- affinity(SiO2 = c(-5, 0, res), `Ca+2` = c(6, 11, res), T = 300, P = 500)
diagram(a, ylab = ratlab("Ca+2"), balance = "Al+3", fill = fill, yline = 1.7)
# (Hmmm... where is clinochlore? it doesn't appear on our diagram)
Modified: pkg/CHNOSZ/demo/go-IU.R
===================================================================
--- pkg/CHNOSZ/demo/go-IU.R 2018-03-27 07:57:23 UTC (rev 308)
+++ pkg/CHNOSZ/demo/go-IU.R 2018-03-27 15:19:33 UTC (rev 309)
@@ -21,18 +21,20 @@
thermo.plot.new(xlim=range(T), ylim=c(-3.5, -1.5), xlab = axis.label("T"), ylab=axis.label("SiO2"))
points(xT, xlogaSiO2)
basis(delete=TRUE)
-## first calculation: CHNOSZ default (SiO2 from SHS89, kaolinite and boehmite from HDNB78)
+## first calculation: after SUPCRT92 (SiO2(aq) from SHS89)
+add.obigt("SUPCRT92") # gets kaolinite and boehmite from HDNB78
r1 <- subcrt(c("boehmite", "H2O", "SiO2", "kaolinite"), c(-1, -0.5, -1, 0.5), T=T, P=1000, exceed.Ttr = TRUE)
# we need exceed.Ttr = TRUE because the T limit for boehmite is 500 K (Helgeson et al., 1978)
## second calculation: kaolinite from Berman, 1988
-Kln_Berman <- info("kaolinite", "cr_Berman")
-r2 <- subcrt(c("boehmite", "H2O", "SiO2", Kln_Berman), c(-1, -0.5, -1, 0.5), T=T, P=1000, exceed.Ttr = TRUE)
+data(thermo)
+add.obigt("SUPCRT92", "boehmite") # gets only boehmite from HDNB78
+r2 <- subcrt(c("boehmite", "H2O", "SiO2", "kaolinite"), c(-1, -0.5, -1, 0.5), T=T, P=1000, exceed.Ttr = TRUE)
## third calculation: boehmite from Hemingway et al., 1991
add.obigt("SUPCRTBL", "boehmite")
-r3 <- subcrt(c("boehmite", "H2O", "SiO2", Kln_Berman), c(-1, -0.5, -1, 0.5), T=T, P=1000)
+r3 <- subcrt(c("boehmite", "H2O", "SiO2", "kaolinite"), c(-1, -0.5, -1, 0.5), T=T, P=1000)
## fourth calculation: SiO2 from Apps and Spycher, 2004
add.obigt("SUPCRTBL", "SiO2")
-r4 <- subcrt(c("boehmite", "H2O", "SiO2", Kln_Berman), c(-1, -0.5, -1, 0.5), T=T, P=1000)
+r4 <- subcrt(c("boehmite", "H2O", "SiO2", "kaolinite"), c(-1, -0.5, -1, 0.5), T=T, P=1000)
## log activity of SiO2 is -ve logK
lines(T, -r1$out$logK)
lines(T, -r2$out$logK, lty=2)
@@ -41,7 +43,7 @@
## add points calculated using the SUPCRTBL package
points(seq(125, 350, 25), -c(3.489, 3.217, 2.967, 2.734, 2.517, 2.314, 2.124, 1.946, 1.781, 1.628), pch=4, col="red")
## add labels, legend, and title
-text(182.5, -3.17, "SUPCRT92\n(CHNOSZ default)", srt=48, cex=0.7, font=2)
+text(182.5, -3.17, "SUPCRT92", srt=48, cex=0.7, font=2)
text(154, -3.04, "circa SUPCRTBL", srt=45, cex=0.7, font=2, col="red")
legend("topleft", lty=c(1, 2, 2, 1, 0), pch=c(NA, NA, NA, NA, 4),
col=c("black", "black", "red", "red", "red"), bty="n", cex=0.9,
Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS 2018-03-27 07:57:23 UTC (rev 308)
+++ pkg/CHNOSZ/inst/NEWS 2018-03-27 15:19:33 UTC (rev 309)
@@ -1,8 +1,27 @@
-CHANGES IN CHNOSZ 1.1.3-16 (2018-03-27)
+CHANGES IN CHNOSZ 1.1.3-17 (2018-03-27)
---------------------------------------
-BERMAN EQUATIONS AND DATA
+THERMODYNAMIC DATA
+- The Berman data (Berman, 1988 and later additions) have replaced the
+ SUPCRT92 data (based on Helgeson et al., 1978) for most minerals in
+ the default database (i.e. the one loaded by data(thermo)). Only
+ native elements, sulfides, halides, sulfates, and selected carbonates
+ and oxides from SUPCRT92 that do not duplicate any in the Berman
+ dataset are loaded by default.
+
+- The superseded SUPCRT92 minerals (primarily the silicates and
+ Al-bearing minerals, as well as calcite, dolomite, hematite, and
+ magnetite) are in the file extdata/OBIGT/SUPCRT92.csv, which can be
+ loaded with add.obigt("SUPCRT92"). This is used in some examples for
+ comparing the datasets (see ?berman and demo(go-IU.R)), but should not
+ be needed by most users.
+
+- In thermo$obigt, the minerals using the Berman equations are
+ identified as those having NA values for all thermodynamic properties
+ (columns 8-20). These minerals have the state of "cr" (not "cr_Berman"
+ as before).
+
- berman() now reads data from a user-supplied file berman.csv if it is
present in the working directory.
Modified: pkg/CHNOSZ/inst/extdata/Berman/unused/BA96_obigt.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/Berman/unused/BA96_obigt.csv 2018-03-27 07:57:23 UTC (rev 308)
+++ pkg/CHNOSZ/inst/extdata/Berman/unused/BA96_obigt.csv 2018-03-27 15:19:33 UTC (rev 309)
@@ -1,21 +1,21 @@
name,abbrv,formula,state,ref1,ref2,date,G,H,S,Cp,V,a1.a,a2.b,a3.c,a4.d,c1.e,c2.f,omega.lambda,z.T
-almandine,Alm,Si3Fe3Al2O12,cr_Berman,BA96.1,NA,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-anthophyllite,Ath,Mg7Si8O24H2,cr_Berman,BA96.1,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-cordierite,Cd,Mg2Al4Si5O18,cr_Berman,Ber88,BA96.2,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-enstatite,En,MgSiO3,cr_Berman,Ber88,BA96.2,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-fayalite,Fa,Fe2SiO4,cr_Berman,BA96.1,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-ferrosilite,Fsl,SiFeO3,cr_Berman,BA96.1,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-forsterite,Fo,Mg2SiO4,cr_Berman,Ber88,BA96.3,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-hematite,Hm,Fe2O3,cr_Berman,Ber88,BA96.2,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-ilmenite,Ilm,FeTiO3,cr_Berman,Ber88,BA96.4,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-magnetite,Mt,Fe3O4,cr_Berman,Ber88,BA96.2,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-pyrope,Py,Mg3Al2Si3O12,cr_Berman,Ber88,BA96.3,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-rutile,Rt,TiO2,cr_Berman,Ber88,BA96.2,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-spinel,Sp,MgAl2O4,cr_Berman,Ber88,BA96.3,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-talc,Tc,Mg3Si4O12H2,cr_Berman,Ber88,BA96.4,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-Fe-cordierite,fCd,Fe2Al4Si5O18,cr_Berman,BA96,NA,12.Dec.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-geikelite,Gk,MgTiO3,cr_Berman,BA96,NA,12.Dec.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-hercynite,Hc,FeAl2O4,cr_Berman,BA96,NA,12.Dec.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-iron-a,aFe,Fe,cr_Berman,BA96,NA,12.Dec.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-iron-g,gFe,Fe,cr_Berman,BA96,NA,12.Dec.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-orthocorundum,Ok,Al2O3,cr_Berman,BA96,NA,12.Dec.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+almandine,Alm,Si3Fe3Al2O12,cr,BA96.1,NA,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+anthophyllite,Ath,Mg7Si8O24H2,cr,BA96.1,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+cordierite,Cd,Mg2Al4Si5O18,cr,Ber88,BA96.2,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+enstatite,En,MgSiO3,cr,Ber88,BA96.2,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+fayalite,Fa,Fe2SiO4,cr,BA96.1,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+ferrosilite,Fsl,SiFeO3,cr,BA96.1,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+forsterite,Fo,Mg2SiO4,cr,Ber88,BA96.3,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+hematite,Hm,Fe2O3,cr,Ber88,BA96.2,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+ilmenite,Ilm,FeTiO3,cr,Ber88,BA96.4,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+magnetite,Mt,Fe3O4,cr,Ber88,BA96.2,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+pyrope,Py,Mg3Al2Si3O12,cr,Ber88,BA96.3,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+rutile,Rt,TiO2,cr,Ber88,BA96.2,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+spinel,Sp,MgAl2O4,cr,Ber88,BA96.3,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+talc,Tc,Mg3Si4O12H2,cr,Ber88,BA96.4,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+Fe-cordierite,fCd,Fe2Al4Si5O18,cr,BA96,NA,12.Dec.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+geikelite,Gk,MgTiO3,cr,BA96,NA,12.Dec.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+hercynite,Hc,FeAl2O4,cr,BA96,NA,12.Dec.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+iron-a,aFe,Fe,cr,BA96,NA,12.Dec.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+iron-g,gFe,Fe,cr,BA96,NA,12.Dec.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+orthocorundum,Ok,Al2O3,cr,BA96,NA,12.Dec.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Modified: pkg/CHNOSZ/inst/extdata/OBIGT/Berman_cr.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/Berman_cr.csv 2018-03-27 07:57:23 UTC (rev 308)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/Berman_cr.csv 2018-03-27 15:19:33 UTC (rev 309)
@@ -1,87 +1,87 @@
name,abbrv,formula,state,ref1,ref2,date,G,H,S,Cp,V,a1.a,a2.b,a3.c,a4.d,c1.e,c2.f,omega.lambda,z.T
-akermanite,Ak,Ca2MgSi2O7,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-albite,Ab,NaAlSi3O8,cr_Berman,Ber88,SHD91,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-"albite,high",hAb,NaAlSi3O8,cr_Berman,Ber88,SHD91,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-"albite,low",lAb,NaAlSi3O8,cr_Berman,Ber88,SHD91,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-almandine,Alm,Si3Fe3Al2O12,cr_Berman,Ber88,Ber90.1,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-andalusite,And,Al2SiO5,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-anorthite,An,Al2CaSi2O8,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-anthophyllite,Ath,Mg7Si8O24H2,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-antigorite,Atg,Mg48Si34O99H62O48,cr_Berman,Ber88,BDat17.1,09.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-brucite,Br,MgO2H2,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-Ca-Al-pyroxene,CTs,CaAl2SiO6,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-calcite,Cc,CaCO3,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-chrysotile,Chr,Mg3Si2O9H4,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-clinochlore,Chl,Mg5Al2Si3O18H8,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-coesite,Cs,SiO2,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-cordierite,Cd,Mg2Al4Si5O18,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-corundum,Co,Al2O3,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-"cristobalite,alpha",aCr,SiO2,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-"cristobalite,beta",bCr,SiO2,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-diaspore,Dsp,AlO2H,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-diopside,Di,MgCaSi2O6,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-dolomite,Do,MgCaC2O6,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-"enstatite,clino",cEn,MgSiO3,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-enstatite,En,MgSiO3,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-"enstatite,proto",pEn,MgSiO3,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-fayalite,Fa,Fe2SiO4,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-ferrosilite,Fsl,SiFeO3,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-forsterite,Fo,Mg2SiO4,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-gehlenite,Ge,Al2Ca2SiO7,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-grossular,Gr,Ca3Al2Si3O12,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-hematite,Hm,Fe2O3,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-ilmenite,Ilm,FeTiO3,cr_Berman,Ber88,Ber90.1,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-jadeite,Jd,NaAlSi2O6,cr_Berman,Ber88,SHD91,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-kaolinite,Kln,Al2Si2O9H4,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-kyanite,Ky,Al2SiO5,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-lawsonite,Lw,CaAl2Si2O10H4,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-lime,Lm,CaO,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-magnesite,Mst,MgCO3,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-magnetite,Mt,Fe3O4,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-margarite,Mrg,CaAl4Si2O12H2,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-meionite,Me,Ca4Al6Si6O27C,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-merwinite,Mw,Ca3MgSi2O8,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-monticellite,Mo,CaMgSiO4,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-muscovite,Ms,KAl3Si3O12H2,cr_Berman,Ber88,SHD91,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-paragonite,Pg,NaAl3Si3O12H2,cr_Berman,Ber88,SHD91,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-periclase,Pe,MgO,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-phlogopite,Phl,KMg3AlSi3O12H2,cr_Berman,Ber88,SHD91.1,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-K-feldspar,Kfs,KAlSi3O8,cr_Berman,Ber88,SHD91,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-"K-feldspar,high",Sa,KAlSi3O8,cr_Berman,Ber88,SHD91,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-"K-feldspar,low",Mcr,KAlSi3O8,cr_Berman,Ber88,SHD91,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-prehnite,Prh,Ca2Al2Si3O12H2,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-pyrope,Py,Mg3Al2Si3O12,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-pyrophyllite,Prl,Al2Si4O12H2,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-quartz,aQz,SiO2,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-"quartz,beta",bQz,SiO2,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-rutile,Rt,TiO2,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-sillimanite,Si,Al2SiO5,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-sphene,Sph,CaTiSiO5,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-spinel,Sp,MgAl2O4,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-talc,Tc,Mg3Si4O12H2,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-tremolite,Tr,Ca2Mg5Si8O24H2,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-"tridymite,high",hTr,SiO2,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-"tridymite,low",lTr,SiO2,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-wollastonite,Wo,CaSiO3,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-pseudowollastonite,pWo,CaSiO3,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-zoisite,Zo,Ca2Al3Si3O13H,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-clinozoisite,cZo,Ca2Al3Si3O13H,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-annite,Ann,Si3Fe3AlKH2O12,cr_Berman,Ber90,SHD91.2,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-fluormuscovite,Flms,KAl3Si3O10F2,cr_Berman,ZS92,NA,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-fluorphlogopite,Fphl,KMg3AlSi3O10F2,cr_Berman,ZS92,NA,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-fluorannite,Flan,Si3Fe3AlKO10F2,cr_Berman,ZS92,NA,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-fluortremolite,Fltr,Ca2Mg5Si8O22F2,cr_Berman,ZS92,NA,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-fluorapatite,Flap,Ca5P3O12F,cr_Berman,ZS92,NA,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-hydroxyapatite,Hyap,Ca5P3O13H,cr_Berman,ZS92,NA,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-chlorapatite,Clap,Ca5P3O12Cl,cr_Berman,ZS92,NA,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-fluortalc,Fltc,Mg3Si4O10F2,cr_Berman,ZS92,NA,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-chlorphlogopite,Cphl,KMg3AlSi3O10Cl2,cr_Berman,ZS92,NA,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-chlorannite,Clan,Si3Fe3AlKO10Cl2,cr_Berman,ZS92,NA,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-glaucophane,Glc,Na2Al2Mg3Si8O24H2,cr_Berman,Eva90,JUN92,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-pumpellyite,Pmp,Ca4Al5MgSi6O28H7,cr_Berman,Eva90,JUN92,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-aragonite,Arg,CaCO3,cr_Berman,FDM+14.1,NA,08.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-hedenbergite,Hd,CaFeSi2O6,cr_Berman,DS10,NA,08.Nov.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-andradite,Adr,Ca3Fe2Si3O12,cr_Berman,DS10,NA,08.Nov.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-ferro-actinolite,Fac,Ca2Fe5Si8O22(OH)2,cr_Berman,DS10,NA,08.Nov.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-grunerite,Gru,Fe7Si8O22(OH)2,cr_Berman,DS10,NA,08.Nov.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-ilvaite,Ilv,CaFe2FeSi2O7O(OH),cr_Berman,DS10,NA,08.Nov.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+akermanite,Ak,Ca2MgSi2O7,cr,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+albite,Ab,NaAlSi3O8,cr,Ber88,SHD91,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+"albite,high",hAb,NaAlSi3O8,cr,Ber88,SHD91,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+"albite,low",lAb,NaAlSi3O8,cr,Ber88,SHD91,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+almandine,Alm,Si3Fe3Al2O12,cr,Ber88,Ber90.1,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+andalusite,And,Al2SiO5,cr,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+anorthite,An,Al2CaSi2O8,cr,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+anthophyllite,Ath,Mg7Si8O24H2,cr,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+antigorite,Atg,Mg48Si34O99H62O48,cr,Ber88,BDat17.1,09.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+brucite,Br,MgO2H2,cr,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+Ca-Al-pyroxene,CTs,CaAl2SiO6,cr,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+calcite,Cc,CaCO3,cr,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+chrysotile,Chr,Mg3Si2O9H4,cr,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+clinochlore,Chl,Mg5Al2Si3O18H8,cr,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+coesite,Cs,SiO2,cr,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+cordierite,Cd,Mg2Al4Si5O18,cr,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+corundum,Co,Al2O3,cr,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/chnosz -r 309
From noreply at r-forge.r-project.org Wed Mar 28 06:31:41 2018
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Wed, 28 Mar 2018 06:31:41 +0200 (CEST)
Subject: [CHNOSZ-commits] r310 - in pkg/CHNOSZ: . R inst inst/extdata/Berman
inst/extdata/Berman/unused inst/extdata/OBIGT man man/macros
Message-ID: <20180328043141.B8517189CB8@r-forge.r-project.org>
Author: jedick
Date: 2018-03-28 06:31:38 +0200 (Wed, 28 Mar 2018)
New Revision: 310
Added:
pkg/CHNOSZ/inst/extdata/Berman/sympy.R
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/R/berman.R
pkg/CHNOSZ/inst/NEWS
pkg/CHNOSZ/inst/extdata/Berman/BDat17.csv
pkg/CHNOSZ/inst/extdata/Berman/Ber88.csv
pkg/CHNOSZ/inst/extdata/Berman/Ber90.csv
pkg/CHNOSZ/inst/extdata/Berman/DS10.csv
pkg/CHNOSZ/inst/extdata/Berman/FDM+14.csv
pkg/CHNOSZ/inst/extdata/Berman/JUN92.csv
pkg/CHNOSZ/inst/extdata/Berman/SHD91.csv
pkg/CHNOSZ/inst/extdata/Berman/ZS92.csv
pkg/CHNOSZ/inst/extdata/Berman/unused/BA96.csv
pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv.xz
pkg/CHNOSZ/man/berman.Rd
pkg/CHNOSZ/man/extdata.Rd
pkg/CHNOSZ/man/macros/macros.Rd
Log:
berman(): add k4, k5, k6 to Cp equation
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2018-03-27 15:19:33 UTC (rev 309)
+++ pkg/CHNOSZ/DESCRIPTION 2018-03-28 04:31:38 UTC (rev 310)
@@ -1,6 +1,6 @@
-Date: 2018-03-27
+Date: 2018-03-28
Package: CHNOSZ
-Version: 1.1.3-17
+Version: 1.1.3-18
Title: Thermodynamic Calculations for Geobiochemistry
Authors at R: c(
person("Jeffrey", "Dick", , "j3ffdick at gmail.com", role = c("aut", "cre"),
Modified: pkg/CHNOSZ/R/berman.R
===================================================================
--- pkg/CHNOSZ/R/berman.R 2018-03-27 15:19:33 UTC (rev 309)
+++ pkg/CHNOSZ/R/berman.R 2018-03-28 04:31:38 UTC (rev 310)
@@ -29,14 +29,10 @@
} else dat <- rbind(BDat17, FDM14, DS10, JUN92, ZS92, SHD91, Ber90, Ber88)
# remove duplicates (only the first, i.e. most recent entry is kept)
dat <- dat[!duplicated(dat$name), ]
- # remove the multipliers
- multexp <- c(0, 0, 0, 0, # Ber88 Table 2
- 0, 0, 0, 0, # Table 3a
- 5, 5, 5, 8, # Table 4
- 0, 0, 0, 0, 0, 0, # Table 3b
- 0, 0, 0, 0, 0, 0, 0, 0 # Table 5
- )
- dat[, 2:27] <- t(t(dat[, 2:27]) / 10^multexp)
+ # remove the multipliers on volume parameters
+ vcols <- 13:16 # columns with v1, v2, v3, v4
+ multexp <- c(5, 5, 5, 8)
+ dat[, vcols] <- t(t(dat[, vcols]) / 10^multexp)
# if name is missing, return the entire data frame (used in test-berman.R)
if(missing(name)) return(dat)
# which row has data for this mineral?
@@ -45,7 +41,8 @@
# the function works fine with just the following assign() call,
# but an explicit dummy assignment here is used to avoid "Undefined global functions or variables" in R CMD check
GfPrTr <- HfPrTr <- SPrTr <- Tlambda <- Tmax <- Tmin <- Tref <- VPrTr <-
- d0 <- d1 <- d2 <- d3 <- d4 <- d5 <- dTdP <- k0 <- k1 <- k2 <- k3 <- l1 <- l2 <- v1 <- v2 <- v3 <- v4 <- NA
+ d0 <- d1 <- d2 <- d3 <- d4 <- d5 <- dTdP <- k0 <- k1 <- k2 <- k3 <-
+ k4 <- k5 <- k6 <- l1 <- l2 <- v1 <- v2 <- v3 <- v4 <- NA
# assign values to the variables used below
for(i in 1:ncol(dat)) assign(colnames(dat)[i], dat[irow, i])
# get the entropy of the elements using the chemical formula in thermo$obigt
@@ -63,26 +60,31 @@
### thermodynamic properties ###
# calculate Cp and V (Berman, 1988 Eqs. 4 and 5)
- Cp <- k0 + k1 * T^-0.5 + k2 * T^-2 + k3 * T^-3
+ # k4, k5, k6 terms from winTWQ documentation (doi:10.4095/223425)
+ Cp <- k0 + k1 * T^-0.5 + k2 * T^-2 + k3 * T^-3 + k4 * T^-1 + k5 * T + k6 * T^2
P_Pr <- P - Pr
T_Tr <- T - Tr
V <- VPrTr * (1 + v1 * P_Pr + v2 * P_Pr^2 + v3 * T_Tr + v4 * T_Tr^2)
- # calculate Ga (Ber88 Eq. 6) --> Berman-Brown convention (DG = DH - T*S)
- Ga <- HfPrTr - T * SPrTr + k0 * ( (T - Tr) - T * (log(T) - log(Tr)) ) +
- 2 * k1 * ( (T^0.5 - Tr^0.5) + T*(T^-0.5 - Tr^-0.5) ) -
- k2 * ( (T^-1 - Tr^-1) - T / 2 * (T^-2 - Tr^-2) ) -
- k3 * ( (T^-2 - Tr^-2) / 2 - T / 3 * (T^-3 - Tr^-3) ) +
- VPrTr * ( (v1 / 2 - v2) * (P^2 - Pr^2) + v2 / 3 * (P^3 - Pr^3) +
- (1 - v1 + v2 + v3 * (T - Tr) + v4 * (T - Tr)^2) * (P - Pr) )
+ ## calculate Ga (Ber88 Eq. 6) (superseded 20180328 as it does not include k4, k5, k6)
+ #Ga <- HfPrTr - T * SPrTr + k0 * ( (T - Tr) - T * (log(T) - log(Tr)) ) +
+ # 2 * k1 * ( (T^0.5 - Tr^0.5) + T*(T^-0.5 - Tr^-0.5) ) -
+ # k2 * ( (T^-1 - Tr^-1) - T / 2 * (T^-2 - Tr^-2) ) -
+ # k3 * ( (T^-2 - Tr^-2) / 2 - T / 3 * (T^-3 - Tr^-3) ) +
+ # VPrTr * ( (v1 / 2 - v2) * (P^2 - Pr^2) + v2 / 3 * (P^3 - Pr^3) +
+ # (1 - v1 + v2 + v3 * (T - Tr) + v4 * (T - Tr)^2) * (P - Pr) )
# calculate Ha (symbolically integrated using sympy - expressions not simplified)
- intCp <- T*k0 - Tr*k0 + k2/Tr - k2/T + k3/(2*Tr^2) - k3/(2*T^2) + 2.0*k1*T^0.5 - 2.0*k1*Tr^0.5
+ intCp <- T*k0 - Tr*k0 + k2/Tr - k2/T + k3/(2*Tr^2) - k3/(2*T^2) + 2.0*k1*T^0.5 - 2.0*k1*Tr^0.5 +
+ k4*log(T) - k4*log(Tr) + k5*T^2/2 - k5*Tr^2/2 - k6*Tr^3/3 + k6*T^3/3
intVminusTdVdT <- -VPrTr + P*(VPrTr + VPrTr*v2 - VPrTr*v1 - Tr*VPrTr*v3 + VPrTr*v4*Tr^2 - VPrTr*v4*T^2) +
P^2*(VPrTr*v1/2 - VPrTr*v2) + VPrTr*v1/2 - VPrTr*v2/3 + Tr*VPrTr*v3 + VPrTr*v4*T^2 - VPrTr*v4*Tr^2 + VPrTr*v2*P^3/3
Ha <- HfPrTr + intCp + intVminusTdVdT
# calculate S (also symbolically integrated)
- intCpoverT <- k0*log(T) - k0*log(Tr) - k3/(3*T^3) + k3/(3*Tr^3) + k2/(2*Tr^2) - k2/(2*T^2) + 2.0*k1*Tr^-0.5 - 2.0*k1*T^-0.5
+ intCpoverT <- k0*log(T) - k0*log(Tr) - k3/(3*T^3) + k3/(3*Tr^3) + k2/(2*Tr^2) - k2/(2*T^2) + 2.0*k1*Tr^-0.5 - 2.0*k1*T^-0.5 +
+ k4/Tr - k4/T + T*k5 - Tr*k5 + k6*T**2/2 - k6*Tr**2/2
intdVdT <- -VPrTr*(v3 + v4*(-2*Tr + 2*T)) + P*VPrTr*(v3 + v4*(-2*Tr + 2*T))
S <- SPrTr + intCpoverT - intdVdT
+ # calculate Ga --> Berman-Brown convention (DG = DH - T*S, no S(element))
+ Ga <- Ha - T * S
### polymorphic transition properties ***
if(!is.na(Tlambda) & !is.na(Tref) & any(T > Tref) & calc.transition) {
Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS 2018-03-27 15:19:33 UTC (rev 309)
+++ pkg/CHNOSZ/inst/NEWS 2018-03-28 04:31:38 UTC (rev 310)
@@ -1,4 +1,4 @@
-CHANGES IN CHNOSZ 1.1.3-17 (2018-03-27)
+CHANGES IN CHNOSZ 1.1.3-18 (2018-03-28)
---------------------------------------
THERMODYNAMIC DATA
@@ -22,6 +22,14 @@
(columns 8-20). These minerals have the state of "cr" (not "cr_Berman"
as before).
+- The heat capacity equation in berman() has been expanded to
+ Cp = k0 + k1T-1/2 + k2T-2 + k3T-3 + k4T-1 + k5T + k6T2 (as used in
+ winTWQ).
+
+- Multipliers on values in the Berman data files (extdata/Berman/*.csv)
+ have been removed, except for 10^5, 10^5, 10^5, and 10^8 on v1 to v4
+ (to be consistent with the winTWQ data format).
+
- berman() now reads data from a user-supplied file berman.csv if it is
present in the working directory.
@@ -30,9 +38,6 @@
- Correct swapped v1 <-> v3 and v2 <-> v4 in extdata/Berman/DS10.csv.
-- Change files in extdata/Berman to be more like winTWQ format (no
- value multipliers, except 10^5, 10^5, 10^5, and 10^8 on v1 to v4).
-
OTHER CHANGES
- Lines in 1-D diagram()s can optionally be drawn as splines using the
Modified: pkg/CHNOSZ/inst/extdata/Berman/BDat17.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/Berman/BDat17.csv 2018-03-27 15:19:33 UTC (rev 309)
+++ pkg/CHNOSZ/inst/extdata/Berman/BDat17.csv 2018-03-28 04:31:38 UTC (rev 310)
@@ -1,2 +1,2 @@
-name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,d5
-antigorite,-66076529,-71364156,3602.996,174.246,7394.51,0,-548363000,87284120000,-0.1485,4E-07,2.72,0.8,,,,,,,,,,,,,,
+name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,k4,k5,k6,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,d5
+antigorite,-66076529,-71364156,3602.996,174.246,7394.51,0,-548363000,87284120000,0,0,0,-0.1485,4E-07,2.72,0.8,,,,,,,,,,,,,,
Modified: pkg/CHNOSZ/inst/extdata/Berman/Ber88.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/Berman/Ber88.csv 2018-03-27 15:19:33 UTC (rev 309)
+++ pkg/CHNOSZ/inst/extdata/Berman/Ber88.csv 2018-03-28 04:31:38 UTC (rev 310)
@@ -1,68 +1,68 @@
-name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,d5
-akermanite,-3663786,-3860441,212,9.252,387.06,-2938.8,0,-40790000,-0.0785,0,2.5011,0.67224,358,298,0,0,0,452,,,,,,,,
-albite,-3703293,-3921618,224.412,10.083,393.64,-2415.5,-7892800,1070640000,-0.1945,4.861E-07,2.6307,0.32407,,,,,,,,,,,,,,
-"albite,high",-3703293,-3921618,224.412,10.083,393.64,-2415.5,-7892800,1070640000,-0.1945,4.861E-07,2.6307,0.32407,,,,,,,,,,,,,,
-"albite,low",-3711715,-3935100,207.443,10.043,393.64,-2415.5,-7892800,1070640000,-0.1945,4.861E-07,2.6307,0.32407,,,,,,,,,,,,,,
-almandine,-4941728,-5265502,339.927,11.511,573.96,-1483.1,-29292000,5022080000,-0.0558,3.21E-08,1.8613,0.74539,,,,,,,,,,,,,,
-andalusite,-2441806,-2589972,91.434,5.147,236.48,-1102.9,-7526800,936440000,-0.077,1.923E-07,2.3443,0.07189,,,,,,,,,,,,,,
-anorthite,-4003221,-4228730,200.186,10.075,439.37,-3734.1,0,-317020000,-0.1272,3.176E-07,1.0918,0.41985,,,,,,,,,,,,,,
-anthophyllite,-11342582,-12069032,535.195,26.56,1219.31,-5766.5,-34766100,4400900000,-0.1259,0,2.706,0.31325,,,,,,,,,,,,,,
-antigorite,-66076529,-71364156,3602.996,174.246,7394.51,0,-548363000,87284120000,-0.1978,4.944E-07,2.4965,0.39444,,,,,,,,,,,,,,
-brucite,-834868,-925937,63.064,2.468,136.84,-537.1,-4361900,552690000,-0.2023,6.726E-07,3.2854,0.1094,,,,,,,,,,,,,,
-Ca-Al-pyroxene,-3122310,-3298767,140.751,6.356,310.7,-1671.6,-7455300,948780000,-0.087,2.171E-07,2.225,0.52863,,,,,,,,,,,,,,
-calcite,-1128295,-1206819,91.725,3.69,178.19,-1657.7,-482700,166600000,-0.14,0,0.8907,2.27402,,,,,,,,,,,,,,
-chrysotile,-4035373,-4363356,220.134,10.72,610.02,-5581.2,-1857300,195470000,-0.181,4.524E-07,2.7151,0.67351,,,,,,,,,,,,,,
-clinochlore,-8250546,-8909590,435.154,21.147,1214.28,-11217.1,0,-1256250000,-0.1819,0,2.6452,0,,,,,,,,,,,,,,
-coesite,-852585,-907604,39.424,2.064,94.907,-767.3,-527900,26270000,-0.1037,3E-07,0.7396,0.43605,,,,,,,,,,,,,,
-cordierite,-8651517,-9158727,417.97,23.311,954.39,-7962.3,-2317300,-370210000,-0.1158,0,0.3003,0.18017,,,,,,,,,,,,,,
-corundum,-1582199,-1675700,50.82,2.558,155.02,-828.4,-3861400,409080000,-0.0385,3.75E-08,2.1342,0.4718,,,,,,,,,,,,,,
-"cristobalite,alpha",-853918,-907753,43.394,2.587,83.51,-374.7,-2455400,280070000,-0.2515,0,2.0824,0,535,298,0.048,-0.14216,0.00044142,0,,,,,,,,
-"cristobalite,beta",-853327,-906377,46.029,2.73,83.51,-374.7,-2455400,280070000,-0.11,5.535E-07,0.3189,0,,,,,,,,,,,,,,
-diaspore,-920806,-999378,35.308,1.776,143.24,-1540.4,-323100,64630000,-0.0599,0,2.9718,0,,,,,,,,,,,,,,
-diopside,-3026202,-3200583,142.5,6.62,305.41,-1604.9,-7166000,921840000,-0.0872,1.707E-07,2.7795,0.83082,,,,,,,,,,,,,,
-dolomite,-2162354,-2325248,154.89,6.432,328.48,-2554.4,-4688500,790380000,-0.107,0,1.423,3.63778,,,,,,,1423,298,-9.42,0,385000,0.01732,5.02E-06,0
-"enstatite,clino",-1458601,-1545926,66.325,3.131,139.96,-497,-4400200,535710000,-0.075,4.48E-08,2.1915,0.7492,,,,,,,,,,,,,,
-enstatite,-1458181,-1545552,66.17,3.133,166.58,-1200.6,-2270600,279150000,-0.0749,4.47E-08,2.4656,0.7467,,,,,,,,,,,,,,
-"enstatite,proto",-1456965,-1543959,67.438,3.242,166.58,-1200.6,-2270600,279150000,-0.075,4.48E-08,1.6832,1.1665,,,,,,,,,,,,,,
-fayalite,-1380154,-1479360,150.93,4.63,248.93,-1923.9,0,-139100000,-0.073,0,2.6546,0.79482,,,,,,,,,,,,,,
-ferrosilite,-1117472,-1194375,95.882,3.296,169.06,-1193,-2097100,292530000,-0.099,0,3.1808,0.7585,,,,,,,,,,,,,,
-forsterite,-2055023,-2174420,94.01,4.366,238.64,-2001.3,0,-116240000,-0.0791,1.351E-07,2.9464,0.88633,,,,,,,,,,,,,,
-gehlenite,-3785954,-3988158,198.6,9.033,373.09,-2276.8,-4778500,477910000,-0.0996,2.488E-07,2.4926,0.05664,,,,,,,1600,698,-221.74,0,17291000,0.3695,-0.0001469,0
-grossular,-6270974,-6632859,255.15,12.538,573.43,-2039.4,-18887200,2319310000,-0.0654,1.635E-07,1.8994,0.79756,,,,,,,,,,,,,,
-hematite,-743681,-825627,87.437,3.027,146.86,0,-5576800,525630000,-0.0479,3.04E-08,3.831,0.0165,955,298,0,-0.07403,0.00027921,1287,,,,,,,,
-ilmenite,-1155320,-1231947,108.628,3.17,150,-441.6,-3323700,348150000,-0.0584,1.23E-07,2.7248,0.29968,,,,,,,,,,,,,,
-jadeite,-2846482,-3025118,133.574,6.034,311.29,-2005.1,-5350300,662570000,-0.086,2.149E-07,2.3118,0.25785,,,,,,,,,,,,,,
-kaolinite,-3799770,-4120327,203.7,9.952,523.23,-4426.7,-2244300,92310000,-0.12,0,3.2,0,,,,,,,,,,,,,,
-kyanite,-2443370,-2594220,82.43,4.412,262.68,-2001.4,-1999700,-63180000,-0.0646,0,2.3973,0,,,,,,,,,,,,,,
-lawsonite,-4509709,-4865666,229.176,10.144,728.67,-8248.1,0,850560000,-0.0769,1.922E-07,2.6283,0,,,,,,,,,,,,,,
-lime,-603350,-635090,37.75,1.676,58.79,-133.9,-1147100,102980000,-0.1022,2.565E-07,3.461,0.67406,,,,,,,,,,,,,,
-magnesite,-1029875,-1113636,65.21,2.803,162.3,-1109.3,-4882600,874660000,-0.089,2.212E-07,1.8436,4.15968,,,,,,,,,,,,,,
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-margarite,-5852244,-6236603,265.084,12.958,699.8,-5587.1,-6807700,734320000,-0.1155,2.886E-07,2.1019,1.24556,,,,,,,,,,,,,,
-meionite,-13105915,-13849723,730,34.036,1511.35,-13243.3,0,-751610000,-0.111,0,0.934,0,,,,,,,,,,,,,,
-merwinite,-4309707,-4537497,251.777,9.847,453.62,-3250,0,-344230000,-0.0551,1.381E-07,2.9376,0.87235,,,,,,,,,,,,,,
-monticellite,-2132222,-2250027,108.3,5.148,226.34,-1542.7,-1179700,-23290000,-0.0904,2E-07,2.7863,0.76339,,,,,,,,,,,,,,
-muscovite,-5596723,-5976740,293.157,14.087,651.49,-3873.2,-18523200,2742470000,-0.1717,4.295E-07,3.3527,0,,,,,,,,,,,,,,
-paragonite,-5563572,-5944208,277.699,13.216,577.57,-1472.8,-32214400,5050080000,-0.1973,4.933E-07,3.9424,0.59701,,,,,,,,,,,,,,
-periclase,-569209,-601500,26.951,1.125,61.11,-296.2,-621200,5840000,-0.0622,1.511E-07,3.7477,0.03556,,,,,,,,,,,,,,
-phlogopite,-5827224,-6207342,334.158,14.977,610.38,-2083.8,-21533000,2841040000,-0.1697,0,3.4447,0,,,,,,,,,,,,,,
-K-feldspar,-3745415,-3970791,214.145,10.869,381.37,-1941,-12037300,1836430000,-0.1805,5.112E-07,1.5145,0.5485,,,,,,,1436,298,282.98,-4830,3621000,-0.15733,3.477E-05,410630
-"K-feldspar,high",-3738804,-3959704,229.157,10.896,381.37,-1941,-12037300,1836430000,-0.1805,5.112E-07,1.5145,0.5485,,,,,,,,,,,,,,
-"K-feldspar,low",-3745415,-3970791,214.145,10.869,381.37,-1941,-12037300,1836430000,-0.1805,5.112E-07,1.5145,0.5485,,,,,,,,,,,,,,
-prehnite,-5820154,-6198606,288.634,14.016,716.05,-6404.6,-2182500,268500000,-0.1427,0,0.1468,11.28353,,,,,,,,,,,,,,
-pyrope,-5936009,-6286548,266.359,11.316,640.72,-4542.1,-4701900,0,-0.0576,4.42E-08,2.2519,0.37044,,,,,,,,,,,,,,
-pyrophyllite,-5266865,-5640781,239.4,12.76,665.93,-5897.4,-4979900,661810000,-0.1354,0,1.2637,3.81661,,,,,,,,,,,,,,
-quartz,-856288,-910700,41.46,2.269,80.01,-240.3,-3546700,491570000,-0.2434,1.0137E-06,2.3895,0,848,373,0.0237,-0.09187,0.00024607,0,,,,,,,,
-"quartz,beta",-855033,-908627,44.207,2.37,80.01,-240.3,-3546700,491570000,-0.1238,7.087E-07,0,0,,,,,,,,,,,,,,
-rutile,-889497,-944750,50.46,1.882,77.84,0,-3367800,402940000,-0.0454,5.84E-08,2.5716,0.15409,,,,,,,,,,,,,,
-sillimanite,-2439265,-2586091,95.93,4.983,256.73,-1887.2,-2977400,250960000,-0.0753,0,1.3431,0,,,,,,,,,,,,,,
-sphene,-2455134,-2596652,129.29,5.565,234.62,-1040.3,-5118300,591460000,-0.059,0,2.52,0,,,,,,,,,,,,,,
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-talc,-5517657,-5897387,261.24,13.61,664.11,-5187.2,-2147200,-327370000,-0.1699,5.665E-07,2.9447,0,,,,,,,,,,,,,,
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-"tridymite,high",-853844,-907045,45.524,2.737,75.37,0,-5958100,958250000,-0.074,3.735E-07,0.4829,0,,,,,,,,,,,,,,
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-zoisite,-6494148,-6889488,297.576,13.588,749.17,-6509.3,-2380500,124860000,-0.0515,1.288E-07,3.467,0,,,,,,,,,,,,,,
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+name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,k4,k5,k6,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,d5
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+lime,-603350,-635090,37.75,1.676,58.79,-133.9,-1147100,102980000,0,0,0,-0.1022,2.565E-07,3.461,0.67406,,,,,,,,,,,,,,
+magnesite,-1029875,-1113636,65.21,2.803,162.3,-1109.3,-4882600,874660000,0,0,0,-0.089,2.212E-07,1.8436,4.15968,,,,,,,,,,,,,,
+magnetite,-1014235,-1117403,146.114,4.452,207.93,0,-7243300,664360000,0,0,0,-0.0582,1.751E-07,3.0291,1.3847,848,298,0,-0.19502,0.00061037,1565,,,,,,,,
+margarite,-5852244,-6236603,265.084,12.958,699.8,-5587.1,-6807700,734320000,0,0,0,-0.1155,2.886E-07,2.1019,1.24556,,,,,,,,,,,,,,
+meionite,-13105915,-13849723,730,34.036,1511.35,-13243.3,0,-751610000,0,0,0,-0.111,0,0.934,0,,,,,,,,,,,,,,
+merwinite,-4309707,-4537497,251.777,9.847,453.62,-3250,0,-344230000,0,0,0,-0.0551,1.381E-07,2.9376,0.87235,,,,,,,,,,,,,,
+monticellite,-2132222,-2250027,108.3,5.148,226.34,-1542.7,-1179700,-23290000,0,0,0,-0.0904,2E-07,2.7863,0.76339,,,,,,,,,,,,,,
+muscovite,-5596723,-5976740,293.157,14.087,651.49,-3873.2,-18523200,2742470000,0,0,0,-0.1717,4.295E-07,3.3527,0,,,,,,,,,,,,,,
+paragonite,-5563572,-5944208,277.699,13.216,577.57,-1472.8,-32214400,5050080000,0,0,0,-0.1973,4.933E-07,3.9424,0.59701,,,,,,,,,,,,,,
+periclase,-569209,-601500,26.951,1.125,61.11,-296.2,-621200,5840000,0,0,0,-0.0622,1.511E-07,3.7477,0.03556,,,,,,,,,,,,,,
+phlogopite,-5827224,-6207342,334.158,14.977,610.38,-2083.8,-21533000,2841040000,0,0,0,-0.1697,0,3.4447,0,,,,,,,,,,,,,,
+K-feldspar,-3745415,-3970791,214.145,10.869,381.37,-1941,-12037300,1836430000,0,0,0,-0.1805,5.112E-07,1.5145,0.5485,,,,,,,1436,298,282.98,-4830,3621000,-0.15733,3.477E-05,410630
+"K-feldspar,high",-3738804,-3959704,229.157,10.896,381.37,-1941,-12037300,1836430000,0,0,0,-0.1805,5.112E-07,1.5145,0.5485,,,,,,,,,,,,,,
+"K-feldspar,low",-3745415,-3970791,214.145,10.869,381.37,-1941,-12037300,1836430000,0,0,0,-0.1805,5.112E-07,1.5145,0.5485,,,,,,,,,,,,,,
+prehnite,-5820154,-6198606,288.634,14.016,716.05,-6404.6,-2182500,268500000,0,0,0,-0.1427,0,0.1468,11.28353,,,,,,,,,,,,,,
+pyrope,-5936009,-6286548,266.359,11.316,640.72,-4542.1,-4701900,0,0,0,0,-0.0576,4.42E-08,2.2519,0.37044,,,,,,,,,,,,,,
+pyrophyllite,-5266865,-5640781,239.4,12.76,665.93,-5897.4,-4979900,661810000,0,0,0,-0.1354,0,1.2637,3.81661,,,,,,,,,,,,,,
+quartz,-856288,-910700,41.46,2.269,80.01,-240.3,-3546700,491570000,0,0,0,-0.2434,1.0137E-06,2.3895,0,848,373,0.0237,-0.09187,0.00024607,0,,,,,,,,
+"quartz,beta",-855033,-908627,44.207,2.37,80.01,-240.3,-3546700,491570000,0,0,0,-0.1238,7.087E-07,0,0,,,,,,,,,,,,,,
+rutile,-889497,-944750,50.46,1.882,77.84,0,-3367800,402940000,0,0,0,-0.0454,5.84E-08,2.5716,0.15409,,,,,,,,,,,,,,
+sillimanite,-2439265,-2586091,95.93,4.983,256.73,-1887.2,-2977400,250960000,0,0,0,-0.0753,0,1.3431,0,,,,,,,,,,,,,,
+sphene,-2455134,-2596652,129.29,5.565,234.62,-1040.3,-5118300,591460000,0,0,0,-0.059,0,2.52,0,,,,,,,,,,,,,,
+spinel,-2176537,-2300313,84.535,3.977,235.9,-1766.6,-1710400,40620000,0,0,0,-0.0489,0,2.1691,0.50528,,,,,,,,,,,,,,
+talc,-5517657,-5897387,261.24,13.61,664.11,-5187.2,-2147200,-327370000,0,0,0,-0.1699,5.665E-07,2.9447,0,,,,,,,,,,,,,,
+tremolite,-11578548,-12305578,551.15,27.268,1229.36,-6401.9,-32089900,4208810000,0,0,0,-0.1392,3.481E-07,2.4374,0.98338,,,,,,,,,,,,,,
+"tridymite,low",-854026,-907750,43.77,2.675,75.37,0,-5958100,958250000,0,0,0,-0.2508,0,1.9339,0,383,298,0,0.4267,-0.00144575,130,,,,,,,,
+"tridymite,high",-853844,-907045,45.524,2.737,75.37,0,-5958100,958250000,0,0,0,-0.074,3.735E-07,0.4829,0,,,,,,,,,,,,,,
+wollastonite,-1546123,-1631500,81.81,3.983,149.07,-690.3,-3659300,484350000,0,0,0,-0.1245,3.113E-07,2.818,0,,,,,,,,,,,,,,
+pseudowollastonite,-1543085,-1627427,85.279,4.016,141.16,-417.2,-5857600,940740000,0,0,0,-0.1245,3.113E-07,2.818,0,,,,,,,,,,,,,,
+zoisite,-6494148,-6889488,297.576,13.588,749.17,-6509.3,-2380500,124860000,0,0,0,-0.0515,1.288E-07,3.467,0,,,,,,,,,,,,,,
+clinozoisite,-6496497,-6894968,287.076,13.673,749.17,-6509.3,-2380500,124860000,0,0,0,-0.0515,1.288E-07,3.467,0,,,,,,,,,,,,,,
Modified: pkg/CHNOSZ/inst/extdata/Berman/Ber90.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/Berman/Ber90.csv 2018-03-27 15:19:33 UTC (rev 309)
+++ pkg/CHNOSZ/inst/extdata/Berman/Ber90.csv 2018-03-28 04:31:38 UTC (rev 310)
@@ -1,5 +1,5 @@
-name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,d5
-almandine,-4943492,-5267216,340.007,11.511,573.96,-1483.1,-29292000,5022080000,-0.0558,3.21E-08,1.8613,0.74539,,,,,,,,,,,,,,
-annite,-4793115,-5142800,420,15.408,727.21,-4775.04,-13831900,2119060000,-0.1697,0,3.4447,0,,,,,,,,,,,,,,
-ilmenite,-1155794,-1232448,108.628,3.17,150,-441.6,-3323700,348150000,-0.0584,1.23E-07,2.7248,0.29968,,,,,,,,,,,,,,
-phlogopite,-5830350,-6210391,334.346,14.977,610.38,-2083.8,-21533000,2841040000,-0.1697,0,3.4447,0,,,,,,,,,,,,,,
+name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,k4,k5,k6,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,d5
+almandine,-4943492,-5267216,340.007,11.511,573.96,-1483.1,-29292000,5022080000,0,0,0,-0.0558,3.21E-08,1.8613,0.74539,,,,,,,,,,,,,,
+annite,-4793115,-5142800,420,15.408,727.21,-4775.04,-13831900,2119060000,0,0,0,-0.1697,0,3.4447,0,,,,,,,,,,,,,,
+ilmenite,-1155794,-1232448,108.628,3.17,150,-441.6,-3323700,348150000,0,0,0,-0.0584,1.23E-07,2.7248,0.29968,,,,,,,,,,,,,,
+phlogopite,-5830350,-6210391,334.346,14.977,610.38,-2083.8,-21533000,2841040000,0,0,0,-0.1697,0,3.4447,0,,,,,,,,,,,,,,
Modified: pkg/CHNOSZ/inst/extdata/Berman/DS10.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/Berman/DS10.csv 2018-03-27 15:19:33 UTC (rev 309)
+++ pkg/CHNOSZ/inst/extdata/Berman/DS10.csv 2018-03-28 04:31:38 UTC (rev 310)
@@ -1,6 +1,6 @@
-name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,d5
-hedenbergite,-2674300,-2837802.5,173.59,6.785,353.31148,-3106.646,2047911.742,-563018581,-0.17457,1.51E-06,2.796487,0,,,,,,,,,,,,,,
-andradite,-5419000,-5761985.8,316.4,13.167,569.7558,-1441.44,-22441040.802,3146543781,-0.06539136,1.635E-07,2.072525,0.561,,,,,,,,,,,,,,
-ferro-actinolite,-9839000,-10518042.6,685.1,28.26,1321.15758,-8966.454,-21705844.286,3236159154,-0.15,0,2.84,0,,,,,,,,,,,,,,
-grunerite,-8964807,-9623000,725,27.8,1347.83,-9356.91,-20228480,3039190000,-0.15,0,2.84,0,,,,,,,,,,,,,,
-ilvaite,-3440000,-3695605.5,291.5,10.016,682.79138,-8787.112,30183568.71,-5666432624,-0.06838,2.4E-08,1.801543,1.152,,,,,,,,,,,,,,
+name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,k4,k5,k6,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,d5
+hedenbergite,-2674300,-2837802.5,173.59,6.785,353.31148,-3106.646,2047911.742,-563018581,0,0,0,-0.17457,1.51E-06,2.796487,0,,,,,,,,,,,,,,
+andradite,-5419000,-5761985.8,316.4,13.167,569.7558,-1441.44,-22441040.802,3146543781,0,0,0,-0.06539136,1.635E-07,2.072525,0.561,,,,,,,,,,,,,,
+ferro-actinolite,-9839000,-10518042.6,685.1,28.26,1321.15758,-8966.454,-21705844.286,3236159154,0,0,0,-0.15,0,2.84,0,,,,,,,,,,,,,,
+grunerite,-8964807,-9623000,725,27.8,1347.83,-9356.91,-20228480,3039190000,0,0,0,-0.15,0,2.84,0,,,,,,,,,,,,,,
+ilvaite,-3440000,-3695605.5,291.5,10.016,682.79138,-8787.112,30183568.71,-5666432624,0,0,0,-0.06838,2.4E-08,1.801543,1.152,,,,,,,,,,,,,,
Modified: pkg/CHNOSZ/inst/extdata/Berman/FDM+14.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/Berman/FDM+14.csv 2018-03-27 15:19:33 UTC (rev 309)
+++ pkg/CHNOSZ/inst/extdata/Berman/FDM+14.csv 2018-03-28 04:31:38 UTC (rev 310)
@@ -1,2 +1,2 @@
-name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,d5
-aragonite,-1128353.67,-1207213.7,88.7,3.42,195,-2100,-10000,220000000,-0.1345,1.7E-07,4.18,0,,,,,,,,,,,,,,
+name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,k4,k5,k6,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,d5
+aragonite,-1128353.67,-1207213.7,88.7,3.42,195,-2100,-10000,220000000,0,0,0,-0.1345,1.7E-07,4.18,0,,,,,,,,,,,,,,
Modified: pkg/CHNOSZ/inst/extdata/Berman/JUN92.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/Berman/JUN92.csv 2018-03-27 15:19:33 UTC (rev 309)
+++ pkg/CHNOSZ/inst/extdata/Berman/JUN92.csv 2018-03-28 04:31:38 UTC (rev 310)
@@ -1,3 +1,3 @@
-name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,d5
-glaucophane,-11225858,-11960500,535,26.05,1717.5,-19272,7050000,0,-0.116,2.9E-07,2.2,0.88,,,,,,,,,,,,,,
-pumpellyite,-13448936,-14402300,584,29.55,1576,-10603.8,-28304200,3838351000,-0.051516,1.288E-07,3.467,0,,,,,,,,,,,,,,
+name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,k4,k5,k6,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,d5
+glaucophane,-11225858,-11960500,535,26.05,1717.5,-19272,7050000,0,0,0,0,-0.116,2.9E-07,2.2,0.88,,,,,,,,,,,,,,
+pumpellyite,-13448936,-14402300,584,29.55,1576,-10603.8,-28304200,3838351000,0,0,0,-0.051516,1.288E-07,3.467,0,,,,,,,,,,,,,,
Modified: pkg/CHNOSZ/inst/extdata/Berman/SHD91.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/Berman/SHD91.csv 2018-03-27 15:19:33 UTC (rev 309)
+++ pkg/CHNOSZ/inst/extdata/Berman/SHD91.csv 2018-03-28 04:31:38 UTC (rev 310)
@@ -1,12 +1,12 @@
-name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,d5
-muscovite,-5603417,-5983434,293.157,14.087,651.49,-3873.2,-18523200,2742470000,-0.1717,4.295E-07,3.3527,0,,,,,,,,,,,,,,
-phlogopite,-5837044,-6217085,334.346,14.977,610.38,-2083.8,-21533000,2841040000,-0.1697,0,3.4447,0,,,,,,,,,,,,,,
-K-feldspar,-3752109,-3977485,214.145,10.869,381.37,-1941,-12037300,1836430000,-0.1805,5.112E-07,1.5145,0.5485,,,,,,,1436,298,282.98,-4830,3621000,-0.15733,3.477E-05,410630
-"K-feldspar,high",-3745498,-3966398,229.157,10.896,381.37,-1941,-12037300,1836430000,-0.1805,5.112E-07,1.5145,0.5485,,,,,,,,,,,,,,
-"K-feldspar,low",-3752109,-3977485,214.145,10.869,381.37,-1941,-12037300,1836430000,-0.1805,5.112E-07,1.5145,0.5485,,,,,,,,,,,,,,
-paragonite,-5570375,-5951011,277.699,13.216,577.57,-1472.8,-32214400,5050080000,-0.1973,4.933E-07,3.9424,0.59701,,,,,,,,,,,,,,
-albite,-3710096,-3928421,224.412,10.083,393.64,-2415.5,-7892800,1070640000,-0.1945,4.861E-07,2.6307,0.32407,,,,,,,,,,,,,,
-"albite,high",-3710096,-3928421,224.412,10.083,393.64,-2415.5,-7892800,1070640000,-0.1945,4.861E-07,2.6307,0.32407,,,,,,,,,,,,,,
-"albite,low",-3718518,-3941903,207.443,10.043,393.64,-2415.5,-7892800,1070640000,-0.1945,4.861E-07,2.6307,0.32407,,,,,,,,,,,,,,
-jadeite,-2853285,-3031921,133.574,6.034,311.29,-2005.1,-5350300,662570000,-0.086,2.149E-07,2.3118,0.25785,,,,,,,,,,,,,,
-annite,-4799809,-5149494,420,15.408,727.21,-4775.04,-13831900,2119060000,-0.1697,0,3.4447,0,,,,,,,,,,,,,,
+name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,k4,k5,k6,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,d5
+muscovite,-5603417,-5983434,293.157,14.087,651.49,-3873.2,-18523200,2742470000,0,0,0,-0.1717,4.295E-07,3.3527,0,,,,,,,,,,,,,,
+phlogopite,-5837044,-6217085,334.346,14.977,610.38,-2083.8,-21533000,2841040000,0,0,0,-0.1697,0,3.4447,0,,,,,,,,,,,,,,
+K-feldspar,-3752109,-3977485,214.145,10.869,381.37,-1941,-12037300,1836430000,0,0,0,-0.1805,5.112E-07,1.5145,0.5485,,,,,,,1436,298,282.98,-4830,3621000,-0.15733,3.477E-05,410630
+"K-feldspar,high",-3745498,-3966398,229.157,10.896,381.37,-1941,-12037300,1836430000,0,0,0,-0.1805,5.112E-07,1.5145,0.5485,,,,,,,,,,,,,,
+"K-feldspar,low",-3752109,-3977485,214.145,10.869,381.37,-1941,-12037300,1836430000,0,0,0,-0.1805,5.112E-07,1.5145,0.5485,,,,,,,,,,,,,,
+paragonite,-5570375,-5951011,277.699,13.216,577.57,-1472.8,-32214400,5050080000,0,0,0,-0.1973,4.933E-07,3.9424,0.59701,,,,,,,,,,,,,,
+albite,-3710096,-3928421,224.412,10.083,393.64,-2415.5,-7892800,1070640000,0,0,0,-0.1945,4.861E-07,2.6307,0.32407,,,,,,,,,,,,,,
+"albite,high",-3710096,-3928421,224.412,10.083,393.64,-2415.5,-7892800,1070640000,0,0,0,-0.1945,4.861E-07,2.6307,0.32407,,,,,,,,,,,,,,
+"albite,low",-3718518,-3941903,207.443,10.043,393.64,-2415.5,-7892800,1070640000,0,0,0,-0.1945,4.861E-07,2.6307,0.32407,,,,,,,,,,,,,,
+jadeite,-2853285,-3031921,133.574,6.034,311.29,-2005.1,-5350300,662570000,0,0,0,-0.086,2.149E-07,2.3118,0.25785,,,,,,,,,,,,,,
+annite,-4799809,-5149494,420,15.408,727.21,-4775.04,-13831900,2119060000,0,0,0,-0.1697,0,3.4447,0,,,,,,,,,,,,,,
Modified: pkg/CHNOSZ/inst/extdata/Berman/ZS92.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/Berman/ZS92.csv 2018-03-27 15:19:33 UTC (rev 309)
+++ pkg/CHNOSZ/inst/extdata/Berman/ZS92.csv 2018-03-28 04:31:38 UTC (rev 310)
@@ -1,11 +1,11 @@
-name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,d5
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/chnosz -r 310
From noreply at r-forge.r-project.org Wed Mar 28 08:01:11 2018
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Wed, 28 Mar 2018 08:01:11 +0200 (CEST)
Subject: [CHNOSZ-commits] r311 - in pkg/CHNOSZ: . R data inst
inst/extdata/Berman man tests/testthat vignettes
Message-ID: <20180328060111.9A9FB1895FF@r-forge.r-project.org>
Author: jedick
Date: 2018-03-28 08:01:10 +0200 (Wed, 28 Mar 2018)
New Revision: 311
Added:
pkg/CHNOSZ/inst/extdata/Berman/testing/
Removed:
pkg/CHNOSZ/inst/extdata/Berman/unused/
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/R/berman.R
pkg/CHNOSZ/data/opt.csv
pkg/CHNOSZ/inst/NEWS
pkg/CHNOSZ/man/berman.Rd
pkg/CHNOSZ/man/data.Rd
pkg/CHNOSZ/man/extdata.Rd
pkg/CHNOSZ/tests/testthat/test-berman.R
pkg/CHNOSZ/vignettes/obigt.Rmd
Log:
berman(): read user-supplied data from file specified in thermo$opt$Berman
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2018-03-28 04:31:38 UTC (rev 310)
+++ pkg/CHNOSZ/DESCRIPTION 2018-03-28 06:01:10 UTC (rev 311)
@@ -1,6 +1,6 @@
Date: 2018-03-28
Package: CHNOSZ
-Version: 1.1.3-18
+Version: 1.1.3-19
Title: Thermodynamic Calculations for Geobiochemistry
Authors at R: c(
person("Jeffrey", "Dick", , "j3ffdick at gmail.com", role = c("aut", "cre"),
Modified: pkg/CHNOSZ/R/berman.R
===================================================================
--- pkg/CHNOSZ/R/berman.R 2018-03-28 04:31:38 UTC (rev 310)
+++ pkg/CHNOSZ/R/berman.R 2018-03-28 06:01:10 UTC (rev 311)
@@ -22,11 +22,19 @@
DS10 <- read.csv(paste0(dir, "/DS10.csv"), as.is=TRUE)
FDM14 <- read.csv(paste0(dir, "/FDM+14.csv"), as.is=TRUE)
BDat17 <- read.csv(paste0(dir, "/BDat17.csv"), as.is=TRUE)
- if(file.exists("berman.csv")) {
- BDat_user <- read.csv("berman.csv", as.is=TRUE)
- # assemble the files in reverse chronological order
- dat <- rbind(BDat_user, BDat17, FDM14, DS10, JUN92, ZS92, SHD91, Ber90, Ber88)
- } else dat <- rbind(BDat17, FDM14, DS10, JUN92, ZS92, SHD91, Ber90, Ber88)
+ userfile <- get("thermo")$opt$Berman
+ userfileexists <- FALSE
+ dat <- rbind(BDat17, FDM14, DS10, JUN92, ZS92, SHD91, Ber90, Ber88)
+ if(!is.na(userfile)) {
+ if(userfile!="") {
+ if(file.exists(userfile)) {
+ userfileexists <- TRUE
+ BDat_user <- read.csv(userfile, as.is=TRUE)
+ # assemble the files in reverse chronological order
+ dat <- rbind(BDat_user, BDat17, FDM14, DS10, JUN92, ZS92, SHD91, Ber90, Ber88)
+ } else stop("the file named in thermo$opt$Berman (", userfile, ") does not exist")
+ }
+ }
# remove duplicates (only the first, i.e. most recent entry is kept)
dat <- dat[!duplicated(dat$name), ]
# remove the multipliers on volume parameters
@@ -37,7 +45,10 @@
if(missing(name)) return(dat)
# which row has data for this mineral?
irow <- which(dat$name == name)
- if(length(irow)==0) stop("Data for ", name, " not available. Please add it to berman.csv")
+ if(length(irow)==0) {
+ if(userfileexists) stop("Data for ", name, " not available. Please add it to ", userfile)
+ if(!userfileexists) stop("Data for ", name, " not available. Please add it to your_data_file.csv and run thermo$obigt$Berman <<- 'path/to/your_data_file.csv'")
+ }
# the function works fine with just the following assign() call,
# but an explicit dummy assignment here is used to avoid "Undefined global functions or variables" in R CMD check
GfPrTr <- HfPrTr <- SPrTr <- Tlambda <- Tmax <- Tmin <- Tref <- VPrTr <-
Modified: pkg/CHNOSZ/data/opt.csv
===================================================================
--- pkg/CHNOSZ/data/opt.csv 2018-03-28 04:31:38 UTC (rev 310)
+++ pkg/CHNOSZ/data/opt.csv 2018-03-28 06:01:10 UTC (rev 311)
@@ -1,2 +1,2 @@
cutoff,E.units,T.units,P.units,state,water,G.tol,Cp.tol,V.tol,varP,IAPWS.sat,paramin,ideal.H,ideal.e,nonideal,Berman
-1E-10,cal,C,bar,aq,SUPCRT92,100,1,1,FALSE,liquid,1000,TRUE,TRUE,Helgeson,FALSE
+1E-10,cal,C,bar,aq,SUPCRT92,100,1,1,FALSE,liquid,1000,TRUE,TRUE,Helgeson,NA
Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS 2018-03-28 04:31:38 UTC (rev 310)
+++ pkg/CHNOSZ/inst/NEWS 2018-03-28 06:01:10 UTC (rev 311)
@@ -1,4 +1,4 @@
-CHANGES IN CHNOSZ 1.1.3-18 (2018-03-28)
+CHANGES IN CHNOSZ 1.1.3-19 (2018-03-28)
---------------------------------------
THERMODYNAMIC DATA
@@ -30,11 +30,12 @@
have been removed, except for 10^5, 10^5, 10^5, and 10^8 on v1 to v4
(to be consistent with the winTWQ data format).
-- berman() now reads data from a user-supplied file berman.csv if it is
- present in the working directory.
+- berman() now reads data from a user-supplied file specified in
+ thermo$opt$Berman.
- Add mineral data from Berman and Aranovich, 1996 to
- extdata/Berman/unused/BA96.csv.
+ extdata/Berman/testing/BA96.csv and an example of using this file via
+ thermo$opt$Berman (see ?berman).
- Correct swapped v1 <-> v3 and v2 <-> v4 in extdata/Berman/DS10.csv.
Modified: pkg/CHNOSZ/man/berman.Rd
===================================================================
--- pkg/CHNOSZ/man/berman.Rd 2018-03-28 04:31:38 UTC (rev 310)
+++ pkg/CHNOSZ/man/berman.Rd 2018-03-28 06:01:10 UTC (rev 311)
@@ -126,6 +126,26 @@
legend=c("Helgeson et al., 1978 (unadjusted)",
"Berman, 1988", " (adjusted by Sverjensky et al., 1991)"), bty="n")
title(main="Comparison of Helgeson and Berman datasets at 1000 bar")
+
+## Getting data from a user-supplied file
+## Ol-Opx exchange equilibrium, after Berman and Aranovich, 1996
+E.units("J")
+species <- c("fayalite", "enstatite", "ferrosilite", "forsterite")
+coeffs <- c(-1, -2, 2, 1)
+T <- seq(600, 1500, 50)
+Gex_Ber88 <- subcrt(species, coeffs, T=T, P=1)$out$G
+# add data from BA96
+datadir <- system.file("extdata/Berman/testing", package="CHNOSZ")
+add.obigt(file.path(datadir, "BA96_obigt.csv"))
+thermo$opt$Berman <<- file.path(datadir, "BA96.csv")
+Gex_BA96 <- subcrt(species, coeffs, T=seq(600, 1500, 50), P=1)$out$G
+# Ber88 is lower than BA96 at low T
+stopifnot((Gex_BA96 - Gex_Ber88)[1] > 0)
+# the curves cross at about 725 deg C (BA96 Fig. 8)
+# (actually, in our calculation they cross closer to 800 deg C)
+stopifnot(T[which.min(abs(Gex_BA96 - Gex_Ber88))] == 800)
+# reset the database (thermo$opt$E.units, thermo$obigt, and thermo$opt$Berman)
+data(thermo)
}
\references{
@@ -133,6 +153,8 @@
Berman, R. G. (1988) Internally-consistent thermodynamic data for minerals in the system Na{\s2}O-K{\s2}O-CaO-MgO-FeO-Fe{\s2}O{\s3}-Al{\s2}O{\s3}-SiO{\s2}-TiO{\s2}-H{\s2}O-CO{\s2}. \emph{J. Petrol.} \bold{29}, 445-522. \url{https://doi.org/10.1093/petrology/29.2.445}
+Berman, R. G. and Aranovich, L. Ya. (1996) Optimized standard state and solution properties of minerals. I. Model calibration for olivine, orthopyroxene, cordierite, garnet, and ilmenite in the system FeO-MgO-CaO-Al{\s2}O{\s3}-TiO{\s2}-SiO{\s2}. \emph{Contrib. Mineral. Petrol.} \bold{126}, 1-24. \url{https://doi.org/10.1007/s004100050233}
+
Berman, R. G. (2007) winTWQ (version 2.3): A software package for performing internally-consistent thermobarometric calculations. \emph{Open File} \bold{5462}, Geological Survey of Canada, 41 p. \url{https://doi.org/10.4095/223425}
Helgeson, H. C., Delany, J. M., Nesbitt, H. W. and Bird, D. K. (1978) Summary and critique of the thermodynamic properties of rock-forming minerals. \emph{Am. J. Sci.} \bold{278-A}, 1--229. \url{http://www.worldcat.org/oclc/13594862}
Modified: pkg/CHNOSZ/man/data.Rd
===================================================================
--- pkg/CHNOSZ/man/data.Rd 2018-03-28 04:31:38 UTC (rev 310)
+++ pkg/CHNOSZ/man/data.Rd 2018-03-28 06:01:10 UTC (rev 311)
@@ -22,7 +22,7 @@
The computational settings are changed using \code{\link{water}}, \code{\link{P.units}}, \code{\link{T.units}}, \code{\link{E.units}}, and some other commands (e.g. \code{\link{mod.buffer}}).
Some settings can only be changed by direct manipulation of \code{thermo$opt}.
-In an interactive session, this should be done using the super-assignment operator (e.g. \code{thermo$opt$Berman <<- TRUE}) so that the \code{thermo} object is not copied to the global environment.
+In an interactive session, this should be done using the super-assignment operator (e.g. \code{thermo$opt$ideal.H <<- FALSE}) so that the \code{thermo} object is not copied to the global environment.
(Doing so would cause problems, as many functions are designed to access the \code{thermo} object in the \code{CHNOSZ} environment.)
To restore the default computational settings, thermodynamic database, and system settings, run \code{data(thermo)}.
@@ -59,7 +59,7 @@
\code{ideal.H} \tab logical \tab Should \code{\link{nonideal}} ignore the proton? [\code{TRUE}] \cr
\code{ideal.e} \tab logical \tab Should \code{\link{nonideal}} ignore the electron? [\code{TRUE}] \cr
\code{nonideal} \tab character \tab Method for \code{\link{nonideal}} [\code{Helgeson}] \cr
- \code{Berman} \tab logical \tab Should \code{\link{info}} preferentially return Berman minerals? [\code{FALSE}]
+ \code{Berman} \tab character \tab User data file for mineral parameters in the Berman equations [\code{NA}]
}
\item \code{thermo$element}
Modified: pkg/CHNOSZ/man/extdata.Rd
===================================================================
--- pkg/CHNOSZ/man/extdata.Rd 2018-03-28 04:31:38 UTC (rev 310)
+++ pkg/CHNOSZ/man/extdata.Rd 2018-03-28 06:01:10 UTC (rev 311)
@@ -17,6 +17,7 @@
Following conventions used in other data files, the names of sanidine and microcline were changed to K-feldspar,high and K-feldspar,low.
\item \code{*.csv} contain thermodynamic data from other sources.
\item \code{sympy.R} is an R script used to symbolically integrate heat capacity and volume (to calculate enthalpy, entropy and Gibbs energy), using \CRANpkg{rSymPy}.
+ \item The \code{testing} directory contains data files based on Berman and Aranovich (1996). These are used to demonstrate the addition of data from a user-supplied file (see \code{\link{berman}}).
}
Files in \code{abundance} contain protein abundance and microbial occurrence data:
@@ -114,6 +115,8 @@
Berman, R. G. (1988) Internally-consistent thermodynamic data for minerals in the system Na{\s2}O-K{\s2}O-CaO-MgO-FeO-Fe{\s2}O{\s3}-Al{\s2}O{\s3}-SiO{\s2}-TiO{\s2}-H{\s2}O-CO{\s2}. \emph{J. Petrol.} \bold{29}, 445-522. \url{https://doi.org/10.1093/petrology/29.2.445}
+Berman, R. G. and Aranovich, L. Ya. (1996) Optimized standard state and solution properties of minerals. I. Model calibration for olivine, orthopyroxene, cordierite, garnet, and ilmenite in the system FeO-MgO-CaO-Al{\s2}O{\s3}-TiO{\s2}-SiO{\s2}. \emph{Contrib. Mineral. Petrol.} \bold{126}, 1-24. \url{https://doi.org/10.1007/s004100050233}
+
Dayhoff, M. O. and Lippincott, E. R. and Eck, R. V. (1964) Thermodynamic Equilibria In Prebiological Atmospheres. \emph{Science} \bold{146}, 1461--1464. \url{https://doi.org/10.1126/science.146.3650.1461}
Dayhoff, M. O. and Lippincott, E. R., Eck, R. V. and Nagarajan (1967) Thermodynamic Equilibrium In Prebiological Atmospheres of C, H, O, N, P, S, and Cl. Report SP-3040, National Aeronautics and Space Administration.
Modified: pkg/CHNOSZ/tests/testthat/test-berman.R
===================================================================
--- pkg/CHNOSZ/tests/testthat/test-berman.R 2018-03-28 04:31:38 UTC (rev 310)
+++ pkg/CHNOSZ/tests/testthat/test-berman.R 2018-03-28 06:01:10 UTC (rev 311)
@@ -79,3 +79,12 @@
# we are less consistent with the reference values at high T
expect_maxdiff(Kfs$G[3:4], Kfs_G[3:4], 350)
})
+
+test_that("nonexistent or incomplete user data file is handled properly", {
+ thermo$opt$Berman <<- "XxXxXx.csv"
+ expect_error(berman("calcite"), "the file named in thermo\\$opt\\$Berman \\(XxXxXx.csv\\) does not exist")
+ thermo$opt$Berman <<- system.file("extdata/Berman/testing/BA96.csv", package="CHNOSZ")
+ expect_error(berman("xxx"), "Data for xxx not available. Please add it to")
+ thermo$opt$Berman <<- NA
+ expect_error(berman("xxx"), "Data for xxx not available. Please add it to your_data_file.csv")
+})
Modified: pkg/CHNOSZ/vignettes/obigt.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/obigt.Rmd 2018-03-28 04:31:38 UTC (rev 310)
+++ pkg/CHNOSZ/vignettes/obigt.Rmd 2018-03-28 06:01:10 UTC (rev 311)
@@ -123,7 +123,7 @@
* Updates included with [SUPCRTBL](http://www.indiana.edu/~hydrogeo/supcrtbl.html) are listed under **Optional Data** / **SUPCRTBL**.
-* Data from SUPCRT92 which have been superseded in CHNOSZ by the Berman data are listed under **Optional Data** / **SUPCRT92**.
+* Data from SUPCRT92 which have been superseded by the Berman data are listed under **Optional Data** / **SUPCRT92**.
# Sources of data {.tabset .tabset-fade}
From noreply at r-forge.r-project.org Fri Mar 30 16:50:10 2018
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Fri, 30 Mar 2018 16:50:10 +0200 (CEST)
Subject: [CHNOSZ-commits] r312 - in pkg/CHNOSZ: . R inst man tests/testthat
Message-ID: <20180330145010.AC4B6188AED@r-forge.r-project.org>
Author: jedick
Date: 2018-03-30 16:50:10 +0200 (Fri, 30 Mar 2018)
New Revision: 312
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/R/equilibrate.R
pkg/CHNOSZ/inst/NEWS
pkg/CHNOSZ/man/berman.Rd
pkg/CHNOSZ/tests/testthat/test-diagram.R
pkg/CHNOSZ/tests/testthat/test-equilibrate.R
Log:
fix minor typos
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2018-03-28 06:01:10 UTC (rev 311)
+++ pkg/CHNOSZ/DESCRIPTION 2018-03-30 14:50:10 UTC (rev 312)
@@ -1,6 +1,6 @@
-Date: 2018-03-28
+Date: 2018-03-30
Package: CHNOSZ
-Version: 1.1.3-19
+Version: 1.1.3-20
Title: Thermodynamic Calculations for Geobiochemistry
Authors at R: c(
person("Jeffrey", "Dick", , "j3ffdick at gmail.com", role = c("aut", "cre"),
Modified: pkg/CHNOSZ/R/equilibrate.R
===================================================================
--- pkg/CHNOSZ/R/equilibrate.R 2018-03-28 06:01:10 UTC (rev 311)
+++ pkg/CHNOSZ/R/equilibrate.R 2018-03-30 14:50:10 UTC (rev 312)
@@ -295,7 +295,7 @@
}
# the name of the basis species (need this if we got ibalance which which.balance, above)
balance <- colnames(aout$species)[ibalance[1]]
- message(paste("balance: from moles of", balance, "in formation reactions"))
+ message(paste("balance: moles of", balance, "in formation reactions"))
# the balance vector
n.balance <- aout$species[, ibalance[1]]
# we check if that all formation reactions contain this basis species
Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS 2018-03-28 06:01:10 UTC (rev 311)
+++ pkg/CHNOSZ/inst/NEWS 2018-03-30 14:50:10 UTC (rev 312)
@@ -1,4 +1,4 @@
-CHANGES IN CHNOSZ 1.1.3-19 (2018-03-28)
+CHANGES IN CHNOSZ 1.1.3-20 (2018-03-30)
---------------------------------------
THERMODYNAMIC DATA
Modified: pkg/CHNOSZ/man/berman.Rd
===================================================================
--- pkg/CHNOSZ/man/berman.Rd 2018-03-28 06:01:10 UTC (rev 311)
+++ pkg/CHNOSZ/man/berman.Rd 2018-03-30 14:50:10 UTC (rev 312)
@@ -33,7 +33,7 @@
The equation used for volume is \I{V}(\P, \T) / \I{V}(1 bar, 298.15 K) = 1 + v1 * (\T - 298.15) + v2 * (\T - 298.15)\S{2} + v3 * (\P - 1) + v4 * (\P - 1)\S{2}.
The parameters correspond to Tables 2 (\code{GfPrTr}, \code{HfPrTr}, \code{SPrTr}, \code{VPrTr}), 3a (\code{k0} to \code{k3}), 4 (\code{v1} to \code{v4}), 3b (transition parameters: \code{Tlambda} to \code{dTH}), and 5 (disorder parameters: \code{Tmax}, \code{Tmin}, and \code{d1} to \code{d5}) of Berman (1988).
Following the winTWQ data format, multipliers are applied to the volume parameters only (see below).
-Note that \code{VPrTr} is tabulated in J mol\S{-1}, which is equal to 10 cm\S{3} mol\S{-1}.
+Note that \code{VPrTr} is tabulated in J bar\S{-1} mol\S{-1}, which is equal to 10 cm\S{3} mol\S{-1}.
A value for \code{GfPrTr} is optional and is not used in the calculations (see below).
Numeric values (possibly 0) should be assigned for all of \code{HfPrTr}, \code{SPrTr}, \code{VPrTr}, \code{k0} to \code{k6} and \code{v1} to \code{v4}.
Modified: pkg/CHNOSZ/tests/testthat/test-diagram.R
===================================================================
--- pkg/CHNOSZ/tests/testthat/test-diagram.R 2018-03-28 06:01:10 UTC (rev 311)
+++ pkg/CHNOSZ/tests/testthat/test-diagram.R 2018-03-30 14:50:10 UTC (rev 312)
@@ -5,7 +5,7 @@
basis("CHNOS")
species(c("glycine", "alanine"))
a <- affinity()
- expect_message(diagram(a, plot.it=FALSE), "balance: from moles of CO2 in formation reactions")
+ expect_message(diagram(a, plot.it=FALSE), "balance: moles of CO2 in formation reactions")
e <- equilibrate(a)
expect_error(diagram(e, "Z"), "Z is not a valid diagram type")
})
@@ -22,7 +22,7 @@
# we can't calculate the equilibrium activity of a basis species if it's externally buffered
expect_error(diagram(a, "O2"), "is not numeric - was a buffer selected\\?")
# this one works - a barplot of A/2.303RT
- expect_message(diagram(a, plot.it=FALSE), "balance: from moles of CO2 in formation reactions")
+ expect_message(diagram(a, plot.it=FALSE), "balance: moles of CO2 in formation reactions")
# if we're plotting A/2.303RT the values can be divided by balancing coefficient or not
d.1 <- diagram(a, balance=1, plot.it=FALSE)
d.CO2 <- diagram(a, plot.it=FALSE)
Modified: pkg/CHNOSZ/tests/testthat/test-equilibrate.R
===================================================================
--- pkg/CHNOSZ/tests/testthat/test-equilibrate.R 2018-03-28 06:01:10 UTC (rev 311)
+++ pkg/CHNOSZ/tests/testthat/test-equilibrate.R 2018-03-30 14:50:10 UTC (rev 312)
@@ -19,7 +19,7 @@
test_that("equilibrate() gives expected messages and errors for balance calculation", {
# the following error is triggered by equil.react, not equil.boltzmann
expect_error(equilibrate(aone), "at least two species needed")
- expect_message(equilibrate(aacid), "balance: from moles of CO2")
+ expect_message(equilibrate(aacid), "balance: moles of CO2")
expect_message(equilibrate(aacid), "n.balance is 2 1 1 2")
expect_message(equilibrate(aacid), "loga.balance is -2.221848")
expect_message(equilibrate(aacid, loga.balance=-3), "loga.balance is -3")
From noreply at r-forge.r-project.org Sat Mar 31 06:45:10 2018
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Sat, 31 Mar 2018 06:45:10 +0200 (CEST)
Subject: [CHNOSZ-commits] r313 - in pkg/CHNOSZ: . R inst inst/extdata/Berman
inst/extdata/Berman/testing man tests/testthat
Message-ID: <20180331044510.7F93D1890DE@r-forge.r-project.org>
Author: jedick
Date: 2018-03-31 06:45:08 +0200 (Sat, 31 Mar 2018)
New Revision: 313
Added:
pkg/CHNOSZ/inst/extdata/Berman/testing/BA96_berman.csv
Removed:
pkg/CHNOSZ/inst/extdata/Berman/testing/BA96.csv
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/R/berman.R
pkg/CHNOSZ/inst/NEWS
pkg/CHNOSZ/inst/extdata/Berman/BDat17.csv
pkg/CHNOSZ/inst/extdata/Berman/Ber88.csv
pkg/CHNOSZ/inst/extdata/Berman/Ber90.csv
pkg/CHNOSZ/inst/extdata/Berman/DS10.csv
pkg/CHNOSZ/inst/extdata/Berman/FDM+14.csv
pkg/CHNOSZ/inst/extdata/Berman/JUN92.csv
pkg/CHNOSZ/inst/extdata/Berman/SHD91.csv
pkg/CHNOSZ/inst/extdata/Berman/ZS92.csv
pkg/CHNOSZ/man/berman.Rd
pkg/CHNOSZ/tests/testthat/test-berman.R
Log:
reorder volume parameters in extdata/Berman/*.csv, following winTWQ format
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2018-03-30 14:50:10 UTC (rev 312)
+++ pkg/CHNOSZ/DESCRIPTION 2018-03-31 04:45:08 UTC (rev 313)
@@ -1,6 +1,6 @@
-Date: 2018-03-30
+Date: 2018-03-31
Package: CHNOSZ
-Version: 1.1.3-20
+Version: 1.1.3-21
Title: Thermodynamic Calculations for Geobiochemistry
Authors at R: c(
person("Jeffrey", "Dick", , "j3ffdick at gmail.com", role = c("aut", "cre"),
Modified: pkg/CHNOSZ/R/berman.R
===================================================================
--- pkg/CHNOSZ/R/berman.R 2018-03-30 14:50:10 UTC (rev 312)
+++ pkg/CHNOSZ/R/berman.R 2018-03-31 04:45:08 UTC (rev 313)
@@ -52,7 +52,7 @@
# the function works fine with just the following assign() call,
# but an explicit dummy assignment here is used to avoid "Undefined global functions or variables" in R CMD check
GfPrTr <- HfPrTr <- SPrTr <- Tlambda <- Tmax <- Tmin <- Tref <- VPrTr <-
- d0 <- d1 <- d2 <- d3 <- d4 <- d5 <- dTdP <- k0 <- k1 <- k2 <- k3 <-
+ d0 <- d1 <- d2 <- d3 <- d4 <- Vad <- dTdP <- k0 <- k1 <- k2 <- k3 <-
k4 <- k5 <- k6 <- l1 <- l2 <- v1 <- v2 <- v3 <- v4 <- NA
# assign values to the variables used below
for(i in 1:ncol(dat)) assign(colnames(dat)[i], dat[irow, i])
@@ -75,24 +75,24 @@
Cp <- k0 + k1 * T^-0.5 + k2 * T^-2 + k3 * T^-3 + k4 * T^-1 + k5 * T + k6 * T^2
P_Pr <- P - Pr
T_Tr <- T - Tr
- V <- VPrTr * (1 + v1 * P_Pr + v2 * P_Pr^2 + v3 * T_Tr + v4 * T_Tr^2)
+ V <- VPrTr * (1 + v1 * T_Tr + v2 * T_Tr^2 + v3 * P_Pr + v4 * P_Pr^2)
## calculate Ga (Ber88 Eq. 6) (superseded 20180328 as it does not include k4, k5, k6)
#Ga <- HfPrTr - T * SPrTr + k0 * ( (T - Tr) - T * (log(T) - log(Tr)) ) +
# 2 * k1 * ( (T^0.5 - Tr^0.5) + T*(T^-0.5 - Tr^-0.5) ) -
# k2 * ( (T^-1 - Tr^-1) - T / 2 * (T^-2 - Tr^-2) ) -
# k3 * ( (T^-2 - Tr^-2) / 2 - T / 3 * (T^-3 - Tr^-3) ) +
- # VPrTr * ( (v1 / 2 - v2) * (P^2 - Pr^2) + v2 / 3 * (P^3 - Pr^3) +
- # (1 - v1 + v2 + v3 * (T - Tr) + v4 * (T - Tr)^2) * (P - Pr) )
+ # VPrTr * ( (v3 / 2 - v4) * (P^2 - Pr^2) + v4 / 3 * (P^3 - Pr^3) +
+ # (1 - v3 + v4 + v1 * (T - Tr) + v2 * (T - Tr)^2) * (P - Pr) )
# calculate Ha (symbolically integrated using sympy - expressions not simplified)
intCp <- T*k0 - Tr*k0 + k2/Tr - k2/T + k3/(2*Tr^2) - k3/(2*T^2) + 2.0*k1*T^0.5 - 2.0*k1*Tr^0.5 +
k4*log(T) - k4*log(Tr) + k5*T^2/2 - k5*Tr^2/2 - k6*Tr^3/3 + k6*T^3/3
- intVminusTdVdT <- -VPrTr + P*(VPrTr + VPrTr*v2 - VPrTr*v1 - Tr*VPrTr*v3 + VPrTr*v4*Tr^2 - VPrTr*v4*T^2) +
- P^2*(VPrTr*v1/2 - VPrTr*v2) + VPrTr*v1/2 - VPrTr*v2/3 + Tr*VPrTr*v3 + VPrTr*v4*T^2 - VPrTr*v4*Tr^2 + VPrTr*v2*P^3/3
+ intVminusTdVdT <- -VPrTr + P*(VPrTr + VPrTr*v4 - VPrTr*v3 - Tr*VPrTr*v1 + VPrTr*v2*Tr^2 - VPrTr*v2*T^2) +
+ P^2*(VPrTr*v3/2 - VPrTr*v4) + VPrTr*v3/2 - VPrTr*v4/3 + Tr*VPrTr*v1 + VPrTr*v2*T^2 - VPrTr*v2*Tr^2 + VPrTr*v4*P^3/3
Ha <- HfPrTr + intCp + intVminusTdVdT
# calculate S (also symbolically integrated)
intCpoverT <- k0*log(T) - k0*log(Tr) - k3/(3*T^3) + k3/(3*Tr^3) + k2/(2*Tr^2) - k2/(2*T^2) + 2.0*k1*Tr^-0.5 - 2.0*k1*T^-0.5 +
k4/Tr - k4/T + T*k5 - Tr*k5 + k6*T**2/2 - k6*Tr**2/2
- intdVdT <- -VPrTr*(v3 + v4*(-2*Tr + 2*T)) + P*VPrTr*(v3 + v4*(-2*Tr + 2*T))
+ intdVdT <- -VPrTr*(v1 + v2*(-2*Tr + 2*T)) + P*VPrTr*(v1 + v2*(-2*Tr + 2*T))
S <- SPrTr + intCpoverT - intdVdT
# calculate Ga --> Berman-Brown convention (DG = DH - T*S, no S(element))
Ga <- Ha - T * S
@@ -152,9 +152,11 @@
d2*(Tds^-1 - Tmin^-1)/-1 + d3*(Tds^2 - Tmin^2)/2 + d4*(Tds^3 - Tmin^3)/3
Sds[iTds] <- d0*(log(Tds) - log(Tmin)) + d1*(Tds^-0.5 - Tmin^-0.5)/-0.5 +
d2*(Tds^-2 - Tmin^-2)/-2 + d3*(Tds - Tmin) + d4*(Tds^2 - Tmin^2)/2
- # Eq. 18; we can't do this if d5 == 0 (dolomite and gehlenite)
# "d5 is a constant computed in such as way as to scale the disordring enthalpy to the volume of disorder" (Berman, 1988)
- if(d5 != 0) Vds <- Hds / d5
+ # 20180331: however, having a "d5" that isn't a coefficient in the same equation as d0, d1, d2, d3, d4 is confusing notation
+ # therefore, CHNOSZ now uses "Vad" for this variable, following the notation in the Theriak-Domino manual
+ # Eq. 18; we can't do this if Vad == 0 (dolomite and gehlenite)
+ if(Vad != 0) Vds <- Hds / Vad
# Berman puts the Vds term directly into Eq. 19 (commented below), but that necessarily makes Gds != Hds - T * Sds
#Gds <- Hds - T * Sds + Vds * (P - Pr)
# instead, we include the Vds term with Hds
Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS 2018-03-30 14:50:10 UTC (rev 312)
+++ pkg/CHNOSZ/inst/NEWS 2018-03-31 04:45:08 UTC (rev 313)
@@ -1,4 +1,4 @@
-CHANGES IN CHNOSZ 1.1.3-20 (2018-03-30)
+CHANGES IN CHNOSZ 1.1.3-21 (2018-03-31)
---------------------------------------
THERMODYNAMIC DATA
@@ -34,11 +34,15 @@
thermo$opt$Berman.
- Add mineral data from Berman and Aranovich, 1996 to
- extdata/Berman/testing/BA96.csv and an example of using this file via
- thermo$opt$Berman (see ?berman).
+ extdata/Berman/testing and an example of loading these data via
+ add.obigt() and thermo$opt$Berman (see ?berman).
- Correct swapped v1 <-> v3 and v2 <-> v4 in extdata/Berman/DS10.csv.
+- To reduce confusion that "d5" might be a coefficient in the same
+ equation as d0 .. d4, rename "d5" (constant that scales disordering
+ enthalpy to volume) to "Vad" (notation used in Theriak-Domino manual).
+
OTHER CHANGES
- Lines in 1-D diagram()s can optionally be drawn as splines using the
Modified: pkg/CHNOSZ/inst/extdata/Berman/BDat17.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/Berman/BDat17.csv 2018-03-30 14:50:10 UTC (rev 312)
+++ pkg/CHNOSZ/inst/extdata/Berman/BDat17.csv 2018-03-31 04:45:08 UTC (rev 313)
@@ -1,2 +1,2 @@
-name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,k4,k5,k6,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,d5
-antigorite,-66076529,-71364156,3602.996,174.246,7394.51,0,-548363000,87284120000,0,0,0,-0.1485,4E-07,2.72,0.8,,,,,,,,,,,,,,
+name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,k4,k5,k6,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,Vad
+antigorite,-66076529,-71364156,3602.996,174.246,7394.51,0,-548363000,87284120000,0,0,0,2.72,0.0008,-0.1485,0.0004,,,,,,,,,,,,,,
Modified: pkg/CHNOSZ/inst/extdata/Berman/Ber88.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/Berman/Ber88.csv 2018-03-30 14:50:10 UTC (rev 312)
+++ pkg/CHNOSZ/inst/extdata/Berman/Ber88.csv 2018-03-31 04:45:08 UTC (rev 313)
@@ -1,68 +1,68 @@
-name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,k4,k5,k6,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,d5
-akermanite,-3663786,-3860441,212,9.252,387.06,-2938.8,0,-40790000,0,0,0,-0.0785,0,2.5011,0.67224,358,298,0,0,0,452,,,,,,,,
-albite,-3703293,-3921618,224.412,10.083,393.64,-2415.5,-7892800,1070640000,0,0,0,-0.1945,4.861E-07,2.6307,0.32407,,,,,,,,,,,,,,
-"albite,high",-3703293,-3921618,224.412,10.083,393.64,-2415.5,-7892800,1070640000,0,0,0,-0.1945,4.861E-07,2.6307,0.32407,,,,,,,,,,,,,,
-"albite,low",-3711715,-3935100,207.443,10.043,393.64,-2415.5,-7892800,1070640000,0,0,0,-0.1945,4.861E-07,2.6307,0.32407,,,,,,,,,,,,,,
-almandine,-4941728,-5265502,339.927,11.511,573.96,-1483.1,-29292000,5022080000,0,0,0,-0.0558,3.21E-08,1.8613,0.74539,,,,,,,,,,,,,,
-andalusite,-2441806,-2589972,91.434,5.147,236.48,-1102.9,-7526800,936440000,0,0,0,-0.077,1.923E-07,2.3443,0.07189,,,,,,,,,,,,,,
-anorthite,-4003221,-4228730,200.186,10.075,439.37,-3734.1,0,-317020000,0,0,0,-0.1272,3.176E-07,1.0918,0.41985,,,,,,,,,,,,,,
-anthophyllite,-11342582,-12069032,535.195,26.56,1219.31,-5766.5,-34766100,4400900000,0,0,0,-0.1259,0,2.706,0.31325,,,,,,,,,,,,,,
-antigorite,-66076529,-71364156,3602.996,174.246,7394.51,0,-548363000,87284120000,0,0,0,-0.1978,4.944E-07,2.4965,0.39444,,,,,,,,,,,,,,
-brucite,-834868,-925937,63.064,2.468,136.84,-537.1,-4361900,552690000,0,0,0,-0.2023,6.726E-07,3.2854,0.1094,,,,,,,,,,,,,,
-Ca-Al-pyroxene,-3122310,-3298767,140.751,6.356,310.7,-1671.6,-7455300,948780000,0,0,0,-0.087,2.171E-07,2.225,0.52863,,,,,,,,,,,,,,
-calcite,-1128295,-1206819,91.725,3.69,178.19,-1657.7,-482700,166600000,0,0,0,-0.14,0,0.8907,2.27402,,,,,,,,,,,,,,
-chrysotile,-4035373,-4363356,220.134,10.72,610.02,-5581.2,-1857300,195470000,0,0,0,-0.181,4.524E-07,2.7151,0.67351,,,,,,,,,,,,,,
-clinochlore,-8250546,-8909590,435.154,21.147,1214.28,-11217.1,0,-1256250000,0,0,0,-0.1819,0,2.6452,0,,,,,,,,,,,,,,
-coesite,-852585,-907604,39.424,2.064,94.907,-767.3,-527900,26270000,0,0,0,-0.1037,3E-07,0.7396,0.43605,,,,,,,,,,,,,,
-cordierite,-8651517,-9158727,417.97,23.311,954.39,-7962.3,-2317300,-370210000,0,0,0,-0.1158,0,0.3003,0.18017,,,,,,,,,,,,,,
-corundum,-1582199,-1675700,50.82,2.558,155.02,-828.4,-3861400,409080000,0,0,0,-0.0385,3.75E-08,2.1342,0.4718,,,,,,,,,,,,,,
-"cristobalite,alpha",-853918,-907753,43.394,2.587,83.51,-374.7,-2455400,280070000,0,0,0,-0.2515,0,2.0824,0,535,298,0.048,-0.14216,0.00044142,0,,,,,,,,
-"cristobalite,beta",-853327,-906377,46.029,2.73,83.51,-374.7,-2455400,280070000,0,0,0,-0.11,5.535E-07,0.3189,0,,,,,,,,,,,,,,
-diaspore,-920806,-999378,35.308,1.776,143.24,-1540.4,-323100,64630000,0,0,0,-0.0599,0,2.9718,0,,,,,,,,,,,,,,
-diopside,-3026202,-3200583,142.5,6.62,305.41,-1604.9,-7166000,921840000,0,0,0,-0.0872,1.707E-07,2.7795,0.83082,,,,,,,,,,,,,,
-dolomite,-2162354,-2325248,154.89,6.432,328.48,-2554.4,-4688500,790380000,0,0,0,-0.107,0,1.423,3.63778,,,,,,,1423,298,-9.42,0,385000,0.01732,5.02E-06,0
-"enstatite,clino",-1458601,-1545926,66.325,3.131,139.96,-497,-4400200,535710000,0,0,0,-0.075,4.48E-08,2.1915,0.7492,,,,,,,,,,,,,,
-enstatite,-1458181,-1545552,66.17,3.133,166.58,-1200.6,-2270600,279150000,0,0,0,-0.0749,4.47E-08,2.4656,0.7467,,,,,,,,,,,,,,
-"enstatite,proto",-1456965,-1543959,67.438,3.242,166.58,-1200.6,-2270600,279150000,0,0,0,-0.075,4.48E-08,1.6832,1.1665,,,,,,,,,,,,,,
-fayalite,-1380154,-1479360,150.93,4.63,248.93,-1923.9,0,-139100000,0,0,0,-0.073,0,2.6546,0.79482,,,,,,,,,,,,,,
-ferrosilite,-1117472,-1194375,95.882,3.296,169.06,-1193,-2097100,292530000,0,0,0,-0.099,0,3.1808,0.7585,,,,,,,,,,,,,,
-forsterite,-2055023,-2174420,94.01,4.366,238.64,-2001.3,0,-116240000,0,0,0,-0.0791,1.351E-07,2.9464,0.88633,,,,,,,,,,,,,,
-gehlenite,-3785954,-3988158,198.6,9.033,373.09,-2276.8,-4778500,477910000,0,0,0,-0.0996,2.488E-07,2.4926,0.05664,,,,,,,1600,698,-221.74,0,17291000,0.3695,-0.0001469,0
-grossular,-6270974,-6632859,255.15,12.538,573.43,-2039.4,-18887200,2319310000,0,0,0,-0.0654,1.635E-07,1.8994,0.79756,,,,,,,,,,,,,,
-hematite,-743681,-825627,87.437,3.027,146.86,0,-5576800,525630000,0,0,0,-0.0479,3.04E-08,3.831,0.0165,955,298,0,-0.07403,0.00027921,1287,,,,,,,,
-ilmenite,-1155320,-1231947,108.628,3.17,150,-441.6,-3323700,348150000,0,0,0,-0.0584,1.23E-07,2.7248,0.29968,,,,,,,,,,,,,,
-jadeite,-2846482,-3025118,133.574,6.034,311.29,-2005.1,-5350300,662570000,0,0,0,-0.086,2.149E-07,2.3118,0.25785,,,,,,,,,,,,,,
-kaolinite,-3799770,-4120327,203.7,9.952,523.23,-4426.7,-2244300,92310000,0,0,0,-0.12,0,3.2,0,,,,,,,,,,,,,,
-kyanite,-2443370,-2594220,82.43,4.412,262.68,-2001.4,-1999700,-63180000,0,0,0,-0.0646,0,2.3973,0,,,,,,,,,,,,,,
-lawsonite,-4509709,-4865666,229.176,10.144,728.67,-8248.1,0,850560000,0,0,0,-0.0769,1.922E-07,2.6283,0,,,,,,,,,,,,,,
-lime,-603350,-635090,37.75,1.676,58.79,-133.9,-1147100,102980000,0,0,0,-0.1022,2.565E-07,3.461,0.67406,,,,,,,,,,,,,,
-magnesite,-1029875,-1113636,65.21,2.803,162.3,-1109.3,-4882600,874660000,0,0,0,-0.089,2.212E-07,1.8436,4.15968,,,,,,,,,,,,,,
-magnetite,-1014235,-1117403,146.114,4.452,207.93,0,-7243300,664360000,0,0,0,-0.0582,1.751E-07,3.0291,1.3847,848,298,0,-0.19502,0.00061037,1565,,,,,,,,
-margarite,-5852244,-6236603,265.084,12.958,699.8,-5587.1,-6807700,734320000,0,0,0,-0.1155,2.886E-07,2.1019,1.24556,,,,,,,,,,,,,,
-meionite,-13105915,-13849723,730,34.036,1511.35,-13243.3,0,-751610000,0,0,0,-0.111,0,0.934,0,,,,,,,,,,,,,,
-merwinite,-4309707,-4537497,251.777,9.847,453.62,-3250,0,-344230000,0,0,0,-0.0551,1.381E-07,2.9376,0.87235,,,,,,,,,,,,,,
-monticellite,-2132222,-2250027,108.3,5.148,226.34,-1542.7,-1179700,-23290000,0,0,0,-0.0904,2E-07,2.7863,0.76339,,,,,,,,,,,,,,
-muscovite,-5596723,-5976740,293.157,14.087,651.49,-3873.2,-18523200,2742470000,0,0,0,-0.1717,4.295E-07,3.3527,0,,,,,,,,,,,,,,
-paragonite,-5563572,-5944208,277.699,13.216,577.57,-1472.8,-32214400,5050080000,0,0,0,-0.1973,4.933E-07,3.9424,0.59701,,,,,,,,,,,,,,
-periclase,-569209,-601500,26.951,1.125,61.11,-296.2,-621200,5840000,0,0,0,-0.0622,1.511E-07,3.7477,0.03556,,,,,,,,,,,,,,
-phlogopite,-5827224,-6207342,334.158,14.977,610.38,-2083.8,-21533000,2841040000,0,0,0,-0.1697,0,3.4447,0,,,,,,,,,,,,,,
-K-feldspar,-3745415,-3970791,214.145,10.869,381.37,-1941,-12037300,1836430000,0,0,0,-0.1805,5.112E-07,1.5145,0.5485,,,,,,,1436,298,282.98,-4830,3621000,-0.15733,3.477E-05,410630
-"K-feldspar,high",-3738804,-3959704,229.157,10.896,381.37,-1941,-12037300,1836430000,0,0,0,-0.1805,5.112E-07,1.5145,0.5485,,,,,,,,,,,,,,
-"K-feldspar,low",-3745415,-3970791,214.145,10.869,381.37,-1941,-12037300,1836430000,0,0,0,-0.1805,5.112E-07,1.5145,0.5485,,,,,,,,,,,,,,
-prehnite,-5820154,-6198606,288.634,14.016,716.05,-6404.6,-2182500,268500000,0,0,0,-0.1427,0,0.1468,11.28353,,,,,,,,,,,,,,
-pyrope,-5936009,-6286548,266.359,11.316,640.72,-4542.1,-4701900,0,0,0,0,-0.0576,4.42E-08,2.2519,0.37044,,,,,,,,,,,,,,
-pyrophyllite,-5266865,-5640781,239.4,12.76,665.93,-5897.4,-4979900,661810000,0,0,0,-0.1354,0,1.2637,3.81661,,,,,,,,,,,,,,
-quartz,-856288,-910700,41.46,2.269,80.01,-240.3,-3546700,491570000,0,0,0,-0.2434,1.0137E-06,2.3895,0,848,373,0.0237,-0.09187,0.00024607,0,,,,,,,,
-"quartz,beta",-855033,-908627,44.207,2.37,80.01,-240.3,-3546700,491570000,0,0,0,-0.1238,7.087E-07,0,0,,,,,,,,,,,,,,
-rutile,-889497,-944750,50.46,1.882,77.84,0,-3367800,402940000,0,0,0,-0.0454,5.84E-08,2.5716,0.15409,,,,,,,,,,,,,,
-sillimanite,-2439265,-2586091,95.93,4.983,256.73,-1887.2,-2977400,250960000,0,0,0,-0.0753,0,1.3431,0,,,,,,,,,,,,,,
-sphene,-2455134,-2596652,129.29,5.565,234.62,-1040.3,-5118300,591460000,0,0,0,-0.059,0,2.52,0,,,,,,,,,,,,,,
-spinel,-2176537,-2300313,84.535,3.977,235.9,-1766.6,-1710400,40620000,0,0,0,-0.0489,0,2.1691,0.50528,,,,,,,,,,,,,,
-talc,-5517657,-5897387,261.24,13.61,664.11,-5187.2,-2147200,-327370000,0,0,0,-0.1699,5.665E-07,2.9447,0,,,,,,,,,,,,,,
-tremolite,-11578548,-12305578,551.15,27.268,1229.36,-6401.9,-32089900,4208810000,0,0,0,-0.1392,3.481E-07,2.4374,0.98338,,,,,,,,,,,,,,
-"tridymite,low",-854026,-907750,43.77,2.675,75.37,0,-5958100,958250000,0,0,0,-0.2508,0,1.9339,0,383,298,0,0.4267,-0.00144575,130,,,,,,,,
-"tridymite,high",-853844,-907045,45.524,2.737,75.37,0,-5958100,958250000,0,0,0,-0.074,3.735E-07,0.4829,0,,,,,,,,,,,,,,
-wollastonite,-1546123,-1631500,81.81,3.983,149.07,-690.3,-3659300,484350000,0,0,0,-0.1245,3.113E-07,2.818,0,,,,,,,,,,,,,,
-pseudowollastonite,-1543085,-1627427,85.279,4.016,141.16,-417.2,-5857600,940740000,0,0,0,-0.1245,3.113E-07,2.818,0,,,,,,,,,,,,,,
-zoisite,-6494148,-6889488,297.576,13.588,749.17,-6509.3,-2380500,124860000,0,0,0,-0.0515,1.288E-07,3.467,0,,,,,,,,,,,,,,
-clinozoisite,-6496497,-6894968,287.076,13.673,749.17,-6509.3,-2380500,124860000,0,0,0,-0.0515,1.288E-07,3.467,0,,,,,,,,,,,,,,
+name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,k4,k5,k6,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,Vad
+akermanite,-3663786,-3860441,212,9.252,387.06,-2938.8,0,-40790000,0,0,0,2.5011,0.00067224,-0.0785,0,358,298,0,0,0,452,,,,,,,,
+albite,-3703293,-3921618,224.412,10.083,393.64,-2415.5,-7892800,1070640000,0,0,0,2.6307,0.00032407,-0.1945,0.0004861,,,,,,,,,,,,,,
+"albite,high",-3703293,-3921618,224.412,10.083,393.64,-2415.5,-7892800,1070640000,0,0,0,2.6307,0.00032407,-0.1945,0.0004861,,,,,,,,,,,,,,
+"albite,low",-3711715,-3935100,207.443,10.043,393.64,-2415.5,-7892800,1070640000,0,0,0,2.6307,0.00032407,-0.1945,0.0004861,,,,,,,,,,,,,,
+almandine,-4941728,-5265502,339.927,11.511,573.96,-1483.1,-29292000,5022080000,0,0,0,1.8613,0.00074539,-0.0558,3.21E-05,,,,,,,,,,,,,,
+andalusite,-2441806,-2589972,91.434,5.147,236.48,-1102.9,-7526800,936440000,0,0,0,2.3443,7.189E-05,-0.077,0.0001923,,,,,,,,,,,,,,
+anorthite,-4003221,-4228730,200.186,10.075,439.37,-3734.1,0,-317020000,0,0,0,1.0918,0.00041985,-0.1272,0.0003176,,,,,,,,,,,,,,
+anthophyllite,-11342582,-12069032,535.195,26.56,1219.31,-5766.5,-34766100,4400900000,0,0,0,2.706,0.00031325,-0.1259,0,,,,,,,,,,,,,,
+antigorite,-66076529,-71364156,3602.996,174.246,7394.51,0,-548363000,87284120000,0,0,0,2.4965,0.00039444,-0.1978,0.0004944,,,,,,,,,,,,,,
+brucite,-834868,-925937,63.064,2.468,136.84,-537.1,-4361900,552690000,0,0,0,3.2854,0.0001094,-0.2023,0.0006726,,,,,,,,,,,,,,
+Ca-Al-pyroxene,-3122310,-3298767,140.751,6.356,310.7,-1671.6,-7455300,948780000,0,0,0,2.225,0.00052863,-0.087,0.0002171,,,,,,,,,,,,,,
+calcite,-1128295,-1206819,91.725,3.69,178.19,-1657.7,-482700,166600000,0,0,0,0.8907,0.00227402,-0.14,0,,,,,,,,,,,,,,
+chrysotile,-4035373,-4363356,220.134,10.72,610.02,-5581.2,-1857300,195470000,0,0,0,2.7151,0.00067351,-0.181,0.0004524,,,,,,,,,,,,,,
+clinochlore,-8250546,-8909590,435.154,21.147,1214.28,-11217.1,0,-1256250000,0,0,0,2.6452,0,-0.1819,0,,,,,,,,,,,,,,
+coesite,-852585,-907604,39.424,2.064,94.907,-767.3,-527900,26270000,0,0,0,0.7396,0.00043605,-0.1037,0.0003,,,,,,,,,,,,,,
+cordierite,-8651517,-9158727,417.97,23.311,954.39,-7962.3,-2317300,-370210000,0,0,0,0.3003,0.00018017,-0.1158,0,,,,,,,,,,,,,,
+corundum,-1582199,-1675700,50.82,2.558,155.02,-828.4,-3861400,409080000,0,0,0,2.1342,0.0004718,-0.0385,3.75E-05,,,,,,,,,,,,,,
+"cristobalite,alpha",-853918,-907753,43.394,2.587,83.51,-374.7,-2455400,280070000,0,0,0,2.0824,0,-0.2515,0,535,298,0.048,-0.14216,0.00044142,0,,,,,,,,
+"cristobalite,beta",-853327,-906377,46.029,2.73,83.51,-374.7,-2455400,280070000,0,0,0,0.3189,0,-0.11,0.0005535,,,,,,,,,,,,,,
+diaspore,-920806,-999378,35.308,1.776,143.24,-1540.4,-323100,64630000,0,0,0,2.9718,0,-0.0599,0,,,,,,,,,,,,,,
+diopside,-3026202,-3200583,142.5,6.62,305.41,-1604.9,-7166000,921840000,0,0,0,2.7795,0.00083082,-0.0872,0.0001707,,,,,,,,,,,,,,
+dolomite,-2162354,-2325248,154.89,6.432,328.48,-2554.4,-4688500,790380000,0,0,0,1.423,0.00363778,-0.107,0,,,,,,,1423,298,-9.42,0,385000,0.01732,5.02E-06,0
+"enstatite,clino",-1458601,-1545926,66.325,3.131,139.96,-497,-4400200,535710000,0,0,0,2.1915,0.0007492,-0.075,4.48E-05,,,,,,,,,,,,,,
+enstatite,-1458181,-1545552,66.17,3.133,166.58,-1200.6,-2270600,279150000,0,0,0,2.4656,0.0007467,-0.0749,4.47E-05,,,,,,,,,,,,,,
+"enstatite,proto",-1456965,-1543959,67.438,3.242,166.58,-1200.6,-2270600,279150000,0,0,0,1.6832,0.0011665,-0.075,4.48E-05,,,,,,,,,,,,,,
+fayalite,-1380154,-1479360,150.93,4.63,248.93,-1923.9,0,-139100000,0,0,0,2.6546,0.00079482,-0.073,0,,,,,,,,,,,,,,
+ferrosilite,-1117472,-1194375,95.882,3.296,169.06,-1193,-2097100,292530000,0,0,0,3.1808,0.0007585,-0.099,0,,,,,,,,,,,,,,
+forsterite,-2055023,-2174420,94.01,4.366,238.64,-2001.3,0,-116240000,0,0,0,2.9464,0.00088633,-0.0791,0.0001351,,,,,,,,,,,,,,
+gehlenite,-3785954,-3988158,198.6,9.033,373.09,-2276.8,-4778500,477910000,0,0,0,2.4926,5.664E-05,-0.0996,0.0002488,,,,,,,1600,698,-221.74,0,17291000,0.3695,-0.0001469,0
+grossular,-6270974,-6632859,255.15,12.538,573.43,-2039.4,-18887200,2319310000,0,0,0,1.8994,0.00079756,-0.0654,0.0001635,,,,,,,,,,,,,,
+hematite,-743681,-825627,87.437,3.027,146.86,0,-5576800,525630000,0,0,0,3.831,1.65E-05,-0.0479,3.04E-05,955,298,0,-0.07403,0.00027921,1287,,,,,,,,
+ilmenite,-1155320,-1231947,108.628,3.17,150,-441.6,-3323700,348150000,0,0,0,2.7248,0.00029968,-0.0584,0.000123,,,,,,,,,,,,,,
+jadeite,-2846482,-3025118,133.574,6.034,311.29,-2005.1,-5350300,662570000,0,0,0,2.3118,0.00025785,-0.086,0.0002149,,,,,,,,,,,,,,
+kaolinite,-3799770,-4120327,203.7,9.952,523.23,-4426.7,-2244300,92310000,0,0,0,3.2,0,-0.12,0,,,,,,,,,,,,,,
+kyanite,-2443370,-2594220,82.43,4.412,262.68,-2001.4,-1999700,-63180000,0,0,0,2.3973,0,-0.0646,0,,,,,,,,,,,,,,
+lawsonite,-4509709,-4865666,229.176,10.144,728.67,-8248.1,0,850560000,0,0,0,2.6283,0,-0.0769,0.0001922,,,,,,,,,,,,,,
+lime,-603350,-635090,37.75,1.676,58.79,-133.9,-1147100,102980000,0,0,0,3.461,0.00067406,-0.1022,0.0002565,,,,,,,,,,,,,,
+magnesite,-1029875,-1113636,65.21,2.803,162.3,-1109.3,-4882600,874660000,0,0,0,1.8436,0.00415968,-0.089,0.0002212,,,,,,,,,,,,,,
+magnetite,-1014235,-1117403,146.114,4.452,207.93,0,-7243300,664360000,0,0,0,3.0291,0.0013847,-0.0582,0.0001751,848,298,0,-0.19502,0.00061037,1565,,,,,,,,
+margarite,-5852244,-6236603,265.084,12.958,699.8,-5587.1,-6807700,734320000,0,0,0,2.1019,0.00124556,-0.1155,0.0002886,,,,,,,,,,,,,,
+meionite,-13105915,-13849723,730,34.036,1511.35,-13243.3,0,-751610000,0,0,0,0.934,0,-0.111,0,,,,,,,,,,,,,,
+merwinite,-4309707,-4537497,251.777,9.847,453.62,-3250,0,-344230000,0,0,0,2.9376,0.00087235,-0.0551,0.0001381,,,,,,,,,,,,,,
+monticellite,-2132222,-2250027,108.3,5.148,226.34,-1542.7,-1179700,-23290000,0,0,0,2.7863,0.00076339,-0.0904,0.0002,,,,,,,,,,,,,,
+muscovite,-5596723,-5976740,293.157,14.087,651.49,-3873.2,-18523200,2742470000,0,0,0,3.3527,0,-0.1717,0.0004295,,,,,,,,,,,,,,
+paragonite,-5563572,-5944208,277.699,13.216,577.57,-1472.8,-32214400,5050080000,0,0,0,3.9424,0.00059701,-0.1973,0.0004933,,,,,,,,,,,,,,
+periclase,-569209,-601500,26.951,1.125,61.11,-296.2,-621200,5840000,0,0,0,3.7477,3.556E-05,-0.0622,0.0001511,,,,,,,,,,,,,,
+phlogopite,-5827224,-6207342,334.158,14.977,610.38,-2083.8,-21533000,2841040000,0,0,0,3.4447,0,-0.1697,0,,,,,,,,,,,,,,
+K-feldspar,-3745415,-3970791,214.145,10.869,381.37,-1941,-12037300,1836430000,0,0,0,1.5145,0.0005485,-0.1805,0.0005112,,,,,,,1436,298,282.98,-4830,3621000,-0.15733,3.477E-05,410630
+"K-feldspar,high",-3738804,-3959704,229.157,10.896,381.37,-1941,-12037300,1836430000,0,0,0,1.5145,0.0005485,-0.1805,0.0005112,,,,,,,,,,,,,,
+"K-feldspar,low",-3745415,-3970791,214.145,10.869,381.37,-1941,-12037300,1836430000,0,0,0,1.5145,0.0005485,-0.1805,0.0005112,,,,,,,,,,,,,,
+prehnite,-5820154,-6198606,288.634,14.016,716.05,-6404.6,-2182500,268500000,0,0,0,0.1468,0.01128353,-0.1427,0,,,,,,,,,,,,,,
+pyrope,-5936009,-6286548,266.359,11.316,640.72,-4542.1,-4701900,0,0,0,0,2.2519,0.00037044,-0.0576,4.42E-05,,,,,,,,,,,,,,
+pyrophyllite,-5266865,-5640781,239.4,12.76,665.93,-5897.4,-4979900,661810000,0,0,0,1.2637,0.00381661,-0.1354,0,,,,,,,,,,,,,,
+quartz,-856288,-910700,41.46,2.269,80.01,-240.3,-3546700,491570000,0,0,0,2.3895,0,-0.2434,0.0010137,848,373,0.0237,-0.09187,0.00024607,0,,,,,,,,
+"quartz,beta",-855033,-908627,44.207,2.37,80.01,-240.3,-3546700,491570000,0,0,0,0,0,-0.1238,0.0007087,,,,,,,,,,,,,,
+rutile,-889497,-944750,50.46,1.882,77.84,0,-3367800,402940000,0,0,0,2.5716,0.00015409,-0.0454,5.84E-05,,,,,,,,,,,,,,
+sillimanite,-2439265,-2586091,95.93,4.983,256.73,-1887.2,-2977400,250960000,0,0,0,1.3431,0,-0.0753,0,,,,,,,,,,,,,,
+sphene,-2455134,-2596652,129.29,5.565,234.62,-1040.3,-5118300,591460000,0,0,0,2.52,0,-0.059,0,,,,,,,,,,,,,,
+spinel,-2176537,-2300313,84.535,3.977,235.9,-1766.6,-1710400,40620000,0,0,0,2.1691,0.00050528,-0.0489,0,,,,,,,,,,,,,,
+talc,-5517657,-5897387,261.24,13.61,664.11,-5187.2,-2147200,-327370000,0,0,0,2.9447,0,-0.1699,0.0005665,,,,,,,,,,,,,,
+tremolite,-11578548,-12305578,551.15,27.268,1229.36,-6401.9,-32089900,4208810000,0,0,0,2.4374,0.00098338,-0.1392,0.0003481,,,,,,,,,,,,,,
+"tridymite,low",-854026,-907750,43.77,2.675,75.37,0,-5958100,958250000,0,0,0,1.9339,0,-0.2508,0,383,298,0,0.4267,-0.00144575,130,,,,,,,,
+"tridymite,high",-853844,-907045,45.524,2.737,75.37,0,-5958100,958250000,0,0,0,0.4829,0,-0.074,0.0003735,,,,,,,,,,,,,,
+wollastonite,-1546123,-1631500,81.81,3.983,149.07,-690.3,-3659300,484350000,0,0,0,2.818,0,-0.1245,0.0003113,,,,,,,,,,,,,,
+pseudowollastonite,-1543085,-1627427,85.279,4.016,141.16,-417.2,-5857600,940740000,0,0,0,2.818,0,-0.1245,0.0003113,,,,,,,,,,,,,,
+zoisite,-6494148,-6889488,297.576,13.588,749.17,-6509.3,-2380500,124860000,0,0,0,3.467,0,-0.0515,0.0001288,,,,,,,,,,,,,,
+clinozoisite,-6496497,-6894968,287.076,13.673,749.17,-6509.3,-2380500,124860000,0,0,0,3.467,0,-0.0515,0.0001288,,,,,,,,,,,,,,
Modified: pkg/CHNOSZ/inst/extdata/Berman/Ber90.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/Berman/Ber90.csv 2018-03-30 14:50:10 UTC (rev 312)
+++ pkg/CHNOSZ/inst/extdata/Berman/Ber90.csv 2018-03-31 04:45:08 UTC (rev 313)
@@ -1,5 +1,5 @@
-name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,k4,k5,k6,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,d5
-almandine,-4943492,-5267216,340.007,11.511,573.96,-1483.1,-29292000,5022080000,0,0,0,-0.0558,3.21E-08,1.8613,0.74539,,,,,,,,,,,,,,
-annite,-4793115,-5142800,420,15.408,727.21,-4775.04,-13831900,2119060000,0,0,0,-0.1697,0,3.4447,0,,,,,,,,,,,,,,
-ilmenite,-1155794,-1232448,108.628,3.17,150,-441.6,-3323700,348150000,0,0,0,-0.0584,1.23E-07,2.7248,0.29968,,,,,,,,,,,,,,
-phlogopite,-5830350,-6210391,334.346,14.977,610.38,-2083.8,-21533000,2841040000,0,0,0,-0.1697,0,3.4447,0,,,,,,,,,,,,,,
+name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,k4,k5,k6,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,Vad
+almandine,-4943492,-5267216,340.007,11.511,573.96,-1483.1,-29292000,5022080000,0,0,0,1.8613,0.00074539,-0.0558,3.21E-05,,,,,,,,,,,,,,
+annite,-4793115,-5142800,420,15.408,727.21,-4775.04,-13831900,2119060000,0,0,0,3.4447,0,-0.1697,0,,,,,,,,,,,,,,
+ilmenite,-1155794,-1232448,108.628,3.17,150,-441.6,-3323700,348150000,0,0,0,2.7248,0.00029968,-0.0584,0.000123,,,,,,,,,,,,,,
+phlogopite,-5830350,-6210391,334.346,14.977,610.38,-2083.8,-21533000,2841040000,0,0,0,3.4447,0,-0.1697,0,,,,,,,,,,,,,,
Modified: pkg/CHNOSZ/inst/extdata/Berman/DS10.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/Berman/DS10.csv 2018-03-30 14:50:10 UTC (rev 312)
+++ pkg/CHNOSZ/inst/extdata/Berman/DS10.csv 2018-03-31 04:45:08 UTC (rev 313)
@@ -1,6 +1,6 @@
-name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,k4,k5,k6,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,d5
-hedenbergite,-2674300,-2837802.5,173.59,6.785,353.31148,-3106.646,2047911.742,-563018581,0,0,0,-0.17457,1.51E-06,2.796487,0,,,,,,,,,,,,,,
-andradite,-5419000,-5761985.8,316.4,13.167,569.7558,-1441.44,-22441040.802,3146543781,0,0,0,-0.06539136,1.635E-07,2.072525,0.561,,,,,,,,,,,,,,
-ferro-actinolite,-9839000,-10518042.6,685.1,28.26,1321.15758,-8966.454,-21705844.286,3236159154,0,0,0,-0.15,0,2.84,0,,,,,,,,,,,,,,
-grunerite,-8964807,-9623000,725,27.8,1347.83,-9356.91,-20228480,3039190000,0,0,0,-0.15,0,2.84,0,,,,,,,,,,,,,,
-ilvaite,-3440000,-3695605.5,291.5,10.016,682.79138,-8787.112,30183568.71,-5666432624,0,0,0,-0.06838,2.4E-08,1.801543,1.152,,,,,,,,,,,,,,
+name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,k4,k5,k6,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,Vad
+hedenbergite,-2674300,-2837802.5,173.59,6.785,353.31148,-3106.646,2047911.742,-563018581,0,0,0,2.796487,0,-0.17457,0.00151,,,,,,,,,,,,,,
+andradite,-5419000,-5761985.8,316.4,13.167,569.7558,-1441.44,-22441040.802,3146543781,0,0,0,2.072525,0.000561,-0.06539136,0.0001635,,,,,,,,,,,,,,
+ferro-actinolite,-9839000,-10518042.6,685.1,28.26,1321.15758,-8966.454,-21705844.286,3236159154,0,0,0,2.84,0,-0.15,0,,,,,,,,,,,,,,
+grunerite,-8964807,-9623000,725,27.8,1347.83,-9356.91,-20228480,3039190000,0,0,0,2.84,0,-0.15,0,,,,,,,,,,,,,,
+ilvaite,-3440000,-3695605.5,291.5,10.016,682.79138,-8787.112,30183568.71,-5666432624,0,0,0,1.801543,0.001152,-0.06838,2.4E-05,,,,,,,,,,,,,,
Modified: pkg/CHNOSZ/inst/extdata/Berman/FDM+14.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/Berman/FDM+14.csv 2018-03-30 14:50:10 UTC (rev 312)
+++ pkg/CHNOSZ/inst/extdata/Berman/FDM+14.csv 2018-03-31 04:45:08 UTC (rev 313)
@@ -1,2 +1,2 @@
-name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,k4,k5,k6,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,d5
-aragonite,-1128353.67,-1207213.7,88.7,3.42,195,-2100,-10000,220000000,0,0,0,-0.1345,1.7E-07,4.18,0,,,,,,,,,,,,,,
+name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,k4,k5,k6,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,Vad
+aragonite,-1128353.67,-1207213.7,88.7,3.42,195,-2100,-10000,220000000,0,0,0,4.18,0,-0.1345,0.00017,,,,,,,,,,,,,,
Modified: pkg/CHNOSZ/inst/extdata/Berman/JUN92.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/Berman/JUN92.csv 2018-03-30 14:50:10 UTC (rev 312)
+++ pkg/CHNOSZ/inst/extdata/Berman/JUN92.csv 2018-03-31 04:45:08 UTC (rev 313)
@@ -1,3 +1,3 @@
-name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,k4,k5,k6,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,d5
-glaucophane,-11225858,-11960500,535,26.05,1717.5,-19272,7050000,0,0,0,0,-0.116,2.9E-07,2.2,0.88,,,,,,,,,,,,,,
-pumpellyite,-13448936,-14402300,584,29.55,1576,-10603.8,-28304200,3838351000,0,0,0,-0.051516,1.288E-07,3.467,0,,,,,,,,,,,,,,
+name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,k4,k5,k6,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,Vad
+glaucophane,-11225858,-11960500,535,26.05,1717.5,-19272,7050000,0,0,0,0,2.2,0.00088,-0.116,0.00029,,,,,,,,,,,,,,
+pumpellyite,-13448936,-14402300,584,29.55,1576,-10603.8,-28304200,3838351000,0,0,0,3.467,0,-0.051516,0.0001288,,,,,,,,,,,,,,
Modified: pkg/CHNOSZ/inst/extdata/Berman/SHD91.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/Berman/SHD91.csv 2018-03-30 14:50:10 UTC (rev 312)
+++ pkg/CHNOSZ/inst/extdata/Berman/SHD91.csv 2018-03-31 04:45:08 UTC (rev 313)
@@ -1,12 +1,12 @@
-name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,k4,k5,k6,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,d5
-muscovite,-5603417,-5983434,293.157,14.087,651.49,-3873.2,-18523200,2742470000,0,0,0,-0.1717,4.295E-07,3.3527,0,,,,,,,,,,,,,,
-phlogopite,-5837044,-6217085,334.346,14.977,610.38,-2083.8,-21533000,2841040000,0,0,0,-0.1697,0,3.4447,0,,,,,,,,,,,,,,
-K-feldspar,-3752109,-3977485,214.145,10.869,381.37,-1941,-12037300,1836430000,0,0,0,-0.1805,5.112E-07,1.5145,0.5485,,,,,,,1436,298,282.98,-4830,3621000,-0.15733,3.477E-05,410630
-"K-feldspar,high",-3745498,-3966398,229.157,10.896,381.37,-1941,-12037300,1836430000,0,0,0,-0.1805,5.112E-07,1.5145,0.5485,,,,,,,,,,,,,,
-"K-feldspar,low",-3752109,-3977485,214.145,10.869,381.37,-1941,-12037300,1836430000,0,0,0,-0.1805,5.112E-07,1.5145,0.5485,,,,,,,,,,,,,,
-paragonite,-5570375,-5951011,277.699,13.216,577.57,-1472.8,-32214400,5050080000,0,0,0,-0.1973,4.933E-07,3.9424,0.59701,,,,,,,,,,,,,,
-albite,-3710096,-3928421,224.412,10.083,393.64,-2415.5,-7892800,1070640000,0,0,0,-0.1945,4.861E-07,2.6307,0.32407,,,,,,,,,,,,,,
-"albite,high",-3710096,-3928421,224.412,10.083,393.64,-2415.5,-7892800,1070640000,0,0,0,-0.1945,4.861E-07,2.6307,0.32407,,,,,,,,,,,,,,
-"albite,low",-3718518,-3941903,207.443,10.043,393.64,-2415.5,-7892800,1070640000,0,0,0,-0.1945,4.861E-07,2.6307,0.32407,,,,,,,,,,,,,,
-jadeite,-2853285,-3031921,133.574,6.034,311.29,-2005.1,-5350300,662570000,0,0,0,-0.086,2.149E-07,2.3118,0.25785,,,,,,,,,,,,,,
-annite,-4799809,-5149494,420,15.408,727.21,-4775.04,-13831900,2119060000,0,0,0,-0.1697,0,3.4447,0,,,,,,,,,,,,,,
+name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,k4,k5,k6,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,Vad
+muscovite,-5603417,-5983434,293.157,14.087,651.49,-3873.2,-18523200,2742470000,0,0,0,3.3527,0,-0.1717,0.0004295,,,,,,,,,,,,,,
+phlogopite,-5837044,-6217085,334.346,14.977,610.38,-2083.8,-21533000,2841040000,0,0,0,3.4447,0,-0.1697,0,,,,,,,,,,,,,,
+K-feldspar,-3752109,-3977485,214.145,10.869,381.37,-1941,-12037300,1836430000,0,0,0,1.5145,0.0005485,-0.1805,0.0005112,,,,,,,1436,298,282.98,-4830,3621000,-0.15733,3.477E-05,410630
+"K-feldspar,high",-3745498,-3966398,229.157,10.896,381.37,-1941,-12037300,1836430000,0,0,0,1.5145,0.0005485,-0.1805,0.0005112,,,,,,,,,,,,,,
+"K-feldspar,low",-3752109,-3977485,214.145,10.869,381.37,-1941,-12037300,1836430000,0,0,0,1.5145,0.0005485,-0.1805,0.0005112,,,,,,,,,,,,,,
+paragonite,-5570375,-5951011,277.699,13.216,577.57,-1472.8,-32214400,5050080000,0,0,0,3.9424,0.00059701,-0.1973,0.0004933,,,,,,,,,,,,,,
+albite,-3710096,-3928421,224.412,10.083,393.64,-2415.5,-7892800,1070640000,0,0,0,2.6307,0.00032407,-0.1945,0.0004861,,,,,,,,,,,,,,
+"albite,high",-3710096,-3928421,224.412,10.083,393.64,-2415.5,-7892800,1070640000,0,0,0,2.6307,0.00032407,-0.1945,0.0004861,,,,,,,,,,,,,,
+"albite,low",-3718518,-3941903,207.443,10.043,393.64,-2415.5,-7892800,1070640000,0,0,0,2.6307,0.00032407,-0.1945,0.0004861,,,,,,,,,,,,,,
+jadeite,-2853285,-3031921,133.574,6.034,311.29,-2005.1,-5350300,662570000,0,0,0,2.3118,0.00025785,-0.086,0.0002149,,,,,,,,,,,,,,
+annite,-4799809,-5149494,420,15.408,727.21,-4775.04,-13831900,2119060000,0,0,0,3.4447,0,-0.1697,0,,,,,,,,,,,,,,
Modified: pkg/CHNOSZ/inst/extdata/Berman/ZS92.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/Berman/ZS92.csv 2018-03-30 14:50:10 UTC (rev 312)
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/chnosz -r 313