[CHNOSZ-commits] r313 - in pkg/CHNOSZ: . R inst inst/extdata/Berman inst/extdata/Berman/testing man tests/testthat

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Sat Mar 31 06:45:10 CEST 2018


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,,,,,,,,,,,,,,
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-"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,,,,,,,,,,,,,,
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-pseudowollastonite,-1543085,-1627427,85.279,4.016,141.16,-417.2,-5857600,940740000,0,0,0,-0.1245,3.113E-07,2.818,0,,,,,,,,,,,,,,
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+"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,,,,,,,,,,,,,,
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+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,,,,,,,,,,,,,,
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+"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,,,,,,,,,,,,,,
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+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


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