Merge pull request #1 from naliboff/new_release_v3

Update ConMan to version 3.0.0

.zenodo.json

@@ -0,0 +1,17 @@
+{
+    "creators": [
+	{
+	    "name": "Scott King",
+	    "affiliation": "Virginia Tech University",
+	    "orcid": "0000-0002-9564-5164"
+	},
+	{
+	    "name": "Arthur Raefsky"
+	},
+	{
+            "name": "Brad H. Hager",
+            "affiliation": "MIT",
+            "orcid": "0000-0002-5643-1374"
+        }
+    ]
+}

CITATION

@@ -0,0 +1,8 @@
+King, S.D., A. Raefsky, and B.H. Hager (1990), ConMan: Vectorizing a finite
+element code for incompressible two-dimensional convection in the Earth’s
+mantle, Phys. Earth Planet. Int., 59, 195-208.
+
+King S. D., C. Lee, P. E. van Keken, W. Leng, S. Zhong, E. Tan, E., M. Gurnis,
+N. Tosi, and M. C.  Kameyama (2010). A community benchmark for 2D Cartesian
+compressible convection in the Earth’s mantle, Geophys. J. Int., 180, 73-87,
+2010. doi:10.1111/j.1365-246X.2009.04413.x

Cookbook1/Make_table.sh

@@ -0,0 +1,253 @@
+# Make a LaTeX table for Benchmarks
+
+#########################################
+#      User Adjustable Parameters       #
+#########################################
+FILE=blankenbach
+LATEX='latex'
+DVIPS='dvips'
+export FILE LATEX DVIPS GHOST
+
+#########################################
+#    End User Adjustable Parameters     #
+#########################################
+
+TEXFILE=$FILE.tex
+DVIFILE=$FILE.dvi
+PSFILE=$FILE.ps
+export TEXFILE DVIFILE PSFILE
+
+/bin/rm -f $TEXFILE
+echo '\documentclass[11pt]{article}' >> $TEXFILE
+echo '\begin{document}' >> $TEXFILE
+#########################################
+#   Rayleigh Number 10,000 Blankenbach  #
+#########################################
+echo '\begin{table}' >> $TEXFILE
+echo '\centering' >> $TEXFILE
+echo '\begin{tabular} {| r c c c c c c r |} \hline ' >> $TEXFILE
+echo '\multicolumn{1}{| c }{Grid} &' >> $TEXFILE
+echo '\multicolumn{1}{ c }{V$_{rms}$} &' >> $TEXFILE
+echo '\multicolumn{1}{ c }{Nusselt No.} &' >> $TEXFILE
+echo '\multicolumn{1}{ c }{Topo$_L$} &' >> $TEXFILE
+echo '\multicolumn{1}{ c }{Topo$_R$} &' >> $TEXFILE
+echo '\multicolumn{1}{ c }{Geoid$_L$} &' >> $TEXFILE
+echo '\multicolumn{1}{ c }{Geoid$_R$} & ' >> $TEXFILE
+echo '\multicolumn{1}{ c |}{Time (sec)} \\ ' >> $TEXFILE
+echo '\hline ' >> $TEXFILE
+  vrms=`tail -1 tser.bm1a50 | awk '{printf "%5.3f", $3}'`
+  nu=`tail -1 tser.bm1a50 | awk '{printf "%5.3f", $2}'`
+  topol=`awk 'NR==54 {printf "%7.3f", $3}' geoid.bm1a50`
+  geoidl=`awk 'NR==54 {printf "%5.3f", $5}' geoid.bm1a50`
+  topor=`awk 'NR==104 {printf "%7.3f", $3}' geoid.bm1a50`
+  geoidr=`awk 'NR==104 {printf "%5.3f", $5}' geoid.bm1a50`
+  time=`awk '$1=="total" {print $2}' out.bm1a50`
+  export vrms nu topol geoidl topor geoidr time
+echo ' 50 &' $vrms '&' $nu '&' $topol '&' $topor '&' $geoidl '&' $geoidr '&' $time '\\' >> $TEXFILE
+  vrms=`tail -1 tser.bm1a100 | awk '{printf "%5.3f", $3}'`
+  nu=`tail -1 tser.bm1a100 | awk '{printf "%5.3f", $2}'`
+  topol=`awk 'NR==104 {printf "%7.3f", $3}' geoid.bm1a100`
+  geoidl=`awk 'NR==104 {printf "%5.3f", $5}' geoid.bm1a100`
+  topor=`awk 'NR==204 {printf "%7.3f", $3}' geoid.bm1a100`
+  geoidr=`awk 'NR==204 {printf "%5.3f", $5}' geoid.bm1a100`
+  time=`awk '$1=="total" {print $2}' out.bm1a100`
+  export vrms nu topol geoidl topor geoidr time
+echo '100 &' $vrms '&' $nu '&' $topol '&' $topor '&' $geoidl '&' $geoidr '&' $time '\\' >> $TEXFILE
+  vrms=`tail -1 tser.bm1a200 | awk '{printf "%5.3f", $3}'`
+  nu=`tail -1 tser.bm1a200 | awk '{printf "%5.3f", $2}'`
+  topol=`awk 'NR==204 {printf "%7.3f", $3}' geoid.bm1a200`
+  geoidl=`awk 'NR==204 {printf "%5.3f", $5}' geoid.bm1a200`
+  topor=`awk 'NR==404 {printf "%7.3f", $3}' geoid.bm1a200`
+  geoidr=`awk 'NR==404 {printf "%5.3f", $5}' geoid.bm1a200`
+  time=`awk '$1=="total" {print $2}' out.bm1a200`
+  export vrms nu topol geoidl topor geoidr time
+echo '200 &' $vrms '&' $nu '&' $topol '&' $topor '&' $geoidl '&' $geoidr '&' $time '\\' >> $TEXFILE
+echo '\hline ' >> $TEXFILE
+echo '\dag C$_{ext}$ & 42.865 & 4.884 & 2254.021 & -2903.221 & 54.822 & -62.622 & \null \\' >> $TEXFILE
+echo '\hline ' >> $TEXFILE
+echo '\multicolumn{8}{|l|}{\dag Christensen$^{\prime}$s extrapolated values.} \\' >> $TEXFILE
+echo '\hline ' >> $TEXFILE
+echo '\end{tabular}' >> $TEXFILE
+echo '\caption{Blankenbach (1989) Benchmark 1a: Steady State, 2D, constant viscosity convection in a 1 by 1 box with Rayleigh number $10^4$ using ConMan} ' >> $TEXFILE
+echo '\end{table}' >> $TEXFILE
+
+#########################################
+#  Rayleigh Number 100,000 Blankenbach  #
+#########################################
+echo '\begin{table}' >> $TEXFILE
+echo '\centering' >> $TEXFILE
+echo '\begin{tabular} {| r c c c c c c r |} \hline ' >> $TEXFILE
+echo '\multicolumn{1}{| c }{Grid} &' >> $TEXFILE
+echo '\multicolumn{1}{ c }{V$_{rms}$} &' >> $TEXFILE
+echo '\multicolumn{1}{ c }{Nusselt No.} &' >> $TEXFILE
+echo '\multicolumn{1}{ c }{Topo$_L$} &' >> $TEXFILE
+echo '\multicolumn{1}{ c }{Topo$_R$} &' >> $TEXFILE
+echo '\multicolumn{1}{ c }{Geoid$_L$} &' >> $TEXFILE
+echo '\multicolumn{1}{ c }{Geoid$_R$} & ' >> $TEXFILE
+echo '\multicolumn{1}{ c |}{Time (sec)} \\ ' >> $TEXFILE
+echo '\hline ' >> $TEXFILE
+  vrms=`tail -1 tser.bm1b50 | awk '{printf "%5.3f", $3}'`
+  nu=`tail -1 tser.bm1b50 | awk '{printf "%5.3f", $2}'`
+  topol=`awk 'NR==54 {printf "%7.3f", $3}' geoid.bm1b50`
+  geoidl=`awk 'NR==54 {printf "%5.3f", $5}' geoid.bm1b50`
+  topor=`awk 'NR==104 {printf "%7.3f", $3}' geoid.bm1b50`
+  geoidr=`awk 'NR==104 {printf "%5.3f", $5}' geoid.bm1b50`
+  time=`awk '$1=="total" {print $2}' out.bm1b50`
+  export vrms nu topol geoidl topor geoidr time
+echo '50 &' $vrms '&' $nu '&' $topol '&' $topor '&' $geoidl '&' $geoidr '&' $time '\\' >> $TEXFILE
+  vrms=`tail -1 tser.bm1b100 | awk '{printf "%5.3f", $3}'`
+  nu=`tail -1 tser.bm1b100 | awk '{printf "%5.3f", $2}'`
+  topol=`awk 'NR==104 {printf "%7.3f", $3}' geoid.bm1b100`
+  geoidl=`awk 'NR==104 {printf "%5.3f", $5}' geoid.bm1b100`
+  topor=`awk 'NR==204 {printf "%7.3f", $3}' geoid.bm1b100`
+  geoidr=`awk 'NR==204 {printf "%5.3f", $5}' geoid.bm1b100`
+  time=`awk '$1=="total" {print $2}' out.bm1b100`
+  export vrms nu topol geoidl topor geoidr time
+echo '100 &' $vrms '&' $nu '&' $topol '&' $topor '&' $geoidl '&' $geoidr '&' $time '\\' >> $TEXFILE
+  vrms=`tail -1 tser.bm1b200 | awk '{printf "%5.3f", $3}'`
+  nu=`tail -1 tser.bm1b200 | awk '{printf "%5.3f", $2}'`
+  topol=`awk 'NR==204 {printf "%7.3f", $3}' geoid.bm1b200`
+  geoidl=`awk 'NR==204 {printf "%5.3f", $5}' geoid.bm1b200`
+  topor=`awk 'NR==404 {printf "%7.3f", $3}' geoid.bm1b200`
+  geoidr=`awk 'NR==404 {printf "%5.3f", $5}' geoid.bm1b200`
+  time=`awk '$1=="total" {print $2}' out.bm1b200`
+  export vrms nu topol geoidl topor geoidr time
+echo '200 &' $vrms '&' $nu '&' $topol '&' $topor '&' $geoidl '&' $geoidr '&' $time '\\' >> $TEXFILE
+echo '\hline ' >> $TEXFILE
+echo '\dag C$_{ext}$ & 193.214 & 10.534 & 1460.986 & -2004.205 & 27.703 & -32.016 & \null \\' >> $TEXFILE
+echo '\hline ' >> $TEXFILE
+echo '\multicolumn{8}{|l|}{\dag Christensen$^{\prime}$s extrapolated values.} \\' >> $TEXFILE
+echo '\hline ' >> $TEXFILE
+echo '\end{tabular}' >> $TEXFILE
+echo '\caption{Blankenbach (1989) Benchmark 1b: Steady State, 2D, constant viscosity convection in a 1 by 1 box with Rayleigh number $10^5$ using ConMan} ' >> $TEXFILE
+echo '\end{table}' >> $TEXFILE
+
+#########################################
+# Rayleigh Number 1,000,000 Blankenbach #
+#########################################
+echo '\begin{table}' >> $TEXFILE
+echo '\centering' >> $TEXFILE
+echo '\begin{tabular} {| r c c c c c c r |} \hline ' >> $TEXFILE
+echo '\multicolumn{1}{| c }{Grid} &' >> $TEXFILE
+echo '\multicolumn{1}{ c }{V$_{rms}$} &' >> $TEXFILE
+echo '\multicolumn{1}{ c }{Nusselt No.} &' >> $TEXFILE
+echo '\multicolumn{1}{ c }{Topo$_L$} &' >> $TEXFILE
+echo '\multicolumn{1}{ c }{Topo$_R$} &' >> $TEXFILE
+echo '\multicolumn{1}{ c }{Geoid$_L$} &' >> $TEXFILE
+echo '\multicolumn{1}{ c }{Geoid$_R$} &' >> $TEXFILE
+echo '\multicolumn{1}{ c |}{Time (sec)} \\ ' >> $TEXFILE
+echo '\hline ' >> $TEXFILE
+  vrms=`tail -1 tser.bm1c50 | awk '{printf "%5.3f", $3}'`
+  nu=`tail -1 tser.bm1c50 | awk '{printf "%5.3f", $2}'`
+  topol=`awk 'NR==54 {printf "%7.3f", $3}' geoid.bm1c50`
+  geoidl=`awk 'NR==54 {printf "%5.3f", $5}' geoid.bm1c50`
+  topor=`awk 'NR==104 {printf "%7.3f", $3}' geoid.bm1c50`
+  geoidr=`awk 'NR==104 {printf "%5.3f", $5}' geoid.bm1c50`
+  time=`awk '$1=="total" {print $2}' out.bm1c50`
+  export vrms nu topol geoidl topor geoidr time
+echo '50 &' $vrms '&' $nu '&' $topol '&' $topor '&' $geoidl '&' $geoidr '&' $time '\\' >> $TEXFILE
+  vrms=`tail -1 tser.bm1c100 | awk '{printf "%5.3f", $3}'`
+  nu=`tail -1 tser.bm1c100 | awk '{printf "%5.3f", $2}'`
+  topol=`awk 'NR==104 {printf "%7.3f", $3}' geoid.bm1c100`
+  geoidl=`awk 'NR==104 {printf "%5.3f", $5}' geoid.bm1c100`
+  topor=`awk 'NR==204 {printf "%7.3f", $3}' geoid.bm1c100`
+  geoidr=`awk 'NR==204 {printf "%5.3f", $5}' geoid.bm1c100`
+  time=`awk '$1=="total" {print $2}' out.bm1c100`
+  export vrms nu topol geoidl topor geoidr time
+echo '100 &' $vrms '&' $nu '&' $topol '&' $topor '&' $geoidl '&' $geoidr '&' $time '\\' >> $TEXFILE
+  vrms=`tail -1 tser.bm1c200 | awk '{printf "%5.3f", $3}'`
+  nu=`tail -1 tser.bm1c200 | awk '{printf "%5.3f", $2}'`
+  topol=`awk 'NR==204 {printf "%7.3f", $3}' geoid.bm1c200`
+  geoidl=`awk 'NR==204 {printf "%5.3f", $5}' geoid.bm1c200`
+  topor=`awk 'NR==404 {printf "%7.3f", $3}' geoid.bm1c200`
+  geoidr=`awk 'NR==404 {printf "%5.3f", $5}' geoid.bm1c200`
+  time=`awk '$1=="total" {print $2}' out.bm1c200`
+  export vrms nu topol geoidl topor geoidr time
+echo '200 &' $vrms '&' $nu '&' $topol '&' $topor '&' $geoidl '&' $geoidr '&' $time '\\' >> $TEXFILE
+echo '\hline ' >> $TEXFILE
+echo '\dag C$_{ext}$ & 833.989 & 21.997 & 931.962 & -1283.813 & 13.452 & -15.034 & \null \\' >> $TEXFILE
+echo '\hline ' >> $TEXFILE
+echo '\multicolumn{8}{|l|}{\dag Christensen$^{\prime}$s extrapolated values.} \\' >> $TEXFILE
+echo '\hline ' >> $TEXFILE
+echo '\end{tabular}' >> $TEXFILE
+echo '\caption{Blankenbach (1989) Benchmark 1c: Steady State, 2D, constant viscosity convection in a 1 by 1 box with Rayleigh number $10^6$ using ConMan.} ' >> $TEXFILE
+echo '\end{table}' >> $TEXFILE
+
+#########################################
+# Rayleigh Number 10,000 Blankenbach TD #
+#########################################
+echo '\begin{table}' >> $TEXFILE
+echo '\centering' >> $TEXFILE
+echo '\begin{tabular} {| r c c c c c c r |} \hline ' >> $TEXFILE
+echo '\multicolumn{1}{| c }{Grid} &' >> $TEXFILE
+echo '\multicolumn{1}{ c }{V$_{rms}$} &' >> $TEXFILE
+echo '\multicolumn{1}{ c }{Nusselt No.} &' >> $TEXFILE
+echo '\multicolumn{1}{ c }{Topo$_L$} &' >> $TEXFILE
+echo '\multicolumn{1}{ c }{Topo$_R$} &' >> $TEXFILE
+echo '\multicolumn{1}{ c }{Geoid$_L$} &' >> $TEXFILE
+echo '\multicolumn{1}{ c }{Geoid$_R$} &' >> $TEXFILE
+echo '\multicolumn{1}{ c |}{Time (sec)} \\ ' >> $TEXFILE
+echo '\hline ' >> $TEXFILE
+  vrms=`tail -1 tser.bm2a50 | awk '{printf "%5.3f", $3}'`
+  nu=`tail -1 tser.bm2a50 | awk '{printf "%5.3f", $2}'`
+  topol=`awk 'NR==54 {printf "%7.3f", $3}' geoid.bm2a50`
+  geoidl=`awk 'NR==54 {printf "%5.3f", $5}' geoid.bm2a50`
+  topor=`awk 'NR==104 {printf "%7.3f", $3}' geoid.bm2a50`
+  geoidr=`awk 'NR==104 {printf "%5.3f", $5}' geoid.bm2a50`
+  time=`awk '$1=="total" {print $2}' out.bm2a50`
+  export vrms nu topol geoidl topor geoidr time
+echo '50 &' $vrms '&' $nu '&' $topol '&' $topor '&' $geoidl '&' $geoidr '&' $time '\\' >> $TEXFILE
+  vrms=`tail -1 tser.bm2a100 | awk '{printf "%5.3f", $3}'`
+  nu=`tail -1 tser.bm2a100 | awk '{printf "%5.3f", $2}'`
+  topol=`awk 'NR==104 {printf "%7.3f", $3}' geoid.bm2a100`
+  geoidl=`awk 'NR==104 {printf "%5.3f", $5}' geoid.bm2a100`
+  topor=`awk 'NR==204 {printf "%7.3f", $3}' geoid.bm2a100`
+  geoidr=`awk 'NR==204 {printf "%5.3f", $5}' geoid.bm2a100`
+  time=`awk '$1=="total" {print $2}' out.bm2a100`
+  export vrms nu topol geoidl topor geoidr time
+echo '100 &' $vrms '&' $nu '&' $topol '&' $topor '&' $geoidl '&' $geoidr '&' $time '\\' >> $TEXFILE
+  vrms=`tail -1 tser.bm2a200 | awk '{printf "%5.3f", $3}'`
+  nu=`tail -1 tser.bm2a200 | awk '{printf "%5.3f", $2}'`
+  topol=`awk 'NR==204 {printf "%7.3f", $3}' geoid.bm2a200`
+  geoidl=`awk 'NR==204 {printf "%5.3f", $5}' geoid.bm2a200`
+  topor=`awk 'NR==404 {printf "%7.3f", $3}' geoid.bm2a200`
+  geoidr=`awk 'NR==404 {printf "%5.3f", $5}' geoid.bm2a200`
+  time=`awk '$1=="total" {print $2}' out.bm2a200`
+  export vrms nu topol geoidl topor geoidr time
+echo '200 &' $vrms '&' $nu '&' $topol '&' $topor '&' $geoidl '&' $geoidr '&' $time '\\' >> $TEXFILE
+#  vrms=`tail -1 tser.bm2a400 | awk '{printf "%5.3f", $3}'`
+#  nu=`tail -1 tser.bm2a400 | awk '{printf "%5.3f", $2}'`
+#  topol=`awk 'NR==404 {printf "%7.3f", $3}' geoid.bm2a400`
+#  geoidl=`awk 'NR==404 {printf "%5.3f", $5}' geoid.bm2a400`
+#  topor=`awk 'NR==804 {printf "%7.3f", $3}' geoid.bm2a400`
+#  geoidr=`awk 'NR==804 {printf "%5.3f", $5}' geoid.bm2a400`
+#  time=`awk '$1=="total" {print $2}' out.bm2a400`
+#  export vrms nu topol geoidl topor geoidr time
+#echo '400 &' $vrms '&' $nu '&' $topol '&' $topor '&' $geoidl '&' $geoidr '&' $time '\\' >> $TEXFILE
+#  vrms=`tail -1 tser.bm2a600 | awk '{printf "%5.3f", $3}'`
+#  nu=`tail -1 tser.bm2a600 | awk '{printf "%5.3f", $2}'`
+#  topol=`awk 'NR==604 {printf "%7.3f", $3}' geoid.bm2a600`
+#  geoidl=`awk 'NR==604 {printf "%5.3f", $5}' geoid.bm2a600`
+#  topor=`awk 'NR==1204 {printf "%7.3f", $3}' geoid.bm2a600`
+#  geoidr=`awk 'NR==1204 {printf "%5.3f", $5}' geoid.bm2a600`
+#  time=`awk '$1=="total" {print $2}' out.bm2a600`
+#  export vrms nu topol geoidl topor geoidr time
+#echo '600 &' $vrms '&' $nu '&' $topol '&' $topor '&' $geoidl '&' $geoidr '&' $time '\\' >> $TEXFILE
+#echo '\hline ' >> $TEXFILE
+echo '\dag C$_{ext}$ & 480.433 & 10.066 & 1010.925 & -4098.073 & 17.343 & -54.598 & \null \\' >> $TEXFILE
+echo '\hline ' >> $TEXFILE
+echo '\multicolumn{8}{|l|}{\dag Christensen$^{\prime}$s extrapolated values.} \\' >> $TEXFILE
+echo '\hline ' >> $TEXFILE
+echo '\end{tabular}' >> $TEXFILE
+echo '\caption{Blankenbach (1989) Benchmark 2a: Steady State, 2D, temperature-dependent viscosity convection (b=6.907755279) in a 1 by 1 box with Rayleigh number $10^4$ using ConMan.} ' >> $TEXFILE
+echo '\end{table}' >> $TEXFILE
+
+
+echo '\end{document}' >> $TEXFILE
+
+#########################################
+#   Run LaTeX and make Postscript file  #
+#########################################
+$LATEX $TEXFILE
+$DVIPS $DVIFILE -o $PSFILE
+open $PSFILE

Cookbook1/RUN_Cookbook1.sh

@@ -0,0 +1,29 @@
+#/bin/bash -f
+# Cookbook 1 run script
+#
+echo 'please be patient, running 50x50 Blankenbach 1989 constant viscosity calculations'
+echo 'estimated completion time: 10 seconds'
+../conman < run.bm1a50
+../conman < run.bm1b50
+../conman < run.bm1c50
+# 
+echo 'please be patient, running 100x100 Blankenbach 1989 constant viscosity calculations'
+echo 'estimated completion time: 30 seconds'
+../conman < run.bm1a100
+../conman < run.bm1b100
+../conman < run.bm1c100
+#
+echo 'please be patient, running 200x200 Blankenbach 1989 constant viscosity calculations'
+echo 'estimated completion time: 5 minutes'
+../conman < run.bm1a200
+../conman < run.bm1b200
+../conman < run.bm1c200
+#
+echo 'please be really patient, running 200x200 Blankenbach 1989 temperature-dependent calculations'
+echo 'estimated completion time: 50 minutes'
+../conman < run.bm2a50
+../conman < run.bm2a100
+../conman < run.bm2a200
+# these take a long, long time (11 hours and 120 hours)
+#../conman < run.bm2a400
+#../conman < run.bm2a600