From b41e0b2036c6688f720e9c31e75c7ce7a18f9cc7 Mon Sep 17 00:00:00 2001
From: Tao Cheng <chengtaoliterature@gmail.com>
Date: Sun, 2 Nov 2014 23:21:36 -0800
Subject: [PATCH] debug

---
 lib/cons.py                |  2 +-
 tools/Lammps/lammps_eos.py |  3 +-
 tools/Lammps/template.py   |  9 ++--
 tools/pbs/exLammps         | 85 ++++++++++++++++++++++++++++++++++++++
 tools/vasp/get_potcar.py   |  2 +-
 5 files changed, 94 insertions(+), 7 deletions(-)
 create mode 100755 tools/pbs/exLammps

diff --git a/lib/cons.py b/lib/cons.py
index 91891cc..57ba064 100644
--- a/lib/cons.py
+++ b/lib/cons.py
@@ -3,7 +3,7 @@
 
 # Atom number - Atom name map
 ELEMENT = {1:"H", 3:"Li", 6:"C", 7:"N",  8:"O", 9:"F", 12: "Mg", 13: "Al", 14:"Si", 
-            15:"P", 16:"S", 17:"Cl", 20:"Ca", 22:"Ti", 31:"Ga", 32:"Ge"}
+            15:"P", 16:"S", 17:"Cl", 20:"Ca", 22:"Ti", 28:"Ni", 31:"Ga", 32:"Ge"}
 # Atom name - Atom number map
 ELEMENT2ATN = {"H":1, "Li":3, "C":6, "N":7,  "O":8, 9:"F", "Na":11, 12: "Mg", "Al":13, "Si":14, 
             "P":15, "S":16, "Cl":17, "Ca":20, "Ti":22, "V":23,"Ni":28, "Pt":78, 32:"Ge", "MO":42, "Mo":42,
diff --git a/tools/Lammps/lammps_eos.py b/tools/Lammps/lammps_eos.py
index 0767701..940deb4 100644
--- a/tools/Lammps/lammps_eos.py
+++ b/tools/Lammps/lammps_eos.py
@@ -35,6 +35,7 @@
     for j in lines:
         o.write(j)
     o.close()
-    shutil.copy("../min.rst", ".")
+    if os.path.exists("../min.rst"):
+        shutil.copy("../min.rst", ".")
     shutil.copy("../ffield", ".")
     os.chdir("..")
diff --git a/tools/Lammps/template.py b/tools/Lammps/template.py
index 19398e4..1de6b6b 100644
--- a/tools/Lammps/template.py
+++ b/tools/Lammps/template.py
@@ -77,7 +77,7 @@
 
 #pair_style      reax/c control
 #pair_style      reax/c NULL lgvdw yes
-pair_style       %reax_potential%
+pair_style       %reax_potential% safezone 1.8 mincap 180
 
 #----Neighbor Section----#
 
@@ -108,22 +108,23 @@
 #--------Output info--------
 
 thermo         400
-thermo_style    custom step etotal ke pe temp press vol v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq cella cellb cellc cellalpha cellbeta cellgamma
+thermo_style    custom step etotal ke pe temp press vol v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq cella cellb cellc cellalpha cellbeta cellgamma pxx pyy pzz
 thermo_modify   line multi
 
 dump            100 all custom 400 dump.lammpstrj id type x y z vx vy vz
 dump_modify     100 sort id
 dump            101 all cfg 400 dump.*.cfg mass type xs ys zs vx vy vz fx fy fz
-dump_modify     101 element %elements%
+dump_modify     101 element %elements% sort id
 
 #--------Analysis-----------
 
-fix             200 all reax/c/bonds 400 bonds.reax
+#fix             200 all reax/c/bonds 400 bonds.reax
 #fix             201 all reax/c/species 1 1 400 species.out
 
 #--------Simulation--------
 
 velocity        all create 300.0 4928459 rot yes dist gaussian
+restart         40000 restart_*.rst
 fix             401 all nvt temp 300 300 50       
 timestep        0.25
 run             80000
diff --git a/tools/pbs/exLammps b/tools/pbs/exLammps
new file mode 100755
index 0000000..622d55e
--- /dev/null
+++ b/tools/pbs/exLammps
@@ -0,0 +1,85 @@
+#!/usr/bin/env python
+
+"""
+Generate pbs script for LAMMPS calculation on HPC.
+exLAMMPS ncpu
+"""
+
+import sys
+import os
+import shutil
+
+INP = """#!/bin/bash
+
+#PBS -A ONRDC33663C5T
+#PBS -V
+#PBS -j oe
+#PBS -N LAMMPS
+#PBS -q challenge
+#PBS -l select=%nnode%:ncpus=32:mpiprocs=32
+#PBS -l walltime=168:00:00
+
+export LAMMPSLOC=/u/taocheng/SOFT/lammps-1Feb14/src
+export exe=$LAMMPSLOC/lmp_pgi
+echo "The LAMMPS executable is: " $exe
+
+export DATADIR=$PBS_O_WORKDIR
+
+export NPROCS=`wc -l $PBS_NODEFILE | cut -f1 -d " "`
+export JOBID=`echo $PBS_JOBID | awk -F'.' '{print $1}'`
+export OUTPUTDIR=$WORKDIR/LAMMPS/$JOBID
+echo "The LAMMPS output will temporarily be written to :" $OUTPUTDIR
+echo "LAMMPS Job: " $JOBID "is starting with " $NPROCS "cores on:"
+cat $PBS_NODEFILE
+echo
+
+# Create Directories
+#
+mkdir -p $OUTPUTDIR
+
+# export job info
+#
+echo $PBS_JOBID >  $DATADIR/jobinfo
+cat $PBS_NODEFILE >>  $DATADIR/jobinfo
+echo $OUTPUTDIR >>  $DATADIR/jobinfo
+
+# Copy executable and any required input files to your work directory
+#
+cp $DATADIR/* $OUTPUTDIR
+cd $OUTPUTDIR
+
+#
+# Run LAMMPS
+#
+date
+aprun -n %ncpu% $exe -in lammps_input > log
+echo
+date
+echo "LAMMPS has finished."
+echo "The LAMMPS output is being copied back to: " $PBS_O_WORKDIR
+cd ..
+tar -cvzf $JOBID.tar.gz $JOBID
+cp -r $JOBID.tar.gz $PBS_O_WORKDIR
+rm $JOBID.tar.gz
+
+exit 0
+
+"""
+
+def main():
+    if len(sys.argv) == 1:
+        ncpu = 32
+    else:
+        ncpu = int(sys.argv[1])
+    nnode = ncpu/32
+        
+    o = open("runLAMMPS.in", "w")
+    lines = INP
+    lines = lines.replace("%nnode%", "%d"%nnode)
+    lines = lines.replace("%ncpu%", "%d"%ncpu)
+    o.write(lines)
+    o.close()
+    os.system("chmod +x runLAMMPS.in")
+
+if __name__ == "__main__":
+    main()
diff --git a/tools/vasp/get_potcar.py b/tools/vasp/get_potcar.py
index d497335..b7a9b55 100644
--- a/tools/vasp/get_potcar.py
+++ b/tools/vasp/get_potcar.py
@@ -23,7 +23,7 @@
 
 POT = {"N":"N", "O":"O", "H":"H", "C":"C", "Li":"Li", "S":"S", "Ti":"Ti", "P":"P", 
        "Ca":"Ca_pv", "Al":"Al", "Cu":"Cu", "Na":"Na", "Cl":"Cl", "Cr":"Cr", "Ga":"Ga",
-        "Br":"Br", "D": "H", "Si": "Si", "Ni": "Ni"}
+        "Br":"Br", "D": "H", "Si": "Si", "Ni": "Ni", "Pt":"Pt"}
 POT_DATA_BASE = "/project/source/VASP/vasp.5.2/potcar/potpaw_PBE"
 
 o = open("POTCAR", "w")