generate hun's analysis code automaticly

tools/hun/Atom.dic

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+     H        1.007900
+     C       12.011000
+     O       15.994000
+     N       14.007000

tools/hun/Cutoff.dic

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+     H     H      0.4000
+     H     C      0.4000
+     H     O      0.4000
+     H     N      0.4000
+     C     C      0.4000
+     C     O      0.4000
+     C     N      0.4000
+     O     O      0.4000
+     O     N      0.4000
+     N     N      0.4000

tools/hun/gen.py

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+import sys
+import os
+import socket
+import argparse
+
+LIB = ''
+
+if socket.gethostname() == "cluster.hpc.org":
+    LIB = "/home/chengtao/packages/simpy/simpy/lib"
+elif socket.gethostname() == "tao-laptop":
+    LIB = "/home/tao/Nutstore/code/simupy/lib"
+elif socket.gethostname() == "atom.wag.caltech.edu":
+    LIB = "/net/hulk/home6/chengtao/soft/simpy/lib"
+elif socket.gethostname() == "ion.wag.caltech.edu":
+    LIB = "/net/hulk/home6/chengtao/soft/simpy/lib"
+elif socket.gethostname() == "giant12":
+    LIB = "/net/hulk/home6/chengtao/soft/simpy/lib"
+
+sys.path.insert(0 , LIB)
+
+from cons import ELEMENT2MASS
+
+def gen_atomdic(atoms):
+    o = open("Atom.dic", "w")
+    for i in atoms:
+        o.write("%s %.6f\n"%(i, ELEMENT2MASS[i]))
+    o.close()
+
+def gen_cutoff(atoms):
+    bo = 0.4
+    o = open("Cutoff.dic", "w")
+    for i in range(len(atoms)):
+        for j in range(i, len(atoms)):
+            o.write("%6s%6s%12.4f\n"%(atoms[i], atoms[j], bo))
+    o.close()
+
+def gen_molfrag():
+    o = open("molfrag.sh", "w")
+    o.write("""
+# argument
+if [ $# -ne 1 ]
+then
+  echo "Usage : molfrag.sh [control.file]"
+  exit
+fi
+
+Logfile="log.molfrag"
+
+echo "Molecular Fragment Analysis Toolkit"
+echo "-----------------------------------"
+echo ""
+echo "Programmed by Hyungjun Kim (linus) at 2007"
+echo ""
+
+#echo "Molecular Fragment Analysis Toolkit" > $Logfile
+#echo "-----------------------------------" >> $Logfile
+#echo "" >> $Logfile
+#echo "Programmed by Hyungjun Kim (linus) at 2007" >> $Logfile
+#echo "" >> $Logfile
+
+echo " *Creating Bond Change Logs."
+#echo " *Creating Bond Change Logs." >> $Logfile
+bondlog $1
+#cp dataTATB/Bond.log dataTATB/Bond.log.bak
+#cp dataTATB/Nbondchg.log dataTATB/Nbondchg.log.bak
+
+echo ""
+echo " *Reducing Bond Change Logs."
+echo " (Deleting Redundant reactions)"
+
+#echo "" >> $Logfile
+#echo " *Reducing Bond Change Logs." >> $Logfile
+#echo " (Deleting Redundant reactions)" >> $Logfile
+netbondlog $1
+
+echo ""
+echo " *Molecular Fragment Analysis"
+
+#echo "" >> $Logfile
+#echo " *Molecular Fragment Analysis" >> $Logfile
+molfrag $1
+molstat $1
+
+MolStatList=$(grep MolStatTotal $1)
+MolStatList=${MolStatList#MolStatTotal}
+
+fragtable $1 $MolStatList
+
+echo ""
+echo " *Rxn Analysis"
+
+#echo "" >> $Logfile
+#echo " *Molecular Fragment Analysis" >> $Logfile
+rxnanal $1
+
+echo "DONE"
+#rm bondlog netbondlog molfrag rxnanal molstat fragtable
+""")
+    o.close()
+    os.system("chmod +x molfrag.sh")
+
+def gen_control():
+    o = open("control.file", "w")
+    o.write("""# Input files
+# Type : Grasp, Reax, Reax2
+Type            Grasp
+Config          config.out
+Bonds           reaxbonds.out
+
+# Simulation Information (fs)
+Timestep        0.5
+
+# Dictionaries
+Atoms           Atom.dic
+Bond-CutOff     Cutoff.dic
+
+# Analysis Parameters
+# 0: Do not create MoleculeData file. 1: Create MoleculeData file.
+MolDataFlag     1
+# Time window for determining important bond breaking (ps)
+TimeWindow      0.05
+
+# Output files
+MoleculeID              data/molid.out
+MoleculeData    data/moldata.out
+
+NofMolecules    data/nmol.out
+MoleculeChanges data/molchg.out
+MoleculeAtom    data/mol.atom
+BondLog         data/Bond.log
+NBondChange     data/Nbondchg.log
+NetBonds        data/netBonds.out
+RxnLog          data/rxn.log
+TemperatureLog  data/temperature.log
+
+# Output files for Molecular Statistics
+MolStatPerStep  data/molstat.step
+MolStatTotal    data/molstat.total
+FragmentTable   data/fragtable
+
+# Basic Settings for Memory Allocation (integer type)
+MaxBondsPerAtom                         50
+MaxAtomsPerMolecule                     2000
+MaxMoleculeChangePerStep        100000
+MaxMoleculeSpecies                      1000000
+MaxMoleculeTrace                        10000
+
+# Analyzing Frequency (integer type)
+# Currently Frequency=1 case is only tested.
+Frequency                       1
+""")
+    o.close()
+
+
+def main():
+    parser = argparse.ArgumentParser()
+    parser.add_argument("-atoms", nargs="+", help="atom types")
+    args = parser.parse_args()
+
+    atoms = []
+    if args.atoms:
+        atoms = args.atoms
+    else:
+        exit("No atoms input!")
+
+    if not os.path.exists("anal"):
+        os.mkdir("anal")
+
+    os.chdir("anal")
+    if not os.path.exists("data"):
+        os.mkdir("data")
+
+    # generate the necessary input files
+    gen_molfrag()
+    gen_atomdic(atoms)
+    gen_cutoff(atoms)
+    gen_control()
+    os.chdir("..")
+
+    os.system("dump2config.py dump.lammpstrj ./anal/config.out")
+    os.system("trj2reaxbonds.py lammps.trj ./anal/reaxbonds.out")
+    os.chdir("anal")
+    os.system("./molfrag.sh control.file")
+
+if __name__ == "__main__":
+    main()

tools/hun/gen.py~

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+import sys
+import os
+import socket
+import argparse
+
+LIB = ''
+
+if socket.gethostname() == "cluster.hpc.org":
+    LIB = "/home/chengtao/packages/simpy/simpy/lib"
+elif socket.gethostname() == "tao-laptop":
+    LIB = "/home/tao/Nutstore/code/simupy/lib"
+elif socket.gethostname() == "atom.wag.caltech.edu":
+    LIB = "/net/hulk/home6/chengtao/soft/simpy/lib"
+elif socket.gethostname() == "ion.wag.caltech.edu":
+    LIB = "/net/hulk/home6/chengtao/soft/simpy/lib"
+elif socket.gethostname() == "giant12":
+    LIB = "/net/hulk/home6/chengtao/soft/simpy/lib"
+
+sys.path.insert(0 , LIB)
+
+from cons import ELEMENT2MASS
+
+def gen_atomdic(atoms):
+    o = open("Atom.dic", "w")
+    for i in atoms:
+        o.write("%6s%16.6f\n"%(i, ELEMENT2MASS[i]))
+    o.close()
+
+def gen_cutoff(atoms):
+    bo = 0.4
+    o = open("Cutoff.dic", "w")
+    for i in range(len(atoms)):
+        for j in range(i, len(atoms)):
+            o.write("%6s%6s%12.4f\n"%(atoms[i], atoms[j], bo))
+    o.close()
+
+def gen_molfrag():
+    o = open("molfrag.sh", "w")
+    o.write("""
+# argument
+if [ $# -ne 1 ]
+then
+  echo "Usage : molfrag.sh [control.file]"
+  exit
+fi
+
+Logfile="log.molfrag"
+
+echo "Molecular Fragment Analysis Toolkit"
+echo "-----------------------------------"
+echo ""
+echo "Programmed by Hyungjun Kim (linus) at 2007"
+echo ""
+
+#echo "Molecular Fragment Analysis Toolkit" > $Logfile
+#echo "-----------------------------------" >> $Logfile
+#echo "" >> $Logfile
+#echo "Programmed by Hyungjun Kim (linus) at 2007" >> $Logfile
+#echo "" >> $Logfile
+
+echo " *Creating Bond Change Logs."
+#echo " *Creating Bond Change Logs." >> $Logfile
+bondlog $1
+#cp dataTATB/Bond.log dataTATB/Bond.log.bak
+#cp dataTATB/Nbondchg.log dataTATB/Nbondchg.log.bak
+
+echo ""
+echo " *Reducing Bond Change Logs."
+echo " (Deleting Redundant reactions)"
+
+#echo "" >> $Logfile
+#echo " *Reducing Bond Change Logs." >> $Logfile
+#echo " (Deleting Redundant reactions)" >> $Logfile
+netbondlog $1
+
+echo ""
+echo " *Molecular Fragment Analysis"
+
+#echo "" >> $Logfile
+#echo " *Molecular Fragment Analysis" >> $Logfile
+molfrag $1
+molstat $1
+
+MolStatList=$(grep MolStatTotal $1)
+MolStatList=${MolStatList#MolStatTotal}
+
+fragtable $1 $MolStatList
+
+echo ""
+echo " *Rxn Analysis"
+
+#echo "" >> $Logfile
+#echo " *Molecular Fragment Analysis" >> $Logfile
+rxnanal $1
+
+echo "DONE"
+#rm bondlog netbondlog molfrag rxnanal molstat fragtable
+""")
+    o.close()
+    os.system("chmod +x molfrag.sh")
+
+# generate the necessary input files
+
+def main():
+    parser = argparse.ArgumentParser()
+    parser.add_argument("-atoms", nargs="+", help="atom types")
+    args = parser.parse_args()
+
+    atoms = []
+    if args.atoms:
+        atoms = args.atoms
+    else:
+        exit("No atoms input!")
+
+    if not os.path.exists("data"):
+        os.mkdir("data")
+
+    gen_molfrag()
+    gen_atomdic(atoms)
+    gen_cutoff(atoms)
+
+if __name__ == "__main__":
+    main()

tools/hun/molfrag.sh

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+
+# argument
+if [ $# -ne 1 ]
+then
+  echo "Usage : molfrag.sh [control.file]"
+  exit
+fi
+
+Logfile="log.molfrag"
+
+echo "Molecular Fragment Analysis Toolkit"
+echo "-----------------------------------"
+echo ""
+echo "Programmed by Hyungjun Kim (linus) at 2007"
+echo ""
+
+#echo "Molecular Fragment Analysis Toolkit" > $Logfile
+#echo "-----------------------------------" >> $Logfile
+#echo "" >> $Logfile
+#echo "Programmed by Hyungjun Kim (linus) at 2007" >> $Logfile
+#echo "" >> $Logfile
+
+echo " *Creating Bond Change Logs."
+#echo " *Creating Bond Change Logs." >> $Logfile
+bondlog $1
+#cp dataTATB/Bond.log dataTATB/Bond.log.bak
+#cp dataTATB/Nbondchg.log dataTATB/Nbondchg.log.bak
+
+echo ""
+echo " *Reducing Bond Change Logs."
+echo " (Deleting Redundant reactions)"
+
+#echo "" >> $Logfile
+#echo " *Reducing Bond Change Logs." >> $Logfile
+#echo " (Deleting Redundant reactions)" >> $Logfile
+netbondlog $1
+
+echo ""
+echo " *Molecular Fragment Analysis"
+
+#echo "" >> $Logfile
+#echo " *Molecular Fragment Analysis" >> $Logfile
+molfrag $1
+molstat $1
+
+MolStatList=$(grep MolStatTotal $1)
+MolStatList=${MolStatList#MolStatTotal}
+
+fragtable $1 $MolStatList
+
+echo ""
+echo " *Rxn Analysis"
+
+#echo "" >> $Logfile
+#echo " *Molecular Fragment Analysis" >> $Logfile
+rxnanal $1
+
+echo "DONE"
+#rm bondlog netbondlog molfrag rxnanal molstat fragtable