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genLanczosHvParamFiles.py
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genLanczosHvParamFiles.py
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####################################################
####################################################
# Usage: pydev genLanczosHvParamFiles.py [outputDir]
####################################################
####################################################
# Written by Joshua Cantin 27 Aug 2013
from numpy import *
import sys
import datetime
import os
import string
####################################################
#Fixed Hv Parameters
####################################################
quadratureConvergenceStudy = "FALSE"
#geometryFilename = "sII_smallCage11_CM_EA_ZYZ.xyz"
totalMass = 2.01588 #g/mol
rotationalConstant = 0.7096487130193394 #kJ/mol
simulationTitlePrefix = "Alavi_SPCE_smallCage11"
rotationalSymmetry = "Even"
####################################################
#Miscellaneous Parameters
####################################################
nthreads = 8
executable = "LanczosTOBY"
H2Allowance = 0.08 #nm
####################################################
#Fixed Lanczos Parameters
####################################################
EigenvalueOpenLowerLimit = -10 #kJ/mol
EigenvalueClosedUpperLimit = 10 #kJ/mol
NumberOfEigenvectorsWord = "none"
NumberOfEigenvectorsNum = 3
HvCalculator = "linRotCartSph_NoQuad_Alavi_SPCE"
OutputDirectoryPath = "/scratch/jtcantin/"
####################################################
#Base Hv Parameters
####################################################
baseHvParamDict = { "gridPoints": 21,
"gridSize": 0.4, #nm
"gridSpacing": 0.02, #nm
"lMax": 5,
"thetaPoints": 70,
"phiPoints": 70,
"potentialGridPoints": 241,
"potentialGridSize": 0.48, #nm
"potentialGridSpacing": 0.002, #nm
"totalMass": totalMass,
"rotationalConstant": rotationalConstant,
"geometryFilename": "sII_smallCage11_CM_EA_ZYZ.xyz",
"simulationTitle": simulationTitlePrefix + "_baseParam",
"ceilingPotential": 18., #kJ/mol
"quadratureConvergenceStudy": quadratureConvergenceStudy,
"rotationalSymmetry": rotationalSymmetry
}
####################################################
#Base Lanczos Parameters
####################################################
baseLanczosParamDict = { "lanczosIterations": 10000,
"EigenvalueOpenLowerLimit": EigenvalueOpenLowerLimit,
"EigenvalueClosedUpperLimit": EigenvalueClosedUpperLimit,
"NumberOfEigenvectorsWord": NumberOfEigenvectorsWord,
"NumberOfEigenvectorsNum": NumberOfEigenvectorsNum,
"HvCalculator": HvCalculator,
"OutputDirectoryPath": OutputDirectoryPath
}
####################################################
#Parameter Ranges
####################################################
#Syntax: numpy.r_[first:last+step:step]
gridSizeArray = r_[0.4:0.5:0.1] #nm
gridSpacingArray = r_[0.02:0.03:0.01] #nm
lMaxArray = r_[5:6:1]
thetaPointsArray = r_[70:80:10]
phiPointsArray = r_[70:80:10]
ceilingPotentialArray = r_[18.:19.:1.] #kJ/mol
#potentialGridSizeArray = gridSizeArray + 0.08 #nm
potentialGridSpacingArray = array([0.0005, 0.001, 0.002, 0.003, 0.004])#r_[0.001:0.004:0.001] #nm
geometryFilenameArray = array(["sII_smallCage11_CM_EA_ZYZ.xyz"])
lanczosIterationsArray = r_[10000:20000:10000]
#Round arrays appropriately
gridSizeArray = around(gridSizeArray, 15)
gridSpacingArray = around(gridSpacingArray, 15)
lMaxArray = rint(lMaxArray).astype(int)
thetaPointsArray = rint(thetaPointsArray).astype(int)
phiPointsArray = rint(phiPointsArray).astype(int)
ceilingPotentialArray = around(ceilingPotentialArray, 15)
#potentialGridSizeArray = around(potentialGridSizeArray, 15)
potentialGridSpacingArray = around(potentialGridSpacingArray, 15)
lanczosIterationsArray = rint(lanczosIterationsArray).astype(int)
rangesList = [ gridSizeArray,
gridSpacingArray,
lMaxArray,
thetaPointsArray,
phiPointsArray,
ceilingPotentialArray,
#potentialGridSizeArray,
potentialGridSpacingArray,
geometryFilenameArray,
lanczosIterationsArray
]
rangesListText = [ "gridSize",
"gridSpacing",
"lMax",
"thetaPoints",
"phiPoints",
"ceilingPotential",
#"potentialGridSize",
"potentialGridSpacing",
"geometryFilename",
"lanczosIterations"
]
print ""
print "The parameter values are: "
print ""
print "gridSizeArray: "
print " ", gridSizeArray
print ""
print "gridSpacingArray: "
print " ", gridSpacingArray
print ""
#print "gridPointsArray: "
#print gridPointsArray
print "lMaxArray: "
print " ", lMaxArray
print ""
print "thetaPointsArray: "
print " ", thetaPointsArray
print ""
print "phiPointsArray: "
print " ", phiPointsArray
print ""
print "ceilingPotentialArray: "
print " ", ceilingPotentialArray
print ""
#print "potentialGridSizeArray: "
#print potentialGridSizeArray
print "potentialGridSpacingArray: "
print " ", potentialGridSpacingArray
print ""
#print "potentialGridPointsArray: "
#print potentialGridPointsArray
print "geometryFilenameArray: "
print " ", geometryFilenameArray
print ""
print "lanczosIterationsArray: "
print " ", lanczosIterationsArray
print ""
print "quadratureConvergenceStudy: "
print " ", quadratureConvergenceStudy
print ""
print "totalMass: "
print " ", totalMass
print ""
print "rotationalConstant: "
print " ", rotationalConstant
print ""
print "simulationTitlePrefix: "
print " ", simulationTitlePrefix
print ""
####################################################
#Function Definitions
####################################################
# Hv Parameter file
####################################################
def writeHvParams(params, filename):
datafile = open(filename, 'w')
#Write header
datafile.write("#" + "\n")
datafile.write("#Make sure that there is no space before the equals sign and only one after; you will get an error or weird results otherwise" + "\n")
###########
#Write data
###########
#Cartesian system grid
datafile.write("nx= %d" % (params["gridPoints"]) + "\n")
datafile.write("x_max(nm)= %.15f" % (params["gridSize"]) + "\n")
datafile.write("ny= %d" % (params["gridPoints"]) + "\n")
datafile.write("y_max(nm)= %.15f" % (params["gridSize"]) + "\n")
datafile.write("nz= %d" % (params["gridPoints"]) + "\n")
datafile.write("z_max(nm)= %.15f" % (params["gridSize"]) + "\n")
#l_max
datafile.write("l_max= %d" % (params["lMax"]) + "\n")
#Angular grid
datafile.write("thetaPoints= %d" % (params["thetaPoints"]) + "\n")
datafile.write("phiPoints= %d" % (params["phiPoints"]) + "\n")
#Cartesian potential grid
datafile.write("pointPotential_nx= %d" % (params["potentialGridPoints"]) + "\n")
datafile.write("pointPotential_x_max(nm)= %.15f" % (params["potentialGridSize"]) + "\n")
datafile.write("pointPotential_ny= %d" % (params["potentialGridPoints"]) + "\n")
datafile.write("pointPotential_y_max(nm)= %.15f" % (params["potentialGridSize"]) + "\n")
datafile.write("pointPotential_nz= %d" % (params["potentialGridPoints"]) + "\n")
datafile.write("pointPotential_z_max(nm)= %.15f" % (params["potentialGridSize"]) + "\n")
#Linear Rotor Parameters
datafile.write("totalMass(g/mol)= %.15f" % (params["totalMass"]) + "\n")
datafile.write("rotationalConstant(kJ/mol)= %.15f" % (params["rotationalConstant"]) + "\n")
#Miscellaneous Parameters
datafile.write("geometryFilename= %s" % (params["geometryFilename"]) + "\n")
datafile.write("simulationTitle= %s" % (params["simulationTitle"]) + "\n")
datafile.write("ceilingPotential(kJ/mol)= %.15f" % (params["ceilingPotential"]) + "\n")
datafile.write("quadratureConvergenceStudy(TRUE/FALSE)= %s" % (params["quadratureConvergenceStudy"]) + "\n")
datafile.write("rotationalSymmetry(All/Even/Odd)= %s" % (params["rotationalSymmetry"]) + "\n")
#Finished
datafile.close()
# Lanczos Parameter file
####################################################
def writeLanczosParams(params, filename):
datafile = open(filename, 'w')
#Write header
datafile.write("#This is the input file for the Boundstate Lanczos Eigenvalue and Eigenvector Calculator" + "\n")
datafile.write("#Make sure that there is no space before the equals sign and only one after; you will get an error or weird results otherwise" + "\n")
###########
#Write data
###########
datafile.write("numberOfIterations= %d" % (params["lanczosIterations"]) + "\n")
datafile.write("EigenvalueOpenLowerLimit(kJ/mol)= %.15f" % (params["EigenvalueOpenLowerLimit"]) + "\n")
datafile.write("EigenvalueClosedUpperLimit(kJ/mol)= %.15f" % (params["EigenvalueClosedUpperLimit"]) + "\n")
datafile.write("NumberOfEigenvectors(all/partial/none)= %s" % (params["NumberOfEigenvectorsWord"]) + "\n")
datafile.write("NumberOfEigenvectors= %d" % (params["NumberOfEigenvectorsNum"]) + "\n")
datafile.write("HvCalculator= %s" % (params["HvCalculator"]) + "\n")
datafile.write("OutputDirectoryPath= %s" % (params["OutputDirectoryPath"]) + "\n")
#Finished
datafile.close()
# Build the simulation title
####################################################
def genSimTitle(pref, HvParams, LanczosParams):
if HvParams["rotationalSymmetry"] == "Odd":
rotSymTitle = "ortho"
elif HvParams["rotationalSymmetry"] == "Even":
rotSymTitle = "para"
else:
print "ERROR: rotational symmetry ill-defined"
sys.exit()
simTitle = pref + "_%s_x%s_dx%s_l%s_t%s_p%s_px%s_pdx%s_cp%s_L%s" % (rotSymTitle,
string.replace(str(HvParams["gridSize"]), ".", ""),
string.replace(str(HvParams["gridSpacing"]), ".", ""),
str(HvParams["lMax"]),
str(HvParams["thetaPoints"]),
str(HvParams["phiPoints"]),
string.replace(str(HvParams["potentialGridSize"]), ".", ""),
string.replace(str(HvParams["potentialGridSpacing"]), ".", ""),
string.replace(str(HvParams["ceilingPotential"]), ".", ""),
str(LanczosParams["lanczosIterations"])
)
return simTitle
# Append to shell script
####################################################
def appendShellFile(executable, nthreads, HvParams, HvFilename, LanczosFilename, logpath, filename):
datafile = open(filename, 'a')
datafile.write("\n")
datafile.write("export OMP_NUM_THREADS=%d" % (nthreads) + "\n")
datafile.write("echo %s" % (HvParams["simulationTitle"]) + "\n")
datafile.write("time ./%s %s %s" % (executable, LanczosFilename, HvFilename))
datafile.write(" > %s/%s" % (logpath, HvParams["simulationTitle"] + "_log") + "\n")
#Finished
datafile.close()
####################################################
####################################################
#Main Program
####################################################
####################################################
####################################################
#Get and make output directory
####################################################
outDir = sys.argv[1] + "_" + datetime.datetime.now().strftime("%Y-%m-%d_%H-%M-%S")
os.system("mkdir ./" + outDir)
HvFilePrefix = "HvInputFile"
LanzcosFilePrefix = "LanczosInputFile"
#Make a directory to contain the files to be placed in Compilation
outDirComp = outDir + "/" + "Compilation"
os.system("mkdir -p ./" + outDirComp)
#Write out base parameters files
baseHvParamDict["simulationTitle"] = genSimTitle(simulationTitlePrefix, baseHvParamDict, baseLanczosParamDict) + "_Base"
HvFileTitle = HvFilePrefix + "_" + baseHvParamDict["simulationTitle"] + ".txt"
LanczosFileTitle = LanzcosFilePrefix + "_" + baseHvParamDict["simulationTitle"] + ".txt"
writeHvParams(baseHvParamDict, outDir + "/" + HvFileTitle)
writeHvParams(baseHvParamDict, outDirComp + "/" + HvFileTitle)
writeLanczosParams(baseLanczosParamDict, outDir + "/" + LanczosFileTitle)
writeLanczosParams(baseLanczosParamDict, outDirComp + "/" + LanczosFileTitle)
appendShellFile(executable, nthreads, baseHvParamDict, HvFileTitle, LanczosFileTitle, OutputDirectoryPath, outDirComp + "/" + "Run.sh")
#Generate parameter files for each range of values, using the base parameters as the starting point for the variations
cnt = 1 #start at 1 to include base parameters
print ""
print "Writing parameter files for:"
for i in range(0,len(rangesList)) :
print ""
print rangesListText[i] + ":"
#Don't make a separate calculation for a single parameter
if len(rangesList[i]) <= 1:
print " Single parameter for %s, value: %s, skipping..." % (rangesListText[i], str(rangesList[i][0]))
continue
#Make a directory for the range of values
outDirRange = outDir + "/" + rangesListText[i]
os.system("mkdir -p ./" + outDirRange)
for value in rangesList[i]:
#Reset to base parameters
HvParamsLocal = baseHvParamDict.copy()
LanczosParamsLocal = baseLanczosParamDict.copy()
if i < (len(rangesList)-1):
HvParamsLocal[rangesListText[i]] = value
else:
LanczosParamsLocal[rangesListText[i]] = value
#Get the potential grid range
HvParamsLocal["potentialGridSize"] = round(HvParamsLocal["gridSize"] + H2Allowance, 15)
#Get the number of grid points
HvParamsLocal["gridPoints"] = int(round((HvParamsLocal["gridSize"] / HvParamsLocal["gridSpacing"]) + 1.))
HvParamsLocal["potentialGridPoints"] = int(round((HvParamsLocal["potentialGridSize"] / HvParamsLocal["potentialGridSpacing"]) + 1.))
#Test if the simulation is the same as the base parameters, if so, don't make a new file for it
shared_items1 = set(HvParamsLocal.items()) & set(baseHvParamDict.items()) #Taken from http://stackoverflow.com/questions/4527942/comparing-two-dictionaries-in-python
shared_items2 = set(LanczosParamsLocal.items()) & set(baseLanczosParamDict.items())
#print rangesListText[i], ": ", value
#print set(HvParamsLocal.items())
#print set(baseHvParamDict.items())
#print shared_items1
#print shared_items1 ^ set(HvParamsLocal.items())
#print shared_items1 ^ set(baseHvParamDict.items())
#print len(set(HvParamsLocal.items()))
#print len(shared_items1)
#raw_input("Press Enter to continue...")
if (len(shared_items1) == len(set(HvParamsLocal.items()))) and (len(shared_items2) == len(set(LanczosParamsLocal.items()))):
datafile = open(outDirRange + "/" + "baseParameters.txt", 'w')
datafile.write("This file indicates that the base parameters are part of this calculation range" + "\n")
datafile.close()
print " %s - identical to value in Base Parameters" % (str(value))
else:
print " %s" % (str(value))
cnt += 1
#Get new simulation title
HvParamsLocal["simulationTitle"] = genSimTitle(simulationTitlePrefix, HvParamsLocal, LanczosParamsLocal)
#Write out data to both range and compilation folders
HvFileTitle = HvFilePrefix + "_" + HvParamsLocal["simulationTitle"] + ".txt"
writeHvParams(HvParamsLocal, outDirRange + "/" + HvFileTitle)
writeHvParams(HvParamsLocal, outDirComp + "/" + HvFileTitle)
LanczosFileTitle = LanzcosFilePrefix + "_" + HvParamsLocal["simulationTitle"] + ".txt"
writeLanczosParams(LanczosParamsLocal, outDirRange + "/" + LanczosFileTitle)
writeLanczosParams(LanczosParamsLocal, outDirComp + "/" + LanczosFileTitle)
#Append execution command to shell script
appendShellFile(executable, nthreads, HvParamsLocal, HvFileTitle, LanczosFileTitle, OutputDirectoryPath, outDirComp + "/" + "Run.sh")
print ""
print "%d simulations prepared." % (cnt)