def rexHist(iterable, title, write=False, imgFilePath=None):
"""
`iterable` *string # An iterable of the CHARMM .out files
`title` string # The title of the plot.
`write` [`False`,`"svg"`,`"png"`] # The plot's output format,
# False won't write a file.
`imgFilePath` string # The plot's file path, defaults
# to `$cwd/default_title`.
"""
fileList = list(iterable)
fileList = map(expandPath, fileList)
tempArray = []
for fileName in fileList:
print 'Processing %s...' % fileName
filePointer = open(fileName)
rawData = getProp(filePointer, 'averener', 'avertemp')
tempArray.append(np.array(rawData['avertemp']).mean()) # Calc Temp
histData = np.histogram(rawData['averener'], 20, new=True)
pyplot.plot(histData[1][1:],histData[0],label=os.path.basename(fileName))
pyplot.legend( ['%3dK' % tempArray[i] for i in xrange(len(fileList))]
,loc=0, ncol=2)
pyplot.xlabel(r'$Energy\ (kcal\ mol^{-1})$')
pyplot.ylabel(r'$Frequency$')
pyplot.title(r'%s' % title)
if write:
if imgFilePath is None:
imgFilePath = '%s/%s.%s' % (os.path.dirname(fileList[0]), title,
write)
else:
imgFilePath = expandPath(imgFilePath)
pyplot.savefig(imgFilePath, format=write)
else:
pyplot.show()
def read_charmm_out(self,filename):
outDict = getprop.getProp(open(filename),'dynatime','dynaener',
'dynapresse','dynapressi','dynatemp') #'averener','dynavdw')
if not self.startedout:
self.ener = np.array(outDict['dynaener'])
self.time = np.array(outDict['dynatime'])
self.presse = np.array(outDict['dynapresse'])
self.pressi = np.array(outDict['dynapressi'])
self.temp = np.array(outDict['dynatemp'])
self.startedout = True
else:
self.ener = np.append(self.ener,outDict['dynaener'])
self.time = np.append(self.time,outDict['dynatime'])
self.presse = np.append(self.presse,outDict['dynapresse'])
self.pressi = np.append(self.pressi,outDict['dynapressi'])
self.temp = np.append(self.temp,outDict['dynatemp'])
def read_charmm_out(self,filename):
outDict = getprop.getProp(open(filename),'dynatime','dynaener',
'dynapresse','dynapressi','dynatemp') #'averener','dynavdw')
if not self.startedout:
self.ener = np.array(outDict['dynaener'])
self.time = np.array(outDict['dynatime'])
self.presse = np.array(outDict['dynapresse'])
self.pressi = np.array(outDict['dynapressi'])
self.temp = np.array(outDict['dynatemp'])
self.startedout = True
else:
self.ener = np.append(self.ener,outDict['dynaener'])
self.time = np.append(self.time,outDict['dynatime'])
self.presse = np.append(self.presse,outDict['dynapresse'])
self.pressi = np.append(self.pressi,outDict['dynapressi'])
self.temp = np.append(self.temp,outDict['dynatemp'])
### Files to extract temperature data from
tempFileList = glob('%s/*out_*' % taco.dcdPathname)
tempFileBase = os.path.basename(tempFileList[0]).split('_')[0]
tempFileList = [ '%s/%s_%d' % (taco.dcdPathname, tempFileBase, i)
for i in xrange(len(tempFileList)) ]
### Files to extract dynamics data from
dcdFileList = glob('%s/*dcd_*' % taco.dcdPathname)
dcdFileBase = os.path.basename(dcdFileList[0]).split('_')[0]
dcdFileList = [ '%s/%s_%d' % (taco.dcdPathname, dcdFileBase, i)
for i in xrange(len(dcdFileList)) ]
### Temperature Data
tempList = []
for tempFile in tempFileList:
tempList.append(np.array(getProp(open(tempFile), 'avertemp',
stopIter=1000)['avertemp']).mean())
#############
# DO Correl #
#############
# Write/Run Correl Jobs
if 0:
taco.correlStart = 0
taco.correlStop = -2
for i, dcdFile in enumerate(dcdFileList):
print "Processing Correl jobs on replica %d." % i
taco.anlPathname = anlPath % (nscale, i)
taco.anlFilename = '%s/gyro_%s.anl' % (taco.anlPathname, taco.correlAtomSelection)
taco.outFilename = '%s/gyro_%s.out' % (taco.anlPathname, taco.correlAtomSelection)
taco.inpFilename = '%s/gyro_%s.inp' % (taco.anlPathname, taco.correlAtomSelection)
