T21 = kf.kffile(T21FileName)

FullList = T21.read("Properties", "CP coordinates")

NumCPs = T21.read("Properties","CP number of")

T21.close()

CoordList = []

for i in range(NumCPs):

tmp = np.empty([3])

k = 0

for j in range(i,NumCPs * 3,NumCPs):

tmp[k] = FullList[j]

k += 1

CoordList.append(tmp)

TypeList = []

T21 = kf.kffile(T21FileName)

Types = T21.stringData("Properties","CP code number for (Rank,Signatu")

Types = Types.split('\n')

Types = Types[3:len(Types)-1]

for i in Types:

for j in i.split():

TypeList.append(int(float(j)))

T21.close()

StepDir = Pt2.__sub__(Pt1)

StepSize = np.linalg.norm(StepDir)

StepDir /= StepSize

StepSize /= (NumPts - 1)

CoordList = [Pt1.__add__(np.multiply(StepDir,Step*StepSize)) for Step in range(NumPts)]

import StringIO

import os

import subprocess

global CurrentDir, T21BaseName, ScriptDir

T41FileName = CurrentDir + '/' + "Tape41_" + str(randint(1,999999)) + ".t41"

DensfScript = StringIO.StringIO()

DensfScript.write('''$ADFBIN/densf << eor

INPUTFILE ''' + T21FileName + '''

OUTPUTFILE ''' + T41FileName + '''

GRID Inline

''')

for i in GridCoords:

for j in i:

DensfScript.write(str(j) + ' ')

DensfScript.write('\n')

DensfScript.write('''End

Density SCF

DenGrad

DenHess

eor''')

DensfScript = DensfScript.getvalue()

#

# print DensfScript

subprocess.Popen(DensfScript, shell=True, stdout=subprocess.PIPE).stdout.read()

try:

os.remove(ScriptDir + '/logfile')

except: pass

subprocess.Popen('rm -rf ' + ScriptDir + '/IINFO*' + ScriptDir + '/SINFO*', shell=True, stdout=subprocess.PIPE).stdout.read()

T41Data = {}

T41VarStrs = ['Density']

for i in ['X','Y','Z']:

T41VarStrs.append('DensityGrad' + i)

for i in ['XX','XY','XZ','YY','YZ','ZZ']:

T41VarStrs.append('DensityHess' + i)

T41 = kf.kffile(T41FileName)

for i in T41VarStrs:

T41Data[i] = T41.read('SCF', i)

T41.close()

T41.delete()

H = np.empty([3,3])

for i in range(3):

for j in range(3):

H[i,j] = T41Data['DensityHess' + HessInd[i][j]][Ind]

G = np.empty([3])

for i in range(3):

G[i] = T41Data['DensityGrad' + GradInd[i]][Ind]

from numpy import linalg as la

NumPts = len(T41Data['Density'])

T41Data['EigVals'] = [None]*NumPts

T41Data['EigVecs'] = [None]*NumPts

for i in range(NumPts):

T41Data['EigVals'][i], T41Data['EigVecs'][i] = la.eigh(GetHessForT41Index(T41Data, i))

# T41Data['EigVecs'][i] = np.transpose(T41Data['EigVecs'][i])

"""

:param text: a plain text message

:return: the message escaped to appear correctly in LaTeX

"""

import re

conv = {

'&': r'\&',

'%': r'\%',

'$': r'\$',

'#': r'\#',

'_': r'\_',

'{': r'\{',

'}': r'\}',

'~': r'\textasciitilde{}',

'^': r'\^{}',

'\\': r'\textbackslash{}',

'<': r'\textless',

'>': r'\textgreater',

}

regex = re.compile('|'.join(re.escape(unicode(key)) for key in sorted(conv.keys(), key = lambda item: - len(item))))

import matplotlib.pyplot as plt

from matplotlib import gridspec

import numpy as np

import Image

import os

# import pylab as plt

# from matplotlib import rc

ValList = [[[0],[0]],[[0],[0]]]

NumPts = len(T41Data['Density'])

global CurrentDir, SubDir

import subprocess

subprocess.Popen('mkdir -p "' + CurrentDir + SubDir + '"', shell=True, stdout=subprocess.PIPE).stdout.read()

OutCSVName = CurrentDir + SubDir + "/" + OutFileName.replace(' ','_')

OutCSVName = OutCSVName.rpartition('_(')[0]

OutCSV = open(OutCSVName + '.csv','w')

Headings = ["PtNum","X","Y","Z","XBohr","YBohr","ZBohr","Rho","Lap"]

for i in ['1','2','3']:

Headings.append('DotPdt_' + i)

for i in ['1','2','3']:

Headings.append('EigVal_' + i)

for i in ['X','Y','Z']:

Headings.append('Grad_' + i)

for i in ['1','2','3']:

for j in ['1','2','3']:

Headings.append('EigVec_' + i + '_' + j)

for i in ['XX','XY','XZ','YY','YZ','ZZ']:

Headings.append('Hess_' + i)

for i in Headings:

OutCSV.write(i + ',')

OutCSV.write('\n')

RCS = [# [[dot products that should be below tolerence],[signs of eigenvalues],[value in plot]]

[[1,2,3],[1,1,1],[6,6]],

[[1,2],[-1,-1],[1,2]],

[[2,3],[1,1],[5,4]],

[[1,3],[1,1],[3,3]]

]

for i in range(NumPts):

G = [T41Data['DensityGrad' + j][i] for j in GradInd]

E = [T41Data['EigVals'][i][j] for j in range(3)]

# EV = np.transpose([T41Data['EigVecs'][i][j] for j in range(3)])

EV = np.transpose(T41Data['EigVecs'][i])

DP = [np.absolute(np.dot(G,j)) for j in EV]

PtNum = float(i + 1)

OutCSV.write(str(i+1) + ',')

for j in [T41Data['Coords'][i]]:

for k in j:

OutCSV.write(str(k) + ',')

for j in [T41Data['CoordsBohr'][i]]:

for k in j:

OutCSV.write(str(k) + ',')

OutCSV.write(str(T41Data['Density'][i]) + ',')

OutCSV.write(str(sum(E)) + ',')

for j in [DP,E,G]:

for k in j:

OutCSV.write(str(k) + ',')

for j in EV:

for k in j:

OutCSV.write(str(k) + ',')

for j in [T41Data['DensityHess' + k][i] for k in ['XX','XY','XZ','YY','YZ','ZZ']]:

OutCSV.write(str(j) + ',')

OutCSV.write('\n')

# HasVal = False

# SameSign = 0

for iRCS in RCS:

HasVal = True

for iDP in range(3):

if ((iDP + 1) in iRCS[0] and DP[iDP] > Tol) or ((iDP + 1) not in iRCS[0] and DP[iDP] <= Tol):

HasVal = False

break

if HasVal:

RCSInd = 0

for ei,es in zip(iRCS[0],iRCS[1]):

if np.sign(E[ei-1]) != es:

RCSInd = 1

break

SignInd = 0 if np.sign(E[iRCS[0][0]-1]) == np.sign(E[iRCS[0][1]-1]) else 1

ValList[SignInd][0].append(PtNum)

ValList[SignInd][1].append(iRCS[2][RCSInd])

# # CP (not used)

# if DP[0] <= Tol and DP[1] <= Tol and DP[2] <= Tol:

# Val = 6

# HasVal = True

#

# # Ridge and r-connector

# elif DP[0] <= Tol and DP[1] <= Tol and DP[2] > Tol:

# HasVal = True

# if E[0] < 0:

# if E[1] < 0: Val = 1

# else:

# SameSign = 1

# Val = 2

# else:

# Val = 2

# if E[1] < 0: SameSign = 1

#

# # Valley and v-connector

# elif DP[1] <= Tol and DP[2] <= Tol and DP[0] > Tol:

# HasVal = True

# if E[1] > 0:

# if E[2] > 0: Val = 5

# else:

# SameSign = 1

# Val = 4

# else:

# Val = 4

# if E[2] > 0: SameSign = 1

#

# # m-connector

# elif DP[0] <= Tol and DP[2] <= Tol and DP[1] > Tol:

# HasVal = True

# Val = 3

# if np.sign(E[2]) != np.sign(E[0]): SameSign = 1

#

# if HasVal:

# ValList[SameSign][0].append(PtNum)

# ValList[SameSign][1].append(Val)

OutCSV.close()

for j in ValList:

j[0].append(NumPts)

j[1].append(0)

NumPts = float(NumPts)

ValList = [[[j / NumPts * 100. for j in k[0]],[j for j in k[1]]] for k in ValList]

xVals = range(0,125,25)

yVals = range(1,7)

fig = plt.figure(figsize=(8,3))

if os.path.isfile(ImgPath):

gs = gridspec.GridSpec(1,2,width_ratios=[5.25,2.75])

ax = fig.add_subplot(gs[0]) # subplot required to change the aspect ratio

else:

ax = fig.add_subplot(111)

# ax.set_aspect(10)

# ax = fig.add_axes([0,0,6*Res,3*Res])

ax.plot(ValList[0][0], ValList[0][1], 'bs', ValList[1][0], ValList[1][1], 'r+')

plt.rc('text', usetex=True)

plt.rc('font', family='sans-serif')

plt.rc('font', size=12)

yLabels = ['Ridge',r'\textit{R}-connector',r'\textit{M}-connector',r'\textit{V}-connector','Valley','Critical point']

plt.xticks(xVals, xVals)

plt.yticks(yVals,yLabels,rotation=0)

plt.axis([-2,103,0.5,5.5])

plt.xlabel('\% of path langth')

fig.set_size_inches(8,3)

if os.path.isfile(ImgPath):

im = Image.open(ImgPath)

# height = im.size[1]

# im = np.array(im).astype(np.float) / 255

c = im.getbbox()

a = 5

cr = (c[0]+a,c[1]+a,c[2]-a,c[3]-a)

im = im.crop(cr).rotate(180)

w = 2.5 * Res

wp = w / float(im.size[0])

h = int(float(im.size[1]) * wp)

w = int(w)

im = im.resize([w,h],Image.BICUBIC)

fig.figimage(im, xo=5.5*Res, yo=0.5*Res + (w-h)/2, origin='lower')

fig.tight_layout()

fig.savefig(CurrentDir + SubDir + "/" + OutFileName.replace(' ','_') + '.png', dpi=Res)

# plt.axis([-2,103,0.5,6.5])

# fig.savefig(CurrentDir + SubDir + "/" + OutFileName.replace(' ','_') + '_wCP.png', dpi=Res)

#

# plt.title(tex_escape(OutFileName.replace('_',' ')))

# plt.axis([-2,103,0.5,5.5])

# fig.savefig(CurrentDir + SubDir + "/" + OutFileName.replace(' ','_') + '_wTitle.png', dpi=Res)

# plt.axis([-2,103,0.5,6.5])

# fig.savefig(CurrentDir + SubDir + "/" + OutFileName.replace(' ','_') + '_wTitle_wCP.png', dpi=Res)

# ax.set_aspect(10)

# f=plt.gcf()

# plt.show()

# fig.set_size_inches(7,4)

# fig.savefig(CurrentDir + SubDir + "/" + OutFileName.replace(' ','_') + '.eps', dpi=Res)

# plt.axis([-2,103,0.5,6.5])

# fig.set_size_inches(7.5,4.5)

# fig.savefig(CurrentDir + SubDir + "/" + OutFileName.replace(' ','_') + '_wCP.eps', dpi=Res)

#

# plt.title(tex_escape(OutFileName.replace('_',' ')))

# plt.axis([-2,103,0.5,5.5])

# fig.set_size_inches(7,4)

# fig.savefig(CurrentDir + SubDir + "/" + OutFileName.replace(' ','_') + '_wTitle.eps', dpi=Res)

# plt.axis([-2,103,0.5,6.5])

# fig.set_size_inches(7.5,4.5)

# fig.savefig(CurrentDir + SubDir + "/" + OutFileName.replace(' ','_') + '_wTitle_wCP.eps', dpi=Res)

# plt.show()

plt.close()

CPNums = []

for CP in CPList:

MinDist = 1e100

MinInd = -1

for i in range(len(NewCoords)):

if NewTypes[i] == OldTypes[CP-1]:

TmpDist = np.linalg.norm(np.subtract(NewCoords[i],OldCoords[CP-1]))

if TmpDist < MinDist:

MinDist = TmpDist

MinInd = i

if MinInd >= 0:

CPNums.append(MinInd + 1)

import ast

import os

import sys

import subprocess

global T21BaseName, ScriptDir, CurrentDir

Res = 1200 # dpi of resulting plots

NumPts = 101

Tols = [10**(-e) for e in range(3,9)]

# InputFilePath = "/Users/Haiiro/Safe/tmp/input.txt"

# InputFilePath = "/Users/Haiiro/ADFdata/1RidgePaper/first_round_data/input.txt"

# InputFilePath = "/Users/Haiiro/ADFdata/1RidgePaper/first_round_data/input_copy.txt"

InputFilePath = "/Users/Haiiro/ADFdata/bondalyzer_math_paper/DiSubstitutedBenzene/LDAautojobs/input.txt"

if len(sys.argv) > 1:

InputFilePath = sys.argv[1]

if len(sys.argv) > 2:

NumPts = int(sys.argv[2])

if len(sys.argv) > 3:

Tols = sys.argv[3]

if len(Tols.split(',')) > 1:

Tols = Tols.split(',')

Tols = [10**(-e) for e in range(int(Tols[0]),int(Tols[1])+1)]

else: Tols = [10**(-int(Tols))]

InputFile = open(InputFilePath, 'r')

InputFileContents = InputFile.readlines()

InputFile.close()

ScriptDir = os.path.dirname(os.path.realpath(__file__))

InputDir = os.path.dirname(os.path.realpath(InputFilePath))

FileNum = 0

for aLine in InputFileContents:

FileNum += 1

print '\nRunning file ' + str(FileNum) + ' of ' + str(len(InputFileContents))

aLine = aLine.split('\t')

if len(aLine) > 0:

InputT21FileName = aLine[0]

TargetCPs = ast.literal_eval(aLine[1])

ImgPaths = []

if len(aLine) > 3:

ImgPaths = aLine[3]

ImgPaths = eval(ImgPaths)

# ImgPaths = ast.literal_eval(ImgPaths)

if len(ImgPaths) < len(TargetCPs):

ImgPaths = [''] * len(TargetCPs)

print "File: %s with CPs: %s" % (InputT21FileName, str(TargetCPs))

T21BaseName = os.path.basename(InputT21FileName)

if T21BaseName != InputT21FileName:

CurrentDir = os.path.dirname(InputT21FileName)

else:

CurrentDir = InputDir

InputT21FileName = CurrentDir + '/' + T21BaseName

print "Adjusted file name: %s" % InputT21FileName

if '?' in InputT21FileName or '*' in InputT21FileName:

T21FileNames = subprocess.Popen("ls " + InputT21FileName, shell=True, stdout=subprocess.PIPE).stdout.read()

T21FileNames = T21FileNames.split('\n')

else:

T21FileNames = [InputT21FileName]

print "All T21s for file: %s" % str(T21FileNames)

OrigCPCoords = []

OrigCPTypes = []

for T21FileName in T21FileNames:

print "Running T21: %s" % T21FileName

if os.path.exists(T21FileName):

T21BaseName = os.path.basename(T21FileName)

if '.' in T21BaseName:

T21BaseName = T21BaseName.rpartition('.')[0]

# T21FileName = "'" + T21FileName + "'"

CPCoords = GetCPCoords(T21FileName)

CPTypes = GetCPTypes(T21FileName)

if len(OrigCPCoords) == 0: OrigCPCoords = CPCoords

if len(OrigCPTypes) == 0: OrigCPTypes = CPTypes

OutFileNames = []

if len(aLine) > 2:

OutFileNames = aLine[2]

OutFileNames = ast.literal_eval(OutFileNames)

if len(OutFileNames) != len(TargetCPs):

OutFileNames = []

break

Tmp = OutFileNames

OutFileNames = []

for i in Tmp:

TmpStr = T21BaseName + '_' + i + '_'

# First = True

# for i in c:

# if First: First = False

# else: TmpStr += '-'

# TmpStr += CPTypeInd[CPTypes[i-1]-1] + str(i)

OutFileNames.append(TmpStr)

if len(OutFileNames) == 0:

for c in TargetCPs:

TmpStr = T21BaseName + '_'

# First = True

# for i in c:

# if First: First = False

# else: TmpStr += '-'

# TmpStr += CPTypeInd[CPTypes[i-1]-1] + str(i)

OutFileNames.append(TmpStr)

global PathCoords

for Pts, PathName, ImgPath in zip(TargetCPs, OutFileNames, ImgPaths):

CPNums = GetCPsFromCoords(Pts, CPCoords, CPTypes, OrigCPCoords, OrigCPTypes)

if not os.path.exists(ImgPath):

ImgPath = CurrentDir + '/' + ImgPath

print "CP pair %s (%s)" % (str(CPNums), Pts)

OutFileName = PathName

First = True

for i in CPNums:

if First: First = False

else: OutFileName += '-'

OutFileName += CPTypeInd[CPTypes[i-1]-1] + str(i)

print "Outfile base: %s" % OutFileName

PathCoords = GenerateCoords(CPCoords[CPNums[0]-1] * B2A, CPCoords[CPNums[1]-1] * B2A, NumPts)

T41FileName = DensfForCoords(T21FileName, PathCoords)

T41Data = GetDataFromT41(T41FileName)

T41Data['Coords'] = PathCoords

T41Data['CoordsBohr'] = GenerateCoords(CPCoords[CPNums[0]-1], CPCoords[CPNums[1]-1], NumPts)

GetEigenSystemForT41(T41Data)

for Tol in Tols:

RCSMake1DPlot(T41Data, Tol, OutFileName + '_(' + '%.0e' % Tol + ')', Res, ImgPath)

# break

else:

print "File not found: %s" % T21FileName

print "Finished"