from __tools__ import XmlWriter from __tools__ import make_sure_path_exists from __tools__ import addsuffixtofile from __cluster__ import write_cluster_batch from __xtpJobfile__ import splittjobfile from __xtpJobfile__ import mergejobfiles from __xtpJobfile__ import infojobfile from __xtpJobfile__ import resetjobfile import lxml.etree as lxml import subprocess as sp import os import sys from __tools__ import cd parser = MyParser( description="Environment to split a jobfile into many and submit to cluster" ) parser.add_argument("--options", "-o", type=str, required=True, help="optionfile") parser.add_argument("--submit", action='store_const', const=1, default=0, help="Submit to cluster") parser.add_argument("--setup", action='store_const', const=1, default=0,
import os import errno import shutil import re import numpy.linalg as lg from __tools__ import MyParser from __tools__ import make_sure_path_exists from __tools__ import XmlParser from __tools__ import cd from __tools__ import XmlWriter from __tools__ import RepresentsInt from __exciton__ import readexcitonlogfile parser = MyParser( description= "Enviroment to do numerical polarisation calculations with gwbse and gaussian" ) parser.add_argument("--template", "-t", type=str, required=True, help="Folder, from which to take votca-optionfiles from") parser.add_argument("--options", "-o", type=str, required=True, help="optionfile") parser.add_argument("--setup", action='store_const', const=1, default=0,
import numpy as np import sys import subprocess as sp import os import errno import shutil import re import argparse import lxml.etree as lxml from __tools__ import MyParser from __tools__ import cd from __tools__ import query_yes_no from __xtpAtom__ import atom from __xtpMolecule__ import molecule parser = MyParser( description="Environment to do run multiple votca calculations") parser.add_argument("--suffix", type=str, default="", help="Suffix to append to foldernames") parser.add_argument("--jobfile", type=str, required=True, help="File with paths to grofiles") parser.add_argument("--template", type=str, required=True, help="Folder, from which to take optionfiles from") parser.add_argument("--mapfile", type=str, default="system.xml",
#!/usr/bin/env python import matplotlib as mpl from mpl_toolkits.mplot3d import Axes3D from mpl_toolkits.mplot3d import proj3d import numpy as np import matplotlib.pyplot as plt import csv import re import sys from __tools__ import MyParser parser=MyParser(description="Tool to visualize kmc trajectory .csv files" ) parser.add_argument("-t","--trajectory",type=str,nargs="+",required=True,help="Files to visualize .csv format") parser.add_argument("--steps",type=int,default=-1,help="Maximum number of steps to read in. default:-1") args=parser.parse_args() #parser.add_argument('-p',"--plot", action='store_const', const=1, default=0,help="Calculate exciton coupling in classical limit") if type(args.trajectory)==str: args.trajectory=[args.trajectory] class carrierstorage(object): numberofobjects= 0 def __init__(self): carrierstorage.numberofobjects+=1 self.id=carrierstorage.numberofobjects self.traj=[]
#!/usr/bin/env python from __tools__ import MyParser from __tools__ import XmlParser from __tools__ import XmlWriter import lxml.etree as lxml parser = MyParser(description="Delete Entries from Jobfile") parser.add_argument("--jobfile", "-j", type=str, required=True, help="jobfile") parser.add_argument("--output", "-o", type=str, default="joboutput.xml", help="jobfile") parser.add_argument("--exclude", type=str, nargs="+", help="Tags to exclude from jobfile e,h,n,s,t") args = parser.parse_args() print "Removing states with tags including: {} ".format(" ".join(args.exclude)) root = XmlParser(args.jobfile) for entry in root.iter('job'): status = entry.find("tag").text for eex in args.exclude: if eex in status: root.remove(entry) break print "Writing to {}".format(args.output) XmlWriter(root, args.output)
import subprocess as sp import os import errno import shutil import re import argparse import lxml.etree as lxml import numpy.linalg as lg import time from __tools__ import MyParser from __tools__ import cd from __tools__ import XmlParser from __xtpAtom__ import atom from __xtpMolecule__ import molecule parser = MyParser(description="Environment to check coupling constants") parser.add_argument( "--template", "-t", type=str, required=True, help= "Folder, from which to take optionfiles from and where the exciton tool had been executed for one molecule" ) parser.add_argument("--xyz", type=str, help="Name of the xyz file for the molecule") parser.add_argument("--mps", type=str, default="",
#!/usr/bin/env python from __tools__ import MyParser from __tools__ import XmlParser #import matplotlib.pyplot as plt import lxml.etree as lxml import subprocess as sp import numpy as np parser = MyParser( description="Tool to create histogramm for iexcitoncl from jobfile") parser.add_argument("--format", type=str, default="Hist_{}", help="Title of histogramm and filename") parser.add_argument("--printing", action='store_const', const=1, default=0, help="Print histogramms to txt file") parser.add_argument("--bins", type=int, default=50, help="Number of bins") parser.add_argument("--jobfiles", type=str, nargs="+", required=True, help="Name of jobfile") parser.add_argument("--min", type=int, default=-14, help="Minimum log10(J2) to still count") args = parser.parse_args()
#!/usr/bin/python import lxml.etree as lxml from __tools__ import MyParser from __tools__ import XmlParser import os parser = MyParser( description= "Assign mpsfile to molecules for iexcitoncl jobs, mps.tab files and ewald jobs" ) parser.add_argument("--path", type=str, required=True, help="Path to mps file folder") parser.add_argument("--jobfile", type=str, required=True, help="file to rewrite") parser.add_argument("--state", type=str, help="State to give tag to, only required for ewald") parser.add_argument( "--format", type=str, required=True, help="Format string into which the id is placed e.g. Molecule_{}_n2s1.mps") parser.add_argument( "--id", nargs="+", type=int,