def orc(path, File, template, sysData, jobTemp):
import re
from supercomp import host
from templates import orc_rjnJob
from write import write_inp
from write import write_job
name = File.replace('.xyz', '').split('_')[0]
# MAKE NEW DIR AND NEW PATH
npath = newDir(path, File, template)
# UNPACK sysData
fragList, atmList, totChrg, totMult = sysData
# CREATE xyzData
xyzData = []
for frag in fragList:
for atm in atmList:
if atm['id'] in frag['ids']:
xyzData.append(
[atm['sym'], atm['nu'], atm["x"], atm["y"], atm["z"]])
# PUT XYZ IN TEMPLATE
input = xyzTemp(path, template, xyzData)
for i in range(len(input)):
if type(input[i]) != list:
# CHANGE CHRG AND MULT
if re.search('^\*xyzfile\s*-?[0-9]\s*-?[0-9]\s*', input[i]):
if totChrg == '?':
print("Cannot determine chrg/mult, using template values")
# IF CHRG = MULT COULD BE TRICKY
else:
line = input[i].split()
if '.xyz' in line[-1]:
input[i] = '*xyzfile ' + str(totChrg) + ' ' + str(
totMult) + ' ' + line[-1]
if re.search('.xyz', input[i]):
line = input[i].strip()
line = line.rsplit(' ', 1)[0]
input[i] = line + ' ' + name + '.xyz\n'
# WRITE INP
write_inp(npath, name, input)
# WRITE JOB
lines = False
if jobTemp:
lines = job_replace(name, jobTemp)
else:
hw = host()
if hw == 'rjn':
lines = orc_rjnJob(name)
if lines:
write_job(npath, name, lines)
def fmo(path, File, template, sysData, jobTemp):
import os, re
from supercomp import host
from chemData import pTable
from templates import fmo_rjnJob
from templates import fmo_mgsJob
from templates import fmo_stmJob
from templates import fmo_gaiJob
from templates import fmo_monJob
from templates import fmo_masJob
from templates import gms_rjnJob
from templates import gms_mgsJob
from templates import gms_masJob
from templates import gms_monJob
from templates import gms_gaiJob
from templates import gms_stmJob
from tempInp import fmo_ions
from write import write_xyz
from write import write_gmsInp
from write import write_job
# NAME FOR WRITING FILE, DIRS
ions = False
name = File.replace('.xyz', '').split('_')[0]
# MAKE NEW DIR AND NEW PATH
npath = newDir(path, File, template)
# UNPACK sysData
mp2 = False
fragList, atmList, totChrg, totMult = sysData
# NUMBER OF FRAGS
nfrags = len(fragList)
# CREATE xyzData
xyzData = []
for frag in fragList:
for atm in atmList:
if atm['id'] in frag['ids']:
xyzData.append(
[atm['sym'], atm['nu'], atm["x"], atm["y"], atm["z"]])
# TEMPLATE LINES
input = xyzTemp(path, template, xyzData)
fmo_input = []
# IF RUNTYP IS ENERGY MAKE ION JOBS
for ind in range(len(input)):
if 'NGROUP' in input[ind]:
spl_line = re.split('=| ', input[ind])
for val, bit in enumerate(spl_line):
if bit == 'NGROUP':
in_grp = spl_line[val + 1]
if in_grp != str(nfrags):
#print('Changing NGROUP to', nfrags)
input[ind] = input[ind].\
replace('NGROUP=' + in_grp, 'NGROUP=' + str(nfrags))
# CHECK NFRAG = NO. OF FOUND FRAGMENTS
if 'NFRAG' in input[ind]:
spl_line = re.split('=| ', input[ind])
for val, bit in enumerate(spl_line):
if bit == 'NFRAG':
in_nfrags = spl_line[val + 1]
if in_nfrags != str(nfrags):
#print('Changing NFRAG to', nfrags)
input[ind] = input[ind].\
replace('NFRAG=' + in_nfrags, 'NFRAG=' + str(nfrags))
# LIST OF CHARGES FOR FRAGMENTS
if 'ICHARG' in input[ind]:
spl_line = re.split('=| ', input[ind])
for val, bit in enumerate(spl_line):
if 'ICHARG' in bit:
in_chrg = spl_line[val + 1]
chrgs = []
for frag in fragList:
chrgs.append(frag['chrg'])
input[ind] = input[ind].replace('ICHARG(1)=' + in_chrg, \
'ICHARG(1)=' + ','.join(str(p) for p in chrgs) + '\n')
# MULT
if 'MULT' in input[ind]:
spl_line = re.split('=', input[ind])
for val, bit in enumerate(spl_line):
if 'MULT' in bit:
mults = []
for frag in fragList:
mults.append(frag['mult'])
in_chrg = spl_line[val + 1]
input[ind] = input[ind].replace('MULT(1)=' + in_chrg,\
'MULT(1)=' + ','.join(str(p) for p in mults) + '\n')
# CHECK IF SPEC FOR ION CALCS
if 'RUNTYP' in input[ind]:
spl_line = re.split('=| ', input[ind])
for val, bit in enumerate(spl_line):
if 'RUNTYP' in bit:
if spl_line[val + 1] == 'ENERGY':
ions = True
# MEMORY USED IN INPUT USED FOR JOB MEMORY
if 'MWORDS' in input[ind]:
spl_line = re.split('=| ', input[ind])
for val, bit in enumerate(spl_line):
if bit == 'MWORDS' in input[ind]:
memory = spl_line[val + 1]
# MEMORY USED IN INPUT FOR JOB MEMORY
ddi = False
if 'MEMDDI' in input[ind]:
spl_line = re.split('=| ', input[ind])
for val, bit in enumerate(spl_line):
if bit == 'MEMDDI' in input[ind]:
ddi = spl_line[val + 1]
# FOR FMO_IONS
if '$MP2' in input[ind]:
mp2 = input[ind]
if "GBASIS" in input[ind]:
spl_line = re.split('=| ', input[ind])
for val, bit in enumerate(spl_line):
if bit == 'GBASIS' in input[ind]:
bset = spl_line[val + 1]
# REMOVE LINES FROM INPUT WITH NEW LIST
# FOR MANY LINE CHANGES - COORDS, INDAT, ATM LIST
atmUniq = []
numUniq = []
seenA = False
for line in input:
if type(line) != list:
# INDAT MAY BE DIFF NUMBER OF LINES TO NEW INDAT
if 'INDAT' in line:
fmo_input.append(' INDAT(1)=0,1,-' +
str(len(fragList[0]['ids'])) + ',\n')
# REMEMBER WHERE LAST FRAG FINISHED
n = len(fragList[0]['ids']) + 1
for frag in fragList:
if not frag is fragList[0]:
fmo_input.append(' '*13 + '0,' + str(n) + \
',-' + str(n + len(frag['ids']) - 1) + ',\n')
n += len(frag['ids'])
fmo_input.append(' ' * 13 + '0\n')
# SO NOT PASSED TO ELSE // EXTRA LINES TO DETERMINE FRAGMENT
elif re.search('^\s*0,[0-9]{1,3},-[0-9]{1,3},\s*$', line) or \
re.search('^\s*0\s*$', line):
pass
# ATOM LIST MAY BE DIFF NUMBER OF LINES TO NEW ATOM LIST
elif re.search('^\s*[A-Za-z]*\s*[0-9]*\.0*$', line):
if not seenA:
for i in xyzData:
atmUniq.append(i[0])
numUniq.append(i[1])
atmUniq = list(set(atmUniq))
for i in range(len(atmUniq)):
for sym, data in pTable.items():
if sym == atmUniq[i]:
fmo_input.append(' ' + str(atmUniq[i]) + ' ' + \
str(data[0]) + '\n')
seenA = True
# EVERY OTHER LINE AS IS
else:
fmo_input.append(line)
else:
fmo_input.append(line)
# HARDWARE FOR WRITING
hw = host()
if ions:
# FOR EACH FRAGMENT
for frag in fragList:
ifrag = []
for ID in frag['ids']:
atm = atmList[ID]
ifrag.append(
[atm['sym'], atm['nu'], atm["x"], atm["y"], atm["z"]])
# MAKE FOLDER AND XYZ
if not os.path.isdir(npath + name + '-' + frag["name"]):
os.mkdir(npath + name + '-' + frag["name"])
write_xyz(npath + name + '-' + frag["name"] + '/',
name + '-' + frag["name"], ifrag)
# INPUT AND OUTPUT FOR JOB
input = fmo_ions(str(frag['chrg']), ifrag, bset, mp2)
write_gmsInp(npath + name + '-' + frag["name"] + '/',
name + '-' + frag["name"], input)
# WRITE JOB
lines = False
if jobTemp:
# lines = job_replace(name, jobTemp)
lines = job_replace(name + '-' + frag["name"], jobTemp)
else:
if hw == 'rjn':
lines = gms_rjnJob(name + '-' + frag["name"])
elif hw == 'mgs':
lines = gms_mgsJob(name + '-' + frag["name"])
elif hw == 'gai':
lines = gms_gaiJob(name + '-' + frag["name"])
elif hw == 'mas':
lines = gms_masJob(name + '-' + frag["name"])
elif hw == 'mon':
lines = gms_monJob(name + '-' + frag["name"])
elif hw == 'stm':
lines = gms_stmJob(name + '-' + frag["name"])
if lines:
write_job(npath + name + '-' + frag["name"] + '/',
name + '-' + frag["name"], lines)
# -------------------------------------------------
# WRITE INP
write_gmsInp(npath, name, fmo_input)
# WRITE JOB
lines = False
if jobTemp:
lines = job_replace(name, jobTemp)
else:
if hw == 'rjn':
lines = fmo_rjnJob(name, nfrags, memory, ddi)
elif hw == 'mgs':
lines = fmo_mgsJob(name, nfrags, memory, ddi)
elif hw == 'stm':
lines = fmo_stmJob(name, nfrags, memory, ddi)
elif hw == 'gai':
lines = fmo_gaiJob(name) #, nfrags, memory, ddi)
elif hw == 'mon':
lines = fmo_monJob(name, nfrags, memory, ddi)
elif hw == 'mas':
lines = fmo_masJob(name, nfrags, memory, ddi)
if lines:
write_job(npath, name, lines)
def gms(path, File, template, sysData, jobTemp):
import re
from supercomp import host
from templates import gms_rjnJob
from templates import gms_mgsJob
from templates import gms_gaiJob
from templates import gms_masJob
from templates import gms_monJob
from templates import gms_stmJob
from write import write_gmsInp
from write import write_job
name = File.replace('.xyz', '').split('_')[0]
# MAKE NEW DIR AND NEW PATH
npath = newDir(path, File, template)
# UNPACK sysData
fragList, atmList, totChrg, totMult = sysData
# CREATE xyzData
xyzData = []
for frag in fragList:
for atm in atmList:
if atm['id'] in frag['ids']:
xyzData.append(
[atm['sym'], atm['nu'], atm["x"], atm["y"], atm["z"]])
# GET TEMPLATE LINES WITH COORDS
input = xyzTemp(path, template, xyzData)
# CHARGE AND MULT
for ind in range(len(input)):
if 'ICHARG' in input[ind]:
if totChrg == '?':
print("Cannot determine chrg/mult, using template values")
else:
spl_line = re.split('=| ', input[ind])
for val, bit in enumerate(spl_line):
if bit == 'ICHARG':
oldChrg = spl_line[val + 1]
input[ind] = input[ind].replace('ICHARG=' + \
oldChrg, 'ICHARG=' + str(totChrg))
if totMult != 0:
if 'CONTRL' in input[ind]:
if totChrg == '?':
print("Cannot determine chrg/mult, using template values")
elif not 'MULT' in input[ind]:
input[ind] = input[ind].\
replace(' RUN',' MULT=' + str(totMult) + ' RUN')
# MEMORY USED IN INPUT
if 'MWORDS' in input[ind]:
spl_line = re.split('=| ', input[ind])
for val, bit in enumerate(spl_line):
if bit == 'MWORDS' in input[ind]:
memory = spl_line[val + 1]
# MEMORY USED IN INPUT
ddi = False
if 'MEMDDI' in input[ind]:
spl_line = re.split('=| ', input[ind])
for val, bit in enumerate(spl_line):
if bit == 'MEMDDI' in input[ind]:
ddi = spl_line[val + 1]
# WRITE INP
write_gmsInp(npath, name, input)
# WRITE JOB
lines = False
if jobTemp:
lines = job_replace(name, jobTemp)
else:
hw = host()
if hw == 'rjn':
lines = gms_rjnJob(name)
elif hw == 'mgs':
lines = gms_mgsJob(name)
elif hw == 'gai':
lines = gms_gaiJob(name)
elif hw == 'mas':
lines = gms_masJob(name)
elif hw == 'mon':
lines = gms_monJob(name)
elif hw == 'stm':
lines = gms_stmJob(name)
if lines:
write_job(npath, name, lines)
def comp_tasks(task, path, filename, jobfile):
import os.path
from general import find_files, software, softInp
from system import systemData
from p_print import stat_print, file_print, e_print
from p_print import noFiles
from logFile import sort
# FORMAT EXPECTED
if filename:
if path is '':
path = './'
Files = [[path, filename]]
else:
Files = False
# GENERATE JOB/INP FROM TEMPLATE
# EXPECTS .template FILE IN PATH DIRECTORY
if task == "1":
import sys
from genJob import g09, gms, psi, fmo, orc
# RECURSIVE FILE CREATION
if not Files:
#level = False # ALL LEVELS
level = input("Number of subdirs [0-9]: ")
file_pattern = ['.xyz'] # FILES TO CHECK
Files = find_files(path, level, file_pattern)
if len(Files) == 0:
noFiles()
for path, File in Files:
# CHECK IF ANY TEMPLATE FILES ARE FMO FOR CORRECT FRAGMENTATION
fmoC = False
templates = []
for template in os.listdir(path):
if template.endswith('template'):
templates.append(template)
with open(template, 'r+') as f:
for line in f:
if '$FMO' in line:
fmoC = True
# CHECK IF TEMPLATE FILE HAS BEEN FOUND
if len(templates) == 0:
sys.exit("No '*template' files found in directory.")
# CHECK IF JOB TEMPLATE
jobTemp = False
if jobfile:
jobTemp = open(path + jobfile, 'r+').read()
elif os.path.isfile(path + 'template.job'):
jobTemp = open(path + 'template.job', 'r+').read()
# SEARCH FILES
print('-' * 40)
file_print(path, File, "Using")
# ONLY HAPPEN ONCE FOR EACH XYZ
sysData = systemData(path, File, fmoC)
# COMPLETE FOR EVERY TEMPLATE
for template in templates:
file_print(path, template, "With template")
soft = softInp(path, template)
if soft == 'g09':
# JOB INCLUDED IN INPUT
g09(path, File, template, sysData)
elif soft == 'gms':
gms(path, File, template, sysData, jobTemp)
elif soft == 'psi':
psi(path, File, template, sysData, jobTemp)
elif soft == 'fmo':
fmo(path, File, template, sysData, jobTemp)
elif soft == 'orc':
orc(path, File, template, sysData, jobTemp)
# WILL TREAT UNKNOWN INPUT FILE AS G09 TYPE
else:
g09(path, File, template, sysData)
### PULL ENERGIES
elif task == "2":
from energy import energy_g09, energy_gms, energy_psi
from write import write_energy
from os import getcwd
cwd = getcwd()
energy = [] # TO PRINT AT END
if not Files:
level = 100 # ALL
file_pattern = ['.log', '.out'] # FILES TO CHECK
Files = find_files(path, level, file_pattern)
if len(Files) == 0:
noFiles()
# SEARCH FILES
for path, File in Files:
# DO NOT SORT PREVIOUS LOG FILES
if not File.startswith('f-') and not File.startswith('slurm'):
soft = software(path, File)
if soft == 'gms':
energy = energy_gms(path, File, energy)
elif soft == 'g09':
energy = energy_g09(path, File, energy)
elif soft == 'psi':
energy = energy_psi(path, File, energy)
mkfi = input("Write to file? (y/n) [n]")
if mkfi == 'n' or mkfi == '':
e_print(energy)
elif mkfi == 'y':
e_print(energy)
write_energy(cwd, energy)
### SORT LOG FILES
elif task == "3":
if not Files:
level = False # ALL LEVELS
level = input("Number of subdirs [0-9]: ")
file_pattern = ['.log', '.out'] # FILES TO CHECK
Files = find_files(path, level, file_pattern)
if len(Files) == 0:
noFiles()
# SEARCH FILES
for path, File in Files:
# DO NOT SORT PREVIOUS LOG FILES
if not File.startswith('f-') and not File.startswith('slurm'):
# GET SOFTWARE OF LOG
soft = software(path, File)
if not soft:
stat_print(path, File, 5)
else:
# MOVE INTO DIRECTORIES & CREATE XYZ's
sort(path, File, soft)
# MASS SED
elif task == "4":
from clean import sed
sed(path)
# MASS RENAME
elif task == "5":
from clean import rename
rename(path)
# DELETE N JOBS FROM QUEUE
elif task == "6":
from supercomp import deleteJob
deleteJob()
# COUNTERPOISE
elif task == '7':
import sys
from genJob import g09, gms, psi, fmo
from genJobCP import psi_cpoise, g09_cpoise, orc_cpoise
if not Files:
level = False # ZERO LEVELS
file_pattern = ['.xyz'] # FILES TO CHECK
Files = find_files(path, level, file_pattern)
if len(Files) == 0:
noFiles()
templates = []
for template in os.listdir(path):
if template.endswith('template'):
templates.append(template)
# CHECK IF TEMPLATE FILE HAS BEEN FOUND
if len(templates) == 0:
sys.exit("No '*template' files found in directory.")
# ASK USER IF SPHERE FOR BSSE
task = input(' \n\
1. Full counterpoise calculation \n\
2. Sphere around each molecule \n\
Task: ')
if task == '2':
# USER DEFINED DISTANCE
dist = input(
"Enter the radius of the solvation shell to include: ")
else:
dist = False
# CHECK IF JOB TEMPLATE
jobTemp = False
if jobfile:
jobTemp = open(path + jobfile, 'r+').read()
elif os.path.isfile(path + 'template.job'):
jobTemp = open(path + 'template.job', 'r+').read()
# SEARCH FILES
for path, File in Files:
file_print(path, File, "Using")
# ONLY HAPPEN ONCE FOR EACH XYZ
sysData = systemData(path, File, True)
# COMPLETE FOR EVERY TEMPLATE
for template in templates:
soft = softInp(path, template)
# PSI4 ONLY
if soft == 'g09':
# JOB INCLUDED IN INPUT
g09_cpoise(path, File, template, sysData, dist)
elif soft == 'gms':
pass
elif soft == 'psi':
psi_cpoise(path, File, template, sysData, jobTemp, dist)
elif soft == 'fmo':
pass
elif soft == 'orc':
orc_cpoise(path, File, template, sysData, jobTemp, dist)
# DISTANCES AND ANGLES
elif task == '8':
from geometry import sysGeom
# GET PATHS
if not Files:
level = 1
file_pattern = ['.xyz'] # FILES TO CHECK
Files = find_files(path, level, file_pattern)
if len(Files) == 0:
noFiles()
# ASK USER QUESTIONS ABOUT WHAT THEY WANT
task = input(' \n\
1. All interionic distances \n\
2. H-bonding data \n\
3. Intramolecular bond lengths \n\
Task: ')
for path, File in Files:
file_print(path, File, "Using")
sysData = systemData(path, File, True)
sysGeom(sysData, task)
# SUBMIT JOBS
elif task == '9':
from supercomp import submit
# GET PATHS
if not Files:
level = False # ALL LEVELS
level = input("Number of subdirs [0-9]: ")
file_pattern = ['.com', '.job'] # FILES TO CHECK
Files = find_files(path, level, file_pattern)
if len(Files) == 0:
noFiles()
# ORIGINAL PATH
os.chdir(path)
cwd = os.getcwd()
# SEARCH FILES
for path2, File in Files:
if File != 'template.job':
os.chdir(path2)
submit(File)
os.chdir(cwd)
# INFLATE SYSTEM
# EXPECTS .xyz FILE IN PATH DIRECTORY
elif task == "A":
import sys
from xyzGenerate import expand
level = False # NO LEVELS
if not Files:
file_pattern = ['.xyz'] # FILES TO CHECK
Files = find_files(path, level, file_pattern)
if len(Files) == 0:
noFiles()
# DISTANCES BY USER
print("Enter the minimum distance you want between fragments")
dist = input("You can provide more than one separated by space: ")
dists = []
# CHECK FLOATS WERE GIVEN
for i in dist.split():
try:
dists.append(float(i))
except TypeError:
sys.exit("Could not convert " + i + " into a float")
# SEARCH FILES
for path, File in Files:
file_print(path, File, "Using")
# ONLY HAPPEN ONCE FOR EACH XYZ
sysData = systemData(path, File, True)
expand(path, File, sysData, dists)
# INTERACTION ENERGY
elif task == 'B':
from xyzGenerate import separate_mols
# MAKE SURE CORRECT FRAGMENTATION
check_frags = True
level = False # NO LEVELS
if not Files:
file_pattern = ['.xyz'] # FILES TO CHECK
Files = find_files(path, level, file_pattern)
if len(Files) == 0:
noFiles()
# SEARCH FILES
for path, File in Files:
use = True
skip = ['anion', 'cation', 'unknown', 'neutral']
for i in skip:
if i in File:
use = False
if use:
print('-' * 40)
file_print(path, File, "Using")
# ONLY HAPPEN ONCE FOR EACH XYZ
sysData = systemData(path, File, check_frags)
separate_mols(path, File, sysData)
# FLUORESCENCE DATA
elif task == 'C':
from extras import get_fluorescence_data
task = input(' \n\
1. Fluorescence Data \n\
Task: ')
if task == '1' or task == "":
get_fluorescence_data()
# GET XYZ SOLVATION SHELL OF EACH FRAGMENT
elif task == 'D':
from xyzGenerate import xyzShell
# USER DEFINED DISTANCE
dist = input("Enter the radius of the solvation shell to include: ")
# MAKE SURE CORRECT FRAGMENTATION
check_frags = True
level = False # NO LEVELS
if not Files:
file_pattern = ['.xyz'] # FILES TO CHECK
Files = find_files(path, level, file_pattern)
if len(Files) == 0:
noFiles()
# SEARCH FILES
for path, File in Files:
use = True
skip = ['anion', 'cation', 'unknown', 'neutral']
for i in skip:
if i in File:
use = False
if use:
print('-' * 40)
file_print(path, File, "Using")
# ONLY HAPPEN ONCE FOR EACH XYZ
sysData = systemData(path, File, check_frags)
xyzShell(path, File, sysData, dist)
# CHECK COMPLETED JOBS
elif task == '10':
from supercomp import host, rjn_q
if os.path.exists(os.path.expanduser('~/sub.txt')):
to_write = []
to_save = []
jobs = open(os.path.expanduser('~/sub.txt'), 'r+').readlines()
hw = host()
if hw == "rjn":
queDicts = rjn_q()
for job in jobs:
found = False
for jobDict in queDicts:
# CHECK IF FILES IN SAVED ARE IN QUEUE
#print(job)
#print(jobDict['id'])
if jobDict['id'] in job:
# IF FINISHED WRITE TO SAVE FILE
to_write.append(job)
found = True
#print('TRUE')
#print(jobDict['status'])
if jobDict['status'] == 'Q':
print('QUEUED\t' + job.replace('\n', ''))
elif jobDict['status'] == 'R':
print('RUNNIN\t' + job.replace('\n', ''))
if not found:
print('FINISH\t' + job.replace('\n', ''))
to_save.append(job)
write = input('Remove data of completed jobs (y/n)? ')
if write == 'y' or write == 'Y':
# REWRITE FILE WITHOUT FINISHED JOBS
f = open(os.path.expanduser('~/sub.txt'), 'w+')
for line in to_write:
f.write(line)
f.close()
# WRITE FINISHED JOBS INTO NEW FILE
f = open(os.path.expanduser('~/jobLog.txt'), 'w+')
for line in to_save:
f.write(line)
f.close()
def deleteJob():
import re, sys
import subprocess as sp
from supercomp import host
que = []
IDs_list = []
nms_list = []
dict_IDs = {}
toDel_list = []
user = sp.Popen("echo $USER", shell=True, stdout=sp.PIPE).stdout
user = user.read().decode("utf-8").split()[0]
hw = host()
if hw == 'rjn':
# GET QUEUE
print('Waiting for qstat from Raijin...')
#print("qstat -u " + user)
pipe = sp.Popen("qstat -u " + user, shell=True, stdout=sp.PIPE).stdout
queue = pipe.read().decode("utf-8")
queue = queue.split('\n')
# REMOVE OTHER LINES
for line in queue:
if user in line:
que.append(line)
# PRINT FOR USER
num_lin = len(que)
for val, line in enumerate(que):
print("{:5}{}".format(str(num_lin - val), line))
# ASK USER NUMBER OF JOBS TO DELETE OR NAME
typ = input("Delete by: 1: Number; 2: All; 3: Name; [Default=1] ")
typ = typ or '1'
# SAVE JOB NUMBERS AND NAMES
for line in que:
#print(que)
ID = re.split(' |\.', line)
ID = list(filter(None, ID))
IDs_list.append(ID[0])
nms_list.append(ID[4])
dict_IDs[ID[0]] = ID[4]
# IF DELETING BY NUMBER
if typ == '1' or typ == '2':
if typ == '2':
sure = input('Are you sure you want to delete all jobs? (y/n) ')
if sure == 'y':
n = len(IDs_list)
else:
n = 0
elif typ == '1':
n = input("Number of jobs to delete from bottom of queue: ")
# IF NO USER INPUT
if not n:
sys.exit("No user input given, exiting",)
start = len(IDs_list) - int(n)
finish = len(IDs_list)
for i in range(len(IDs_list)):
if start <= i < finish:
sp.call("qdel " + IDs_list[i], shell=True)
print("Removed " + IDs_list[i] + " from queue")
# IF DELETING BY NAME
elif typ == '3':
subnm = input("Part of name unique to all jobs to delete: ")
# FIND JOBS WITH NAME
for ID, name in dict_IDs.items():
if subnm in name:
print("To delete: ", name, ID)
toDel_list.append(ID)
# DELETE
toDel = input("Are you sure? y/n ")
if toDel == 'y':
for ID in toDel_list:
sp.call("qdel " + ID, shell=True)
print("Removed " + ID + " from queue")
elif hw == 'mgs':
print('Not written for magnus yet')
elif hw == 'gai':
print('Waiting for qstat from MCC...')
pipe = sp.Popen("qstat -u " + user, shell=True, stdout=sp.PIPE).stdout
queue = pipe.read().decode("utf-8")
queue = queue.split('\n')
# REMOVE OTHER LINES
for line in queue:
if user in line:
que.append(line)
# PRINT FOR USER
num_lin = len(que)
for val, line in enumerate(que):
print("{:5}{}".format(str(num_lin - val), line))
# ASK USER NUMBER OF JOBS TO DELETE OR NAME
typ = input("Delete by: 1: Number; 2: All; 3: Name; [Default=1] ")
typ = typ or '1'
# SAVE JOB NUMBERS AND NAMES
for line in que:
#print(que)
ID = re.split(' |\.', line)
ID = list(filter(None, ID))
IDs_list.append(ID[0])
nms_list.append(ID[3])
dict_IDs[ID[0]] = ID[3]
# IF DELETING BY NUMBER
if typ == '1' or typ == '2':
if typ == '2':
sure = input('Are you sure you want to delete all jobs? (y/n) ')
if sure == 'y':
n = len(IDs_list)
else:
n = 0
elif typ == '1':
n = input("Number of jobs to delete from bottom of queue: ")
start = len(IDs_list) - int(n)
finish = len(IDs_list)
for i in range(len(IDs_list)):
if start <= i < finish:
sp.call("qdel " + IDs_list[i], shell=True)
print("Removed " + IDs_list[i] + " from queue")
# IF DELETING BY NAME
elif typ == '3':
subnm = input("Part of name unique to all jobs to delete: ")
print(subnm)
print(dict_IDs)
# FIND JOBS WITH NAME
for ID, name in dict_IDs.items():
if subnm in name:
print("To delete: ", name, ID)
toDel_list.append(ID)
# DELETE
toDel = input("Are you sure? y/n ")
if toDel == 'y':
for ID in toDel_list:
sp.call("qdel " + ID, shell=True)
print("Removed " + ID + " from queue")
def orc_cpoise(path, File, template, sysData, jobTemp, dist):
import os, re
from supercomp import host
from genJob import xyzTemp
from genJob import job_replace
from templates import orc_rjnJob
from write import write_inp
from write import write_xyz
from write import write_job
name = File.replace('.xyz', '').split('_')[0]
# MAKE NEW DIR AND NEW PATH
npath = newDirCP(path, File, template)
# UNPACK sysData
fragList, atmList, totChrg, totMult = sysData
# IF NOT RADIAL CUTOFF FOR MOLS INCLUDED DO ALL
if not dist:
# FOR EACH FRAGMENT
for frag in fragList:
ifrag = []
for atm in atmList:
if atm['id'] in frag['ids']:
ifrag.append([atm['sym'], atm['nu'], atm["x"], atm["y"], atm["z"]])
else:
# MAKE OTHER FRAGS GHOST
ifrag.append([atm['sym'] + ':'] + [atm['nu'], atm["x"], atm["y"], atm["z"]])
# MAKE FOLDERS
if not os.path.isdir(npath + frag["name"]):
os.mkdir(npath + frag["name"])
# PUT XYZ IN TEMP FOR EACH FRAG
input = xyzTemp(path, template, ifrag)
# CHANGE CHARGE AND MULTIPLICITY/MEMORY
for i in range(len(input)):
if type(input[i]) != list:
# CHANGE CHRG AND MULT
if re.search('^\*xyzfile\s*-?[0-9]\s*-?[0-9]\s*', input[i]):
if totChrg == '?':
print("Cannot determine chrg/mult, using template values")
# IF CHRG = MULT COULD BE TRICKY
else:
line = input[i].split()
if '.xyz' in line[-1]:
input[i] = '*xyz ' + str(frag["chrg"]) + ' ' + str(frag["mult"]) + '\n'
# ADD XYZ AS GHOST ATOMS
for atm in ifrag:
i += 1
input.insert(i, atm)
# END XYZ
input.insert(i+1, '*')
# WILL CHANGE NUMBER OF LINES - DO NOT CONTINUE THIS LOOP
break
# WRITE INPUT FILE FOR EACH FRAG
write_inp(npath + frag["name"] + '/', name +'-'+ frag["name"], input)
# WRITE JOB
lines = False
if jobTemp:
lines = job_replace(name +'-'+ frag["name"], jobTemp)
else:
hw = host()
if hw == 'rjn':
lines = orc_rjnJob(name +'-'+ frag["name"])
if lines:
write_job(npath + frag["name"] + '/', name +'-'+ frag["name"], lines)
# IF RADIAL CUTOFF FOR MOLS INCLUDED IN EACH FILE
else:
from xyzGenerate import xyzShell
# GET < DIST SEPARATED FRAGS
# xyzList = [frag, mol, ghost atoms]
xyzList = xyzShell(path, File, sysData, dist, returnList=True)
# FOR EACH FRAGMENT CENTER
for frag, firstMol, otherMol in xyzList:
ifrag = []
for atm in firstMol:
ifrag.append([atm['sym'], atm['nu'], atm["x"], atm["y"], atm["z"]])
for atm in otherMol:
ifrag.append([atm['sym'] + ":"] + [atm['nu'], atm["x"], atm["y"], atm["z"]])
# MAKE FOLDERS
if not os.path.isdir(npath + frag["name"]):
os.mkdir(npath + frag["name"])
# PUT XYZ IN TEMP FOR EACH FRAG
input = xyzTemp(path, template, ifrag)
# CHANGE CHARGE AND MULTIPLICITY/MEMORY
# MEMORY OF INPUT NEEDS TO BE >>> MEM JOB
for i in range(len(input)):
if type(input[i]) != list:
# CHANGE CHRG AND MULT
if re.search('^\*xyzfile\s*-?[0-9]\s*-?[0-9]\s*', input[i]):
if totChrg == '?':
print("Cannot determine chrg/mult, using template values")
# IF CHRG = MULT COULD BE TRICKY
else:
line = input[i].split()
if '.xyz' in line[-1]:
input[i] = '*xyzfile ' + str(totChrg) + ' ' + str(totMult) + ' ' +line[-1]
if re.search('.xyz', input[i]):
line = input[i].strip()
line = line.rsplit(' ', 1)[0]
input[i] = line+' '+name+'-ghost.xyz\n'
# WRITE GHOST FILE XYZ
write_xyz(npath + frag["name"] + '/', frag["name"] + "-ghost", ifrag)
# WRITE INPUT FILE FOR EACH FRAG
write_inp(npath + frag["name"] + '/', frag["name"], input)
# WRITE JOB
lines = False
if jobTemp:
lines = job_replace(frag["name"], jobTemp)
else:
hw = host()
if hw == 'rjn':
lines = orc_rjnJob(frag["name"])
if lines:
write_job(npath + frag["name"] + '/', frag["name"], lines)
def psi_cpoise(path, File, template, sysData, jobTemp, dist):
import os, re
from supercomp import host
from genJob import xyzTemp
from genJob import job_replace
from templates import psi_rjnJob
from templates import psi_gaiJob
from templates import psi_masJob
from write import write_inp
from write import write_job
name = File.replace('.xyz', '').split('_')[0]
# MAKE NEW DIR AND NEW PATH
npath = newDirCP(path, File, template)
# UNPACK sysData
fragList, atmList, totChrg, totMult = sysData
# CREATE xyzData
xyzData = []
for frag in fragList:
for atm in atmList:
if atm['id'] in frag['ids']:
xyzData.append([atm['sym'], atm['nu'], atm["x"], atm["y"], atm["z"]])
# PUT XYZ IN TEMPLATE
input = xyzTemp(path, template, xyzData)
# IF bsse_type='cp' PSI4 ONLY ONE CALC
cp_type = False
for line in input:
if "bsse_type=" in line and "'cp'" in line:
cp_type = True
# IF bsse_type='cp' PSI4 ONLY ONE CALC
if cp_type:
# REMOVE EXTRA '--' AND CHARGE MULTIPLICITY
cp_input = []
for line in input:
if type(line) != list:
if '--' in line:
pass
elif re.search('\s*-?[0-9]\s*[0-9]\s*', line):
pass
else:
cp_input.append(line)
else:
cp_input.append(line)
# COUNT WHICH ATOM UP TO
count = 0
input = []
for i in range(len(cp_input)):
# IF ATOM LINE
if type(cp_input[i]) is list:
# FOR EACH FRAG
put = False
for frag in fragList:
# IF ATOM NUMBER LAST ATOMS OF FRAG
if count == frag['ids'][0]:
# IF NOT FIRST FRAG
if not count == fragList[0]['ids'][0]:
input.append('--\n')
input.append(str(frag['chrg'])+' '+str(frag['mult'])+'\n')
input.append(cp_input[i])
put = True
if not put:
input.append(cp_input[i])
count += 1
else:
input.append(cp_input[i])
# WRITE INP
write_inp(npath, name, input)
# WRITE JOB
lines = False
if jobTemp:
lines = job_replace(name, jobTemp)
else:
hw = host()
if hw == 'rjn':
lines = psi_rjnJob(name)
elif hw == 'gai':
lines = psi_gaiJob(name)
elif hw == 'mas':
lines = psi_masJob(name)
if lines:
write_job(npath, name, lines)
# NORMAL INPUT -------------------------
else:
# IF NOT RADIAL CUTOFF FOR MOLS INCLUDED DO ALL
if not dist:
for i in range(len(input)):
if type(input[i]) != list:
# CHANGE MEMORY to 64
#if 'memory' in input[i]:
# line = input[i].split()
# memory = line[1]
# input[i] = input[i].replace(memory, '64')
# CHANGE CHRG AND MULT
if re.search('^\s*-?[0-9]\s*-?[0-9]\s*$', input[i]):
# IF CHRG = MULT COULD BE TRICKY
input[i] = ' ' + str(totChrg) + ' ' + str(totMult) + '\n'
# WRITE INP
write_inp(npath, name, input)
# WRITE JOB
lines = False
if jobTemp:
lines = job_replace(name, jobTemp)
else:
hw = host()
if hw == 'rjn':
lines = psi_rjnJob(name)
elif hw == 'gai':
lines = psi_gaiJob(name)
elif hw == 'mas':
lines = psi_masJob(name)
if lines:
write_job(npath, name, lines)
# FOR EACH FRAGMENT
for frag in fragList:
ifrag = []
for atm in atmList:
if atm['id'] in frag['ids']:
ifrag.append([atm['sym'], atm['nu'], atm["x"], atm["y"], atm["z"]])
else:
# MAKE OTHER FRAGS GHOST
ifrag.append(['@' + atm['sym']] + [atm['nu'], atm["x"], atm["y"], atm["z"]])
# MAKE FOLDERS
if not os.path.isdir(npath + frag["name"]):
os.mkdir(npath + frag["name"])
# PUT XYZ IN TEMP FOR EACH FRAG
input = xyzTemp(path, template, ifrag)
# CHANGE CHARGE AND MULTIPLICITY/MEMORY
# MEMORY OF INPUT NEEDS TO BE >>> MEM JOB
for i in range(len(input)):
if type(input[i]) != list:
# CHANGE CHRG AND MULT
if re.search('^\s*-?[0-9]\s*-?[0-9]\s*$', input[i]):
# IF CHRG = MULT COULD BE TRICKY
input[i] = ' ' + str(frag['chrg']) + ' ' + str(totMult) + '\n'
# WRITE INPUT FILE FOR EACH FRAG
write_inp(npath + frag["name"] + '/', frag["name"], input)
# WRITE JOB
lines = False
if jobTemp:
lines = job_replace(frag["name"], jobTemp)
else:
hw = host()
if hw == 'rjn':
lines = psi_rjnJob(frag["name"])
elif hw == 'gai':
lines = psi_gaiJob(frag["name"])
elif hw == 'mas':
lines = psi_masJob(frag["name"])
if lines:
write_job(npath + frag["name"] + '/', frag["name"], lines)
# IF RADIAL CUTOFF FOR MOLS INCLUDED IN EACH FILE
else:
from xyzGenerate import xyzShell
# GET < DIST SEPARATED FRAGS
# xyzList = [frag, mol, ghost atoms]
xyzList = xyzShell(path, File, sysData, dist, returnList=True)
# FOR EACH FRAGMENT CENTER
for frag, firstMol, otherMol in xyzList:
ifrag = []
for atm in firstMol:
ifrag.append([atm['sym'], atm['nu'], atm["x"], atm["y"], atm["z"]])
for atm in otherMol:
ifrag.append(['@' + atm['sym']] + [atm['nu'], atm["x"], atm["y"], atm["z"]])
# MAKE FOLDERS
if not os.path.isdir(npath + frag["name"]):
os.mkdir(npath + frag["name"])
# PUT XYZ IN TEMP FOR EACH FRAG
input = xyzTemp(path, template, ifrag)
# CHANGE CHARGE AND MULTIPLICITY/MEMORY
# MEMORY OF INPUT NEEDS TO BE >>> MEM JOB
for i in range(len(input)):
if type(input[i]) != list:
# CHANGE CHRG AND MULT
if re.search('^\s*-?[0-9]\s*-?[0-9]\s*$', input[i]):
# IF CHRG = MULT COULD BE TRICKY
input[i] = ' ' + str(frag['chrg']) + ' ' + str(totMult) + '\n'
# CHANGE MEMORY
if re.search('memory', input[i]):
line = re.split(' |G|g', input[i])
for bit in line:
if re.search('[0-9]', bit):
input[i] = input[i].replace(bit, '64')
break
# WRITE INPUT FILE FOR EACH FRAG
write_inp(npath + frag["name"] + '/', frag["name"], input)
# WRITE JOB
lines = False
if jobTemp:
lines = job_replace(frag["name"], jobTemp)
else:
hw = host()
if hw == 'rjn':
lines = psi_rjnJob(frag["name"])
elif hw == 'gai':
lines = psi_gaiJob(frag["name"])
elif hw == 'mas':
lines = psi_masJob(frag["name"])
if lines:
write_job(npath + frag["name"] + '/', frag["name"], lines)
