from __future__ import division;
import numpy as np;
import simpleHole as hole;
from MDmanager import MDmanager as mdm;
from combineFiles import combiner;
import os;
import shutil;
import sys;
import multiprocessing as mpi;
import datetime;
import MDdata as mdd; usc = mdd.usc();
#Length (in timesteps) of simulation
sim = 750;
step = 150;
#Timestep length (fs)
dt = 0.25;
therm = 150;
thermstep = 160;
stab = 150;
stabstep = 150
dateAndTime = datetime.datetime.now().strftime("%Y-%m-%d_%H:%M:%S");
runName = dateAndTime
if(len(sys.argv) > 1):
runName = sys.argv[1];
#end
path = os.path.expanduser("~/clayff_h2o/" + runName);
#Removes path if exists, resetting data
if(os.path.exists(path)):
from __future__ import division; import numpy as np; import MDmanager as mdm; mdm = mdm.MDmanager(); import sys; import os; import MDdata; usc = MDdata.usc(); import shutil; dt = 0.25; dtsio2 = 1.25; tauTherm = 50*dt; tauNH = 25*dt; sim = 100; step = 12500; simSample = 100; stepSample = 7500; simTherm = 100; simStab = 100; stepTherm = 100; stepStab = 100; # p = np.zeros(3); # p[0] = sys.argv[1]; # p[1] = sys.argv[2]; # p[2] = sys.argv[3]; runName = sys.argv[1];
from __future__ import division
import numpy as np
import os
import shutil
from math import floor
import multiprocessing as mp
import MDdata as mdd
mdd = mdd.usc()
def makeDirs(last, path, step=1, reset=False):
if reset and os.path.exists(path):
shutil.rmtree(path)
# end
if not os.path.exists(path):
os.makedirs(path)
# end
for i in range(0, last + step, step):
dirname = path + ("/%05d" % i)
if not os.path.exists(dirname):
os.makedirs(dirname)
# end
# end
# end
def split(path, p, s, dest=None, source=None, remove=0):
if dest == None:
from __future__ import division;
import numpy as np;
import os;
import shutil;
from math import floor;
import multiprocessing as mp;
import MDdata as mdd; mdd = mdd.usc();
def makeDirs(last, path, step = 1, reset = False):
if(reset and os.path.exists(path)):
shutil.rmtree(path);
#end
if(not os.path.exists(path)):
os.makedirs(path);
#end
for i in range(0, last + step, step):
dirname = path + ("/%05d"%i);
if(not os.path.exists(dirname)):
os.makedirs(dirname);
#end
#end
#end
def split(path, p, s, dest = None, source = None, remove = 0):
if(dest == None):
dest = path + "/00000";
#end
if(source == None):
source = path + "/00000/combined.xyz";
#end
if(not os.path.exists(dest)):