def makeLens(this, r0, d, h, direction = [1, 0, 0], invert = False, simulation = -1):
length = this.stateNumbers[simulation];
lastSim = this.simulations[simulation];
splitted = this.splitted[simulation];
path = this.path;
simNumber = len(this.splitted) - 1;
if(splitted):
mdf.combine(lastSim, length, states = "last");
#end
loadfile = lastSim + "/%05d/combined.xyz"%length;
newPath = path + "/" + str(simNumber + 1) + "_lens";
#Creating new directories and data
if(not os.path.exists(newPath + "/init")):
os.makedirs(newPath + "/init");
#end
datafilename = newPath + "/init/data.dat"
datafile = open(datafilename, 'w');
datafile.write(str(this.p[0]) + " " + str(this.p[1]) + " " + str(this.p[2]) + "\n");
datafile.write(str(this.s[0]) + " " + str(this.s[1]) + " " + str(this.s[2]) + "\n");
datafile.write("0\n0\n");
#Creating directory to hold xyz files
directory = newPath + "/00000";
this.resetRun(directory);
os.makedirs(directory);
savefile = directory + "/combined.xyz";
N = mdm.makeLens(loadfile, savefile, r0, h, d, this.s, direction, invert);
datafile.write(str(N) + "\n");
datafile.close();
mdf.split(newPath, this.p, this.s, source = newPath + "/00000/combined.xyz");
this.simulations.append(newPath);
this.stateNumbers.append(0);
this.splitted.append(True);
return simNumber + 1;
def radialDistribution(this, bins, simulation = -1, states = "all", label = ''): print "Calculating radial distribution"; simPath = this.simulations[simulation]; length = this.stateNumbers[simulation]; mdf.combine(simPath, length, ); r, g = mda.calculateRadialDistribution(simPath, bins, length, states); mdplot.plotRadialDistribution(this.path, g, r, label = label); return r, g;
def angularDistribution(this, bins, states = "all", simulation = -1, label = ''): print "Calculating angular distribution"; length = this.stateNumbers[simulation]; runName = this.simulations[simulation]; mdf.combine(runName, length); angle, angleDistribution = mda.angularDistribution(bins, runName, length, states); mdplot.plotAngularDistribution(this.path, angleDistribution, angle*180/np.pi, label = label); return angle, angleDistribution;
def makeInitState(this, path, state, dest): mdf.combine(path, state, states = "last"); splitDir = path + "/%05d"%state; #Removes all files in directory before recreating shutil.rmtree(dest); os.makedirs(dest); mdf.split(path, this.p, this.s, dest, splitDir + "/combined.xyz"); #Get number of particles from datafile datafile = open(path + "/init/data.dat"); lines = [l for l in datafile]; N = int(lines[4]); return N;
def selectBox(this, r0, r1, simulation = -1, types = "all"): splitted = this.splitted[simulation]; length = this.stateNumbers[simulation]; lastSim = this.simulations[simulation]; if(splitted): mdf.combine(lastSim, length, states = "last"); #end markFile = lastSim + "/init/mark_%d.dat"%this.selections; this.selections += 1; filename = lastSim + "/%05d/combined.xyz"%length; mdm.selectBox(filename, markFile, r0, r1, types); return this.selections - 1;
def angularDistribution(this, bins, states = "all", simulation = -1, label = ''): print "Calculating angular distribution"; length = this.stateNumbers[simulation]; runName = this.simulations[simulation]; mdf.combine(runName, length); angle, angleDistribution = mda.angularDistribution(bins, runName, length, states); datadirname = this.path + "/data/"; if(not os.path.exists(datadirname)): os.makedirs(datadirname); #end np.save(datadirname + "/angle" + label + ".npy", angle); np.save(datadirname + "/angleData" + label + ".npy", angleDistribution); # mdplot.plotAngularDistribution(this.path, angleDistribution, angle*180/np.pi, label = label); return angle, angleDistribution;
def moveParticles(this, dr, simulation = -1):
length = this.stateNumbers[simulation];
lastSim = this.simulations[simulation];
splitted = this.splitted[simulation];
path = this.path;
simNumber = len(this.splitted) - 1;
if(splitted):
mdf.combine(lastSim, length, states = "last");
#end
loadfile = lastSim + "/%05d/combined.xyz"%length;
newPath = path + "/" + str(simNumber + 1) + "_displaced";
#Creating new directories and data
if(not os.path.exists(newPath + "/init")):
os.makedirs(newPath + "/init");
#end
datafilename = newPath + "/init/data.dat"
datafile = open(datafilename, 'w');
datafile.write(str(this.p[0]) + " " + str(this.p[1]) + " " + str(this.p[2]) + "\n");
datafile.write(str(this.s[0]) + " " + str(this.s[1]) + " " + str(this.s[2]) + "\n");
datafile.write("0\n0\n");
#Number of particles
lastDatafile = open(lastSim + "/init/data.dat");
lines = [l for l in lastDatafile];
N = int(lines[4]);
datafile.write(str(N) + "\n");
lastDatafile.close();
datafile.close();
#Copying mark files
initfiles = os.listdir(lastSim + "/init");
for f in initfiles:
if(f != "data.dat"):
shutil.copyfile(lastSimPath + "/init/" + f, newSimPath + "/init/" + f);
#end
#end
#Creating directory to hold xyz files
directory = newPath + "/00000";
this.resetRun(directory);
os.makedirs(directory);
savefile = directory + "/combined.xyz";
mdm.moveParticles(loadfile, savefile, dr, this.s);
mdf.split(newPath, this.p, this.s, source = newPath + "/00000/combined.xyz");
this.simulations.append(newPath);
this.stateNumbers.append(0);
this.splitted.append(True);
return simNumber + 1;
def radialDistribution(this, bins, simulation = -1, states = "all", label = ''): print "Calculating radial distribution"; simPath = this.simulations[simulation]; length = this.stateNumbers[simulation]; mdf.combine(simPath, length, ); r, g = mda.calculateRadialDistribution(simPath, bins, length, states); datadirname = this.path + "/data/"; if(not os.path.exists(datadirname)): os.makedirs(datadirname); #end np.save(datadirname + "/radial" + label + ".npy", r); np.save(datadirname + "/radialData" + label + ".npy", g); # mdplot.plotRadialDistribution(this.path, g, r, label = label); return r, g;
def freeze(this, r1, r2, v = [0, 0, 0], types = "all", simulation = -1): if(types == "all"): types = [0, 1, 2]; elif(types == "Si"): types = [0]; elif(types == "O"): types = [1]; elif(types == "H"): types = [2]; #end splitted = this.splitted[simulation]; length = this.stateNumbers[simulation]; lastSim = this.simulations[simulation]; if(splitted): mdf.combine(lastSim, length, states = "last"); #end filename = lastSim + "/%05d/combined.xyz"%length; markFilename = lastSim + "/init/mark.dat"; mdm.freeze(filename, markFilename, r1, r2, v, types);
def displaceCylindrical(this, R, direction, simulation = -1):
length = this.stateNumbers[simulation];
lastSim = this.simulations[simulation];
splitted = this.splitted[simulation];
path = this.path;
simNumber = len(this.splitted) - 1;
if(splitted):
mdf.combine(lastSim, length, states = "last");
#end
loadfile = lastSim + "/%05d/combined.xyz"%length;
newPath = path + "/" + str(simNumber + 1) + "_cylindricallyDisplaced";
#Creating new directories and data
this.resetRun(newPath);
os.makedirs(newPath + "/00000");
os.makedirs(newPath + "/init");
#Creatign data file
datafilename = newPath + "/init/data.dat"
datafile = open(datafilename, 'w');
datafile.write(str(this.p[0]) + " " + str(this.p[1]) + " " + str(this.p[2]) + "\n");
datafile.write(str(this.s[0]) + " " + str(this.s[1]) + " " + str(this.s[2]) + "\n");
datafile.write("0\n0\n");
lastDatafile = open(lastSim + "/init/data.dat");
lines = [l for l in lastDatafile];
N = int(lines[4]);
datafile.write(str(N) + "\n");
lastDatafile.close();
datafile.close();
#Copying mark files
initfiles = os.listdir(lastSim + "/init");
for i in range(len(initfiles)):
if(initfiles[i][0:4] == "mark"):
shutil.copyfile(lastSim + "/init/" + initfiles[i], newPath + "/init/" + initfiles[i]);
#end
#end
#Displacing particles
mdm.displaceCylindrical(lastSim, newPath, R, direction)
mdf.split(newPath, this.p, this.s, source = newPath + "/00000/combined.xyz");
this.simulations.append(newPath);
this.stateNumbers.append(0);
this.splitted.append(True);
return simNumber + 1;
def combine(this, simulation1, simulation2):
path = this.path;
simNumber = len(this.splitted) - 1;
length1 = this.stateNumbers[simulation1];
lastSim1 = this.simulations[simulation1];
splitted1 = this.splitted[simulation1];
length2 = this.stateNumbers[simulation2];
lastSim2 = this.simulations[simulation2];
splitted2 = this.splitted[simulation2];
if(splitted1):
mdf.combine(lastSim1, length1, states = "last");
#end
if(splitted2):
mdf.combine(lastSim2, length2, states = "last");
#end
loadfile1 = lastSim1 + "/%05d/combined.xyz"%length1;
loadfile2 = lastSim2 + "/%05d/combined.xyz"%length2;
newPath = path + "/" + str(simNumber + 1) + "_combined";
#Creating new directories and data
if(not os.path.exists(newPath + "/init")):
os.makedirs(newPath + "/init");
#end
datafilename = newPath + "/init/data.dat"
datafile = open(datafilename, 'w');
datafile.write(str(this.p[0]) + " " + str(this.p[1]) + " " + str(this.p[2]) + "\n");
datafile.write(str(this.s[0]) + " " + str(this.s[1]) + " " + str(this.s[2]) + "\n");
datafile.write("0\n0\n");
#Number of particles
lastDatafile = open(lastSim1 + "/init/data.dat");
lines = [l for l in lastDatafile];
N1 = int(lines[4]);
lastDatafile.close();
lastDatafile = open(lastSim2 + "/init/data.dat");
lines = [l for l in lastDatafile];
N2 = int(lines[4]);
lastDatafile.close();
datafile.write(str(N1 + N2) + "\n");
datafile.close();
#Creating directory to hold xyz files
directory = newPath + "/00000";
this.resetRun(directory);
os.makedirs(directory);
savefile = directory + "/combined.xyz";
markFile1 = lastSim1 + "/init/mark.dat";
markFile2 = lastSim2 + "/init/mark.dat";
markFileSave = newPath + "/init/mark.dat";
mdm.combine(loadfile1, loadfile2, savefile, markFile1, markFile2, markFileSave);
mdf.split(newPath, this.p, this.s, source = newPath + "/00000/combined.xyz");
this.simulations.append(newPath);
this.stateNumbers.append(0);
this.splitted.append(True);
return simNumber + 1;
def thermalize(this, length, dt, tau, avglength, timesteps, combine = False, resume = -1): #Berendsen thermostat lastSimPath = this.simulations[resume]; lastState = this.stateNumbers[resume]; lastSim = len(this.simulations) - 1; T = this.T; path = this.path if(path == ""): print "A save directory is needed to run simulation"; print "Use setDir(<dirName>) to set a save directory"; return; #end #Creating path of new simulation newSimPath = path + "/" + str(lastSim + 1) + "_thermalization"; #Copy old datafile to new location if(lastSim == -1): print "A initial state is needed for simulation"; return; #end #Creating new directories and copy data mdf.makeDirs(length, newSimPath, reset = True); N = this.makeInitState(lastSimPath, lastState, newSimPath + "/00000"); os.makedirs(newSimPath + "/init"); datafilename = newSimPath + "/init/data.dat" datafile = open(datafilename, 'w'); datafile.write(str(this.p[0]) + " " + str(this.p[1]) + " " + str(this.p[2]) + "\n"); datafile.write(str(this.s[0]) + " " + str(this.s[1]) + " " + str(this.s[2]) + "\n"); datafile.write(str(dt) + "\n"); datafile.write(str(timesteps) + "\n"); datafile.write(str(int(N)) + "\n"); datafile.close(); #Copy all other files in init directory initfiles = os.listdir(lastSimPath + "/init"); for f in initfiles: if(f != "data.dat"): shutil.copyfile(lastSimPath + "/init/" + f, newSimPath + "/init/" + f); #end #end mds.thermalize(length, dt, tau, T, avglength, newSimPath, timesteps = timesteps); if(combine): print "Combining files"; mdf.combine(length, newSimPath); print "Sorting files"; mdf.sortStates(length, newSimPath); #end this.simulations.append(newSimPath); this.stateNumbers.append(length); this.splitted.append(True); return lastSim + 1;
def combine(this, simulation1, simulation2):
path = this.path;
simNumber = len(this.splitted) - 1;
length1 = this.stateNumbers[simulation1];
lastSim1 = this.simulations[simulation1];
splitted1 = this.splitted[simulation1];
length2 = this.stateNumbers[simulation2];
lastSim2 = this.simulations[simulation2];
splitted2 = this.splitted[simulation2];
if(splitted1):
mdf.combine(lastSim1, length1, states = "last");
#end
if(splitted2):
mdf.combine(lastSim2, length2, states = "last");
#end
newPath = path + "/" + str(simNumber + 1) + "_combined";
#Creating new directories and data
this.resetRun(newPath);
os.makedirs(newPath + "/init");
#Creating datafile
datafilename = newPath + "/init/data.dat"
datafile = open(datafilename, 'w');
datafile.write(str(this.p[0]) + " " + str(this.p[1]) + " " + str(this.p[2]) + "\n");
datafile.write(str(this.s[0]) + " " + str(this.s[1]) + " " + str(this.s[2]) + "\n");
datafile.write("0\n0\n");
#Number of particles
lastDatafile = open(lastSim1 + "/init/data.dat");
lines = [l for l in lastDatafile];
N1 = int(lines[4]);
lastDatafile.close();
lastDatafile = open(lastSim2 + "/init/data.dat");
lines = [l for l in lastDatafile];
N2 = int(lines[4]);
lastDatafile.close();
datafile.write(str(N1 + N2) + "\n");
datafile.close();
#Combining files and splitting xyz file
mdm.combine(lastSim1, lastSim2, newPath);
mdf.split(newPath, this.p, this.s, source = newPath + "/00000/combined.xyz");
this.simulations.append(newPath);
this.stateNumbers.append(0);
this.splitted.append(True);
return simNumber + 1;
def makeVmdData(this, simulation = -1): print "Making vmd input files"; path = this.simulations[simulation]; length = this.stateNumbers[simulation]; mdf.makeVmdData(path, length); mdf.combine(path, length);
def makeVmdData(this, simulation = -1, processors = "all"): path = this.simulations[simulation]; length = this.stateNumbers[simulation]; mdf.makeVmdData(path, length); mdf.combine(path, length, processors = processors);