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 forceDistribution(this, z0, z1, bins, simulation = -1, states = "all", label = ''):
length = this.stateNumbers[simulation];
runName = this.simulations[simulation];
f, r = mda.forceDistribution(z0, z1, bins, runName, length, states, label);
plt.figure(10);
plt.plot(r, f);
plt.savefig("/home/andre/Dropbox/plot/radialForceDistribution_%s.pdf"%label, bbox_inches = 'tight');
plt.close();
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 numberOfSilanol(this, A, t, simulation = -1, states = "all", label = ''): length = this.stateNumbers[simulation]; runName = this.simulations[simulation]; N = mda.silanolGroups(runName, length, states); if(states == "all"): states = np.arange(0, last + 1); #end print np.shape(N), np.shape(t); mdplot.plotSilanol(this.path, N, t, A, label = label); return t, N;
def forceDistribution(this, bins, senderMark, direction, simulation = -1, states = "all", label = ''): length = this.stateNumbers[simulation]; runName = this.simulations[simulation]; r, data = mda.forceDistribution(runName, bins, senderMark, states, direction, length); fz = data[0, :]; fr = data[1, :]; ft = data[2, :]; plt.figure(10); plt.plot(r, fz, '-b'); plt.figure(11); plt.plot(r, fr, '-g'); plt.figure(12); plt.plot(r, ft, '-r'); plt.show();
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 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 analyze(this, simulation = -1, label = ''): simPath = this.simulations[simulation]; length = this.stateNumbers[simulation]; #Read dt and step from file datafile = open(simPath + "/init/data.dat"); datafile.readline(); datafile.readline(); dt = float(datafile.readline()); step = int(datafile.readline()); datafile.close(); t = step*dt*np.arange(0, length + 1); K, V, T, r2 = mda.getAnalysis(simPath, length); mdplot.plotEnergy(this.path, V, K, t, label = label); mdplot.plotTemperature(this.path, T, t, label = label); mdplot.plotDisplacement(this.path, r2, t, label = label); D = np.zeros(np.shape(r2)); for i in range(0, 3): D[1:, i] = r2[1:, i]/(6*t[1:]); #end return K, V, T, r2, D, t;
def forceDistribution(this, bins, senderMark, direction, simulation = -1, states = "all", label = ''):
length = this.stateNumbers[simulation];
runName = this.simulations[simulation];
x, y, data = mda.forceDistribution(runName, bins, senderMark, states, direction, length);
save = this.path + "/data";
if(not os.path.exists(save)):
os.makedirs(save)
#end
saveZ = save + "/z" + label;
saveX = save + "/x" + label;
saveY = save + "/y" + label;
np.save(saveZ, data);
np.save(saveX, x);
np.save(saveY, y);
X, Y = np.meshgrid(x, y)
Z = data[0, :, :];
if(not noplt):
from mpl_toolkits.mplot3d import Axes3D
from matplotlib import cm
from matplotlib.ticker import LinearLocator, FormatStrFormatter
# import matplotlib.pyplot as plt
# import numpy as np
print np.shape(data), np.shape(x), np.shape(y);
# print data[0, :, :];
fig = plt.figure()
ax = fig.gca(projection = '3d')
surf = ax.plot_surface(X, Y, Z, rstride=1, cstride=1, cmap=cm.coolwarm,
linewidth=0, antialiased=False)
# ax.set_zlim(-1.01, 1.01)
ax.zaxis.set_major_locator(LinearLocator(10))
ax.zaxis.set_major_formatter(FormatStrFormatter('%.02f'))
fig.colorbar(surf, shrink=0.5, aspect=5)
plt.axis('off');
plt.show();
def numberOfSilanol(this, simulation = -1, states = "all"): length = this.stateNumbers[simulation]; runName = this.simulations[simulation]; return mda.silanolGroups(runName, length, states);
def visualize(this): #Visualize using vmd mda.vmdVisualize();
def calculateDisplacement(this, simulation = -1): path = this.simulations[simulation]; length = this.stateNumbers[simulation]; return mda.calculateDisplacement(path, length);
def visualize(this): #Visualize using vmd this.makeVmdData(); mda.vmdVisualize();
