sys.path.append('/home/kevin/projects/ntpl/Codes') # Needed to recognize ntpy module
import ntpy.param.lj as lj
import ntpy.param.const as ct
import ntpy.gulp as gp
temps = [20, 50, 80]
strains = [-0.12, -0.10, -0.08, -0.06, -0.04, -0.02, -0.01, 0.0, \
0.005, 0.01, 0.015, 0.02, 0.04, 0.06, 0.08, 0.10, 0.12]
numTemps = len(temps)
numStrains = len(strains)
# numKpts = 100
numKpts = 50
numAtomsUC = 4 # Number of atoms in the unit cell
numFreq = 3 * numAtomsUC
numVel = numFreq
mass = 1.0 * lj.value('mass') * ct.value('kilo') * ct.value('avog')
gulpName = 'gulp.temp' # Gulp template file
tempName = 'input.gulp'
# Lattice Constants
alat = np.array( [lj.value('lat20'), lj.value('lat50'), lj.value('lat80')] )
# Data Arrays
vel = np.zeros( (numTemps, numStrains, numKpts, 3, numFreq, 3), dtype=float)
freqConv = 2.0 * np.pi * ct.value('c') * ct.value('tocenti') * lj.value('tau')
# velConv = ((1.0 / ct.value('centi')) * ct.value('c')) / (1.0 / (lj.value('lat20') * ct.value('ang')))
# print velConv
for itemp in range(numTemps):
# from scipy.optimize import leastsq
import numpy as np
import operator
import sys
sys.path.append('/home/kevin/projects/ntpl/Codes')
import ntpy.param.lj as lj
temps = [20, 50, 80]
strains = [-.12, -.10, -.08, -.06, -.04, -.02, -.01, 0, .005, .01, .015, .02, .04, .06, .08, .10, .12]
numTemps = len(temps)
numStrains = len(strains)
numFreqs = 12
# Lattice Constants
alat = np.array( [lj.value('lat20'), lj.value('lat50'), lj.value('lat80')] )
print "Begin Load Sequence"
## ## ## Load freq from file
freq = np.load('post.freq.npy')
## ## ## Load vel from file
vel = np.load('post.vel.npy')
print vel[0,0,:,0,0,0]
## ## ## Load freqStep from file
freqStep = np.load('post.freqStep.npy')
## ## ## Load freqdos from file
freqdos = np.load('post.freq.dos.npy')
## ## ## Kevin Parrish - 7/31/12 - lammps pos script ## ## ##
import sys
sys.path.append('/home/kevin/projects/ntpl/Codes') # Needed to recognize ntpy module
import ntpy.lattice as lt # Lattice module
import ntpy.param.lj as lj # Parameter module
## Set lattice constants
lat20 = (lj.value('lat20') / lj.value('sigma')) * 1e-10
lat50 = (lj.value('lat50') / lj.value('sigma')) * 1e-10
lat80 = (lj.value('lat80') / lj.value('sigma')) * 1e-10
lat100 = lat80
## Automated using a loop
lats = [lat20, lat50, lat80, lat100]
for index, lat in zip(range(len(lats)), lats):
mylamp = lt.Lammps('in.pos.'+ str(index))
mylat = lt.Block([lats[index], lats[index], lats[index]], 'fcc', [6, 6, 6], atom_mass = [1])
mylamp.buildLammps([mylat])
sys.path.append('/home/kevin/projects/ntpl/Codes') # Needed to recognize ntpy module
import ntpy.lattice as lt
import ntpy.param.lj as lj
import ntpy.param.const as ct
import ntpy.gulp as gp
temps = [20, 50, 80]
strains = [-0.12, -0.10, -0.08, -0.06, -0.04, -0.02, -0.01, 0.0, \
0.005, 0.01, 0.015, 0.02, 0.04, 0.06, 0.08, 0.10, 0.12]
numTemps = len(temps)
numStrains = len(strains)
numKpts = 100
numAtomsUC = 4 # Number of atoms in the unit cell
numFreq = 3 * numAtomsUC
numVel = numFreq
mass = 1.0 * lj.value('mass') * ct.value('kilo') * ct.value('avog')
gulpName = 'gulp.temp' # Gulp template file
tempName = 'input.gulp'
# Lattice Constants
alat = np.array( [lj.value('lat20'), lj.value('lat50'), lj.value('lat80')] )
# Data Arrays
eig = np.zeros( (numTemps, numStrains, numKpts, 3, numFreq, numFreq), \
dtype=complex)
for itemp in range(numTemps):
for istrain in range(numStrains):
# 100 Direction, Create kpts
kpt = np.zeros( (numKpts, 3), dtype=float)
kpt[:, 0] = np.linspace(0, 0.5, num=numKpts)
## ## ## Kevin Parrish ## ## ##
## ## ## nmd.py config file ## ## ##
import numpy as np
import sys
ntpyPath = '/opt/mcgaugheygroup/ntpy'
sys.path.append(ntpyPath) # Needed to recognize ntpy module
import ntpy.lattice as lt
import ntpy.param.lj as lj
import ntpy.param.const as ct
## ## ## BEGIN USER INPUT ## ## ##
## Lattice Parameters
dim = [4, 4, 4]
latType = 'fcc'
realMass = 1.0 * lj.value('mass') * ct.value('kilo') * ct.value('avog')
ljMass = 1.0
realLat = lj.value('lat20') * (1.0+ 0.0)
ljLat = ((lj.value('lat20') / lj.value('sigma')) * 1e-10) * (1.0 + 0.0)
## Name Parameters
gulpName = 'gulp.template' # Gulp Template Name
gulpTrans = 'input.gulp' # Gulp Transient Name
gulpExe = 'gulp_ifort' # Gulp Executable Name
lammpsName = 'lammps.template' # Lammps Template Name
lammpsRunName = 'in.lammps' # Lammps Run Name
lammpsSubName = 'lammps.sub.template' # Lammps Submission Template Name
lammpsSubRunName = 'tmp.lammps.sub' # Lammps Submission Run Name
# np.savez('post.ald.new.'+ str(2)+ '.'+ str(8)+ '.'+ \
# str(0)+ '.npz', newKpt=newKpt, newFreq=newFreq, \
# newLife=newLife, newVel=newVel)
# print 'finish'
# sys.exit()
##########################
for tStr, itemp in zip(strTemps, range(len(strTemps))):
for i, sStr, sNum, istrain in zip(colors, strStrains, rStrains, range(len(strStrains))):
for zStr, isize, zNum in zip(strSizes, range(len(strSizes)), rSizes):
print tStr + "/" + sStr + "/" + zStr + "/"
# # Create volume
latType = "fcc"
ljLat = ((lj.value("lat" + str(rTemps[itemp])) / lj.value("sigma")) * 1e-10) * (1.0 + sNum)
myBox = lt.Block([ljLat, ljLat, ljLat], latType, [zNum, zNum, zNum])
Lx = myBox.Lx()
Ly = myBox.Ly()
Lz = myBox.Lz()
numAtomsUC = myBox.numAtomsUcell()
numModes = 3 * numAtomsUC
V = (Lx * Ly * Lz) * (1.0 * lj.value("sigma") ** 3)
# # Extract Data
pathName = basePathName + tStr + "/" + sStr + "/" + zStr + "/"
jobName = pathName + fileData
kpt, freq, freqShiftQ, lifeQ, freqShiftC, lifeC, vg = aldLife(jobName)
rKpt = lt.kpt([zNum, zNum, zNum], conv=True)
# EigenVectors
