import numpy as np
import matplotlib.pyplot as plt
import os
import time
##############################################################################
# Code
##############################################################################
# data_path='/Users/shenglanqiao/Documents/GitHub/waterMD/data'
data_path = os.getcwd()+'/data'
traj = md.load_trr(data_path+'/nvt-pr_run1.trr', top = data_path+'/water-sol_run1.gro')
print ('here is some info about the trajectory we are looking at:')
print traj
test = WaterStats(traj,'run1',read_mod = 'r')
R_water = 0.3
# output_path = '/Users/shenglanqiao/Documents/GitHub/waterMD/output'
output_path = '/home/shenglan/GitHub/waterMD/output'
def test_rdf(r_range):
test.radial_dist(r_range)
rs, g_R, g_err = test.rdf[0],test.rdf[1],test.rdf[2]
fig = plt.figure()
plt.errorbar(rs,g_R, yerr=g_err)
plt.title('gn(r)')
plt.xlabel('r (nm)')
plt.ylabel('gn(r)')
plt.ylim(0,max(g_R)*1.2)
def main(argv):
# default values for options
run_name = None
outputfile = None
number_qs = 10
frame_start = 1
frame_end = None
# q_inverse = 0.3
q_range = [0.3]
phi_range = [0, 1.0]
try:
opts, args = getopt.getopt(argv, "hi:o:q:r:p:s:e:", [
"ifile=", "ofile=", "q_inv=", "n_phi=", "phi_range=", "fstart=",
"fend="
])
except getopt.GetoptError:
usage()
sys.exit(2)
for opt, arg in opts:
if opt == '-h':
usage()
sys.exit()
elif opt in ("-i", "--ifile"):
run_name = arg
elif opt in ("-o", "--ofile"):
outputfile = arg
elif opt in ("-q", "--q_inv"):
qs = arg.split('/')
print qs
if len(qs) > 1:
try:
q_range = [float(this_q) for this_q in qs]
except ValueError:
print 'Enter a single value of q of a range of values separated by /'
sys.exit(2)
else:
try:
q_range = [float(arg)]
except ValueError:
print 'Enter a single value of q of a range of values separated by space'
sys.exit(2)
elif opt in ("-p", "--n_phi"):
number_qs = int(arg)
elif opt in ("-r", "--phi_range"):
phis = arg.split('/')
if len(phis) == 2:
try:
phi_range = [float(this_phi) for this_phi in phis]
except ValueError:
print 'Enter two values (in units of pi) for starting and ending phi separated by /. '
sys.exit(2)
else:
print 'Enter two values (in units of pi) for starting and ending phi separated by /. '
sys.exit(2)
elif opt in ("-s", "--fstart"):
frame_start = int(arg)
elif opt in ("-e", "--fend"):
frame_end = int(arg)
print 'Input run is %s' % run_name
print 'Output file is %s' % outputfile
print 'Number of phi used is %d from phi = %.3g pi to phi = %.3g pi' % (
number_qs, phi_range[0], phi_range[1])
# print 'Inverse of q is %.2f nm'%q_inverse
print 'Computing correlators for the following q_inverse values in nm:'
print q_range
if run_name == None:
print '<runname> must be provided.'
usage()
sys.exit(2)
# data_path = os.getcwd()+'/data'
data_path = '/home/shenglan/MD_simulations/water_box/cubic_2nm_' + run_name
traj = md.load_trr(data_path + '/nvt-pr_' + run_name + '.trr',
top=data_path + '/water-sol_' + run_name + '.gro')
print('here is some info about the trajectory we are looking at:')
print traj
run = WaterStats(traj, run_name, read_mod='r')
if frame_start >= run.n_frames:
print 'Starting frame cannot be greater than the number of frames in simulation.'
usage()
sys.exit(2)
elif frame_end == None:
frames = np.arange(run.n_frames)[frame_start:]
else:
frames = np.arange(run.n_frames)[frame_start:frame_end]
print("frames %d to %d are used for averaging." % (frames[0], frames[-1]))
# wavelength of laser
wavelength = 0.1
phi = np.linspace(phi_range[0] * np.pi, phi_range[1] * np.pi, number_qs)
dt = 1.0 # ps
for q_inverse in q_range:
print('computing for q_invers = %.3g nm' % q_inverse)
q = 1 / q_inverse * np.pi * 2.0
if outputfile == None:
outputfile = 'corr_'+run_name+\
'_'+str(q_inverse)+'q_'+str(number_qs)+'p_'+\
str(frames[0])+\
'.csv'
tic = time.clock()
run.correlator(q,
wavelength,
frames,
phi,
cut_off=0.5,
output=outputfile)
toc = time.clock()
print("Correlator process time for %.3g nm: %.2f" % (q_inverse,
(toc - tic)))
outputfile = None
run.all_tthds.close()
run.nearest_tthds.close()
from water_stats import WaterStats
import numpy as np
import os
import time
##############################################################################
# Code
##############################################################################
run_name = 'run9'
data_path = '/home/shenglan/MD_simulations/water_box/cubic_2nm_run9'
traj = md.load_trr(data_path+'/nvt-pr.trr', top = data_path+'/water-sol.gro')
print ('here is some info about the trajectory we are looking at:')
print traj
ws = WaterStats(traj,run_name)
cut_off = 0.5
tic = time.clock()
for this_frame in range(ws.n_frames):
tic_loop = time.clock()
print 'finding tthds for frame %d' % this_frame
if str(this_frame) in ws.nearest_tthds:
pass
else:
tthds = ws.make_nearest_nb_tthds(cut_off,this_frame)
ws.nearest_tthds.create_dataset(str(this_frame),data = tthds)
toc_loop = time.clock()
print('Total time for this frame: %.2f' %(toc_loop-tic_loop))
toc = time.clock()
def main(argv):
# default values for options
run_name = None
outputfile = None
number_qs = 10
frame_start = 1
frame_end = None
# q_inverse = 0.3
q_range = [0.3]
phi_range = [0, 1.0]
try:
opts, args = getopt.getopt(
argv, "hi:o:q:r:p:s:e:", ["ifile=", "ofile=", "q_inv=", "n_phi=", "phi_range=", "fstart=", "fend="]
)
except getopt.GetoptError:
usage()
sys.exit(2)
for opt, arg in opts:
if opt == "-h":
usage()
sys.exit()
elif opt in ("-i", "--ifile"):
run_name = arg
elif opt in ("-o", "--ofile"):
outputfile = arg
elif opt in ("-q", "--q_inv"):
qs = arg.split("/")
print qs
if len(qs) > 1:
try:
q_range = [float(this_q) for this_q in qs]
except ValueError:
print "Enter a single value of q of a range of values separated by /"
sys.exit(2)
else:
try:
q_range = [float(arg)]
except ValueError:
print "Enter a single value of q of a range of values separated by space"
sys.exit(2)
elif opt in ("-p", "--n_phi"):
number_qs = int(arg)
elif opt in ("-r", "--phi_range"):
phis = arg.split("/")
if len(phis) == 2:
try:
phi_range = [float(this_phi) for this_phi in phis]
except ValueError:
print "Enter two values (in units of pi) for starting and ending phi separated by /. "
sys.exit(2)
else:
print "Enter two values (in units of pi) for starting and ending phi separated by /. "
sys.exit(2)
elif opt in ("-s", "--fstart"):
frame_start = int(arg)
elif opt in ("-e", "--fend"):
frame_end = int(arg)
print "Input run is %s" % run_name
print "Output file is %s" % outputfile
print "Number of phi used is %d from phi = %.3g pi to phi = %.3g pi" % (number_qs, phi_range[0], phi_range[1])
# print 'Inverse of q is %.2f nm'%q_inverse
print "Computing correlators for the following q_inverse values in nm:"
print q_range
if run_name == None:
print "<runname> must be provided."
usage()
sys.exit(2)
# data_path = os.getcwd()+'/data'
data_path = "/home/shenglan/MD_simulations/water_box/cubic_2nm_" + run_name
traj = md.load_trr(data_path + "/nvt-pr_" + run_name + ".trr", top=data_path + "/water-sol_" + run_name + ".gro")
print ("here is some info about the trajectory we are looking at:")
print traj
run = WaterStats(traj, run_name, read_mod="r")
if frame_start >= run.n_frames:
print "Starting frame cannot be greater than the number of frames in simulation."
usage()
sys.exit(2)
elif frame_end == None:
frames = np.arange(run.n_frames)[frame_start:]
else:
frames = np.arange(run.n_frames)[frame_start:frame_end]
print ("frames %d to %d are used for averaging." % (frames[0], frames[-1]))
# wavelength of laser
wavelength = 0.1
phi = np.linspace(phi_range[0] * np.pi, phi_range[1] * np.pi, number_qs)
dt = 1.0 # ps
for q_inverse in q_range:
print ("computing for q_invers = %.3g nm" % q_inverse)
q = 1 / q_inverse * np.pi * 2.0
if outputfile == None:
outputfile = (
"corr_" + run_name + "_" + str(q_inverse) + "q_" + str(number_qs) + "p_" + str(frames[0]) + ".csv"
)
tic = time.clock()
run.correlator(q, wavelength, frames, phi, cut_off=0.5, output=outputfile)
toc = time.clock()
print ("Correlator process time for %.3g nm: %.2f" % (q_inverse, (toc - tic)))
outputfile = None
run.all_tthds.close()
run.nearest_tthds.close()
from water_stats import WaterStats
import numpy as np
import os
import time
##############################################################################
# Code
##############################################################################
run_name = 'run9'
data_path = '/home/shenglan/MD_simulations/water_box/cubic_2nm_run9'
traj = md.load_trr(data_path + '/nvt-pr.trr', top=data_path + '/water-sol.gro')
print('here is some info about the trajectory we are looking at:')
print traj
ws = WaterStats(traj, run_name)
cut_off = 0.5
tic = time.clock()
for this_frame in range(ws.n_frames):
tic_loop = time.clock()
print 'finding tthds for frame %d' % this_frame
if str(this_frame) in ws.nearest_tthds:
pass
else:
tthds = ws.make_nearest_nb_tthds(cut_off, this_frame)
ws.nearest_tthds.create_dataset(str(this_frame), data=tthds)
toc_loop = time.clock()
print('Total time for this frame: %.2f' % (toc_loop - tic_loop))
toc = time.clock()
import matplotlib.pyplot as plt
import os
import time
##############################################################################
# Code
##############################################################################
# data_path='/Users/shenglanqiao/Documents/GitHub/waterMD/data'
data_path = os.getcwd() + '/data'
traj = md.load_trr(data_path + '/nvt-pr_run1.trr',
top=data_path + '/water-sol_run1.gro')
print('here is some info about the trajectory we are looking at:')
print traj
test = WaterStats(traj, 'run1', read_mod='r')
R_water = 0.3
# output_path = '/Users/shenglanqiao/Documents/GitHub/waterMD/output'
output_path = '/home/shenglan/GitHub/waterMD/output'
def test_rdf(r_range):
test.radial_dist(r_range)
rs, g_R, g_err = test.rdf[0], test.rdf[1], test.rdf[2]
fig = plt.figure()
plt.errorbar(rs, g_R, yerr=g_err)
plt.title('gn(r)')
plt.xlabel('r (nm)')
plt.ylabel('gn(r)')
import h5py
from water_stats import WaterStats
import numpy as np
import os
##############################################################################
# Code
##############################################################################
run_name = "run4"
data_path = os.getcwd() + "/data"
traj = md.load_trr(data_path + "/nvt-pr_" + run_name + ".trr", top=data_path + "/water-sol_" + run_name + ".gro")
print ("here is some info about the trajectory we are looking at:")
print traj
ws = WaterStats(traj, run_name)
cut_off = 0.5
for this_frame in range(ws.n_frames):
if str(this_frame) in ws.all_tthds:
pass
else:
tthds = []
for this_water in ws.water_inds:
tthds.extend(ws.make_tthd(this_water, cut_off, this_frame))
ws.all_tthds.create_dataset(str(this_frame), data=tthds)
# print len(tthds)
# print tthds[0][0]
import h5py
from water_stats import WaterStats
import numpy as np
import os
##############################################################################
# Code
##############################################################################
run_name = 'run4'
data_path = os.getcwd() + '/data'
traj = md.load_trr(data_path + '/nvt-pr_' + run_name + '.trr',
top=data_path + '/water-sol_' + run_name + '.gro')
print('here is some info about the trajectory we are looking at:')
print traj
ws = WaterStats(traj, run_name)
cut_off = 0.5
for this_frame in range(ws.n_frames):
if str(this_frame) in ws.all_tthds:
pass
else:
tthds = []
for this_water in ws.water_inds:
tthds.extend(ws.make_tthd(this_water, cut_off, this_frame))
ws.all_tthds.create_dataset(str(this_frame), data=tthds)
# print len(tthds)
# print tthds[0][0]
#ws.all_tthds['1'][:]= tthds
from water_stats import WaterStats
import numpy as np
import os
import time
##############################################################################
# Code
##############################################################################
run_name = 'run5'
data_path = os.getcwd()+'/data'
traj = md.load_trr(data_path+'/nvt-pr_'+run_name+'.trr', top = data_path+'/water-sol_'+run_name+'.gro')
print ('here is some info about the trajectory we are looking at:')
print traj
ws = WaterStats(traj,run_name)
cut_off = 0.5
frame_ind = 1
half_box = ws.traj.unitcell_lengths[0][0]/2.*10
inds = range(1001)[101:]
count = 33897
for frame_ind in inds:
nbs = ws.find_nearest_nbs(cut_off,frame_ind,3)
xyz_pos = ws.traj[frame_ind].xyz
with open(os.getcwd()+'/output_data/tthd_pdb_1000.pdb','a') as f:
for this_nb in nbs:
r1 = xyz_pos[0,this_nb[0],:]*10
