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Initialized with files on caviness #1

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39 changes: 9 additions & 30 deletions zacros_wrapper/IO_data.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,11 +9,9 @@
from zacros_wrapper.utils import ReturnUnique as _ReturnUnique
from zacros_wrapper.utils import rawbigcount as _rawbigcount

try:
from pMuTT.io.excel import read_excel
from pMuTT.empirical.zacros import Zacros
except:
pass
# from pmutt.io.excel import read_excel
# from pmutt.empirical.zacros import Zacros


'''
Class definitions for:
Expand Down Expand Up @@ -1053,15 +1051,15 @@ def ReadSeed(self, nSites = 1):
# take the line with seed indices
seed_lines = [li for li in lines if (li[0] == 'seed_on_sites')]
seed_indices = np.array([int(si[2]) for si in seed_lines])

# save to a snap matrix (nSites by 4)
snap_data = np.array([[0]*4]*nSites)
snap_data[:,0] = np.arange(1, nSites+1) # 1st column is the site number
snap_data[:,1] = np.arange(1, nSites+1) # 2nd column wont be used
snap_data[:,3] = 1 # 4th column dentate number, default is 1
snap_data[seed_indices,2] = 1 # 3rd column, occupancy, set as 1
snap_data[:,3] = 1 # 3rd column dentate number, default is 1
snap_data[seed_indices,2] = 1 # 2nd column, occupancy, set as 1
self.initialsnap = snap_data


def WriteIn(self, fldr, surf_spec):

Expand Down Expand Up @@ -1413,12 +1411,7 @@ def Read_propensities(path, nRxn):
for dub in LineSplit:
line_data.append(np.float(dub))
prop.append(line_data)


prop = np.array(prop)
nNum = prop.shape[0]
prop = np.reshape(prop, [int(nNum/nRxn), nRxn])
return prop
return np.array(prop)

else:
return None
Expand Down Expand Up @@ -1466,11 +1459,7 @@ def Read_time_integrated_propensities(path, nRxn):
line_data.append(np.float(dub))
propCounter.append(line_data)


propCounter = np.array(propCounter)
nNum = propCounter.shape[0]
propCounter = np.reshape(propCounter, [int(nNum/nRxn), nRxn])
return propCounter
return np.array(propCounter)
else:
return None

Expand Down Expand Up @@ -1508,11 +1497,6 @@ def Read_trajectory_derivatives(path, nRxn):
for dub in LineSplit:
line_data.append(np.float(dub))
W_sen_anal.append(line_data)


W_sen_anal = np.array(W_sen_anal)
nNum = W_sen_anal.shape[0]
W_sen_anal = np.reshape(W_sen_anal, [int(nNum/nRxn), nRxn])
return np.array(W_sen_anal)
else:
return None
Expand Down Expand Up @@ -1551,11 +1535,6 @@ def Read_time_integrated_species(path, n_surf_specs):
for dub in LineSplit:
line_data.append(np.float(dub))
spec_num_int.append(line_data)


spec_num_int = np.array(spec_num_int)
nNum = spec_num_int.shape[0]
spec_num_int = np.reshape(spec_num_int, [int(nNum/n_surf_specs), n_surf_specs])
return np.array(spec_num_int)

else:
Expand Down
27 changes: 15 additions & 12 deletions zacros_wrapper/KMC_Run.py
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Original file line number Diff line number Diff line change
Expand Up @@ -53,8 +53,8 @@ def __init__(self, path = None):
self.propCounter = None # data from timeintprop_output.txt
self.W_sen_anal = None # data from trajderiv_output.txt
self.spec_num_int = None # data from timeintspecs_output.txt
self.TS_site_props_list = None
self.TS_site_props_ss = None # steady state site propensities
#self.TS_site_props_list = None
#self.TS_site_props_ss = None # steady state site propensities


'''
Expand Down Expand Up @@ -95,6 +95,8 @@ def ReadAllOutput(self, build_lattice=False):
False - reads lattice_output.txt as text only
'''

#print 'Reading kMC trajectory data from ' + self.Path

self.ReadAllInput()

if self.CheckComplete():
Expand All @@ -117,18 +119,19 @@ def ReadAllOutput(self, build_lattice=False):

# Extra output files
# Disable for simplicity
self.prop = Read_propensities(self.Path, len( self.genout.RxnNameList ) )
self.propCounter = Read_time_integrated_propensities(self.Path, len( self.genout.RxnNameList ) )
self.W_sen_anal = Read_trajectory_derivatives(self.Path, len( self.genout.RxnNameList ))
self.spec_num_int = Read_time_integrated_species(self.Path, len( self.simin.surf_spec ))
self.TS_site_props_list = Read_time_integrated_site_props(self.Path, nSites, len( self.genout.RxnNameList ), self.histout.n_snapshots )
#self.prop = Read_propensities(self.Path, len( self.genout.RxnNameList ) )
#self.propCounter = Read_time_integrated_propensities(self.Path, len( self.genout.RxnNameList ) )
#self.W_sen_anal = Read_trajectory_derivatives(self.Path, len( self.genout.RxnNameList ))
#self.spec_num_int = Read_time_integrated_species(self.Path, len( self.simin.surf_spec ))
#self.TS_site_props_list = Read_time_integrated_site_props(self.Path, nSites, len( self.genout.RxnNameList ), self.histout.n_snapshots )

if not self.TS_site_props_list is None:

if self.histout.snap_times[-1] == 0.: # only 1 entry in history output
self.TS_site_props_ss = self.TS_site_props_list[-1]
else:
self.TS_site_props_ss = ( self.TS_site_props_list[-1] - self.TS_site_props_list[0] ) / ( self.histout.snap_times[-1] - self.histout.snap_times[0] )
#if not self.TS_site_props_list is None:

#if self.histout.snap_times[-1] == 0.: # only 1 entry in history output
#self.TS_site_props_ss = self.TS_site_props_list[-1]
#else:
#self.TS_site_props_ss = ( self.TS_site_props_list[-1] - self.TS_site_props_list[0] ) / ( self.histout.snap_times[-1] - self.histout.snap_times[0] )

else:
print('general_output.txt not found in ' + self.Path)
Expand Down
2 changes: 1 addition & 1 deletion zacros_wrapper/Lattice.py
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Original file line number Diff line number Diff line change
Expand Up @@ -393,7 +393,7 @@ def Build_neighbor_list_3D(self, cut_range=(0.9, 1.1), cart_coords_3d = None):
self.neighbor_list = []
self.cell_list = [] # self, north, northeast, east, or southeast

n_sites = self.cart_coords_3d.shape[0]
n_sites = len(self.site_type_inds)

# Loop through all sites
for site_1 in range(n_sites):
Expand Down
6 changes: 2 additions & 4 deletions zacros_wrapper/__init__.py
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Original file line number Diff line number Diff line change
@@ -1,9 +1,7 @@
import matplotlib as mat
import platform
if platform.system() == 'Linux':
mat.use('Agg')

mat.use('Agg')
import matplotlib.pyplot as plt

from zacros_wrapper.utils import *
from zacros_wrapper.IO_data import *
from zacros_wrapper.Lattice import Lattice
Expand Down