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cl_water.py
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cl_water.py
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from numpy import *
import libwater as f_water
from cl_set import *
from cl_net import *
import copy as ccopy
import pickle as pic
#####################################################################################
##### Water tools
#####################################################################################
# Turning on the pynoramix option in the fortran code:
f_water.main.python=1
#########################
def hbonds_type(option=None,verbose=True):
hbs_type={}
hbs_info={}
hbs_type['Skinner']=1; hbs_info['Skinner']='R.Kumar, J.R. Schmidt and J.L. Skinner. J. Chem. Phys. 126, 204107 (2007)'
hbs_type['R(o,h)']=2; hbs_info['R(o,h)']='V. J. Buch. J. Chem. Phys. 96, 3814-3823 (1992)'
hbs_type['R(o,o)-Ang(o,o,h)']=3; hbs_info['R(o,o)-Ang(o,o,h)']='A. Luzar, D. Chandler. Phys. Rev. Lett. 76, 928-931 (1996)'
hbs_type['Donor-Acceptor-Number']=4; hbs_info['Donor-Acceptor-Number']='A. D. Hammerich, V. J. Buch. J. Chem. Phys. 128, 111101 (2008)'
hbs_type['Topological']=5; hbs_info['Topological']='R. H. Henchman and S. J. Irudayam. J. Phys. Chem. B. 114, 16792-16810 (2010)'
hbs_type['Donor-Number-Ang(o,o,h)']=6; hbs_info['Donor-Number-Ang(o,o,h)']='J. D. Smith, C. D. Cappa, et al. Proc. Natl. Acad. Sci. U.S.A. 102, 14171 (2005).'
hbs_type['Nearest-Neighbour']=7; hbs_info['Nearest-Neighbour']='This is not a hydrogen bond definition but just a topological characterization.'
if verbose:
if option not in hbs_type.keys():
for ii in hbs_type.keys():
if len(ii)<=12: tab='\t\t\t'
if 12<len(ii)<=18: tab='\t\t'
if 18<len(ii): tab='\t'
print ' ',ii,tab+'[',hbs_info[ii],']'
return
if option != None :
if option not in hbs_type.keys():
print option, ': Hbond type not defined.'
print 'List of definitions:'
for ii in hbs_type.keys():
if len(ii)<=12: tab='\t\t\t'
if 12<len(ii)<=18: tab='\t\t'
if 18<len(ii): tab='\t'
print ' ',ii,tab+'[',hbs_info[ii],']'
return 0
return hbs_type[option]
def hbonds_water(definition=None,system1=None,system2=None,frame=None,sk_param=0.00850,roh_param=2.3000,roo_param=3.5,angooh_param=30.0,optimize=False,verbose=False):
# Setting up the hbond definition:
f_water.hbonds.hb_def=hbonds_type(definition,verbose=False)
if f_water.hbonds.hb_def == 0 : return
if f_water.hbonds.hb_def == 1 : f_water.hbonds.sk_param=sk_param
if f_water.hbonds.hb_def == 2 : f_water.hbonds.roh_param= roh_param
if f_water.hbonds.hb_def == 3 : f_water.hbonds.roo_param, f_water.hbonds.cos_angooh_param= roo_param, cos(radians(angooh_param))
if f_water.hbonds.hb_def == 4 : pass
if f_water.hbonds.hb_def == 5 : pass
if f_water.hbonds.hb_def == 6 : f_water.hbonds.cos_angooh_param= cos(radians(angooh_param))
if f_water.hbonds.hb_def == 7 : pass
# Reset of previous hbonds
for ii in system1.atom :
ii.hbonds=[]
for ii in system1.water :
ii.O.hbonds=[]
ii.H1.hbonds=[]
ii.H2.hbonds=[]
# Frame to be analysed:
if system2==None and optimize==False:
if frame==None:
frame=system1.last_frame
# Setting up the fortran variables:
if not optimize :
f_water.main.list_neighbours=0 # Optimization for hbonds=False
f_water.main.nw=system1.num_waters
f_water.main.initialize_coors_memory()
__coors2fortran(system1,frame=0)
f_water.hbonds.initialize_hbonds_memory()
# Analysis
f_water.hbonds.hbonds_box()
# hbonds already in fortran variables... :
## f_water.hbonds.num_o2h[i] number of hbonds of the atom O of water i
## f_water.hbonds.o2h[i,dim=6] list of water index bonded to water i because of the O
## f_water.hbonds.o2which[i,dim=6] index of hydrogen -1 or 2- corresponding to f_water.hbonds.o2h
## f_water.hbonds.strength_o2h[i,dim=6] skinner parameter corresponding to f_water.hbonds.o2h
## f_water.hbonds.num_h2i[i,j-1] number of hbonds of the atom Hj of water i
## f_water.hbonds.h2o[i,j-1,dim=6] list of water index bonded to water i because of the atom Hj
## f_water.hbonds.strength_h2o[i,j-1,dim=6] skinner parameter corresponding to f_water.hbonds.h2o
# Reformatting data:
list_hbonds={}
for ii in range(system1.num_waters):
index_water_o=ii
index_o=system1.water[ii].O.index
for jj in range(f_water.hbonds.num_o2h[ii]):
index_water_h=f_water.hbonds.o2h[ii,jj]-1
if f_water.hbonds.o2which[ii,jj]==1:
index_h=system1.water[index_water_h].H1.index
aux_link_h=system1.water[index_water_h].H1.hbonds
else:
index_h=system1.water[index_water_h].H2.index
aux_link_h=system1.water[index_water_h].H2.hbonds
list_hbonds[str(index_o)+'-'+str(index_h)]=f_water.hbonds.strength_o2h[ii,jj]
system1.water[index_water_o].O.hbonds.append([index_h,f_water.hbonds.strength_o2h[ii,jj]])
system1.atom[index_o].hbonds.append([index_h,f_water.hbonds.strength_o2h[ii,jj]])
aux_link_h.append([index_o,f_water.hbonds.strength_o2h[ii,jj]])
system1.atom[index_h].hbonds.append([index_o,f_water.hbonds.strength_o2h[ii,jj]])
# Free memory:
f_water.main.free_coors_memory()
f_water.hbonds.free_hbonds_memory()
if verbose :
return list_hbonds # dict: 'index_O'-'indexH'=Skinner_parameter
else:
return
def skinner_parameter(system=None,index_wat_o=None,index_wat_h=None,index_h=None,frame=None):
if frame==None:
frame=system.last_frame
f_water.main.nw=system.num_waters
f_water.main.initialize_coors_memory()
__coors2fortran(system,frame=0)
sk=f_water.hbonds.skinner_parameter(index_wat_o,index_wat_h,index_h)
f_water.main.free_coors_memory()
return sk
def mss_water (system=None,output_array=None,definition='Skinner',sk_param=0.00850,roh_param=2.3000,roo_param=3.5,angooh_param=30.0,verbose=True):
"""output_array=['None','microstates','indexes_waters'] """
if system==None:
print 'Error: input variables needed'
print 'mss_water(system=None)'
return None
# Setting up the hbond definition:
f_water.hbonds.hb_def=hbonds_type(definition,verbose=False)
if f_water.hbonds.hb_def == 0 : return
if f_water.hbonds.hb_def == 1 : f_water.hbonds.sk_param=sk_param
if f_water.hbonds.hb_def == 2 : f_water.hbonds.roh_param= roh_param
if f_water.hbonds.hb_def == 3 : f_water.hbonds.roo_param, f_water.hbonds.cos_angooh_param= roo_param, cos(radians(angooh_param))
if f_water.hbonds.hb_def == 4 : pass
if f_water.hbonds.hb_def == 5 : pass
if f_water.hbonds.hb_def == 6 : f_water.hbonds.cos_angooh_param= cos(radians(angooh_param))
if f_water.hbonds.hb_def == 7 : pass
# Initialize Fortran objects:
f_water.main.nw=system.num_waters
f_water.main.initialize_coors_memory()
# Data in Fortran for the frame:
f_water.main.list_neighbours=0 ## Optimization for hbonds=False in first frame
__coors2fortran(system,frame=0)
# Analysis:
if output_array=='indexes_waters' :
mss=f_water.microstates.microstates_box_ind_wat(system.num_waters)
else :
mss=f_water.microstates.microstates_box(system.num_waters)
for ii in range(system.num_waters):
label=str(mss[ii][0])+' |'
for jj in range(1,5):
label+=' '+str(mss[ii][jj])
label+=' |'
for jj in range(5,8):
label+=' '+str(mss[ii][jj])
label+=' |'
for jj in range(8,11):
label+=' '+str(mss[ii][jj])
label+=' |'
for jj in range(11,14):
label+=' '+str(mss[ii][jj])
label+=' |'
for jj in range(14,17):
label+=' '+str(mss[ii][jj])
system.water[ii].microstate=label
if verbose: print "# Water microstates updated"
# Deallocating Fortran Memory:
f_water.main.free_coors_memory()
if output_array in ['indexes_waters','microstates']:
return mss
else:
pass
### Private methods for the code:
def coors2fortran(system,frame=None):
f_water.main.lbox[:,:]=system.frame[frame].box[:,:]
for jj in range(system.num_waters):
f_water.main.xarr[jj,0,:]=system.frame[frame].coors[system.water[jj].O.index,:]
f_water.main.xarr[jj,1,:]=system.frame[frame].coors[system.water[jj].H1.index,:]
f_water.main.xarr[jj,2,:]=system.frame[frame].coors[system.water[jj].H2.index,:]
pass
###class kinetic_network(network):
###
### def __init__(self,system=None,file_traj=None,begin=None,end=None,definition='Skinner',sk_param=0.00850,roh_param=2.3000,roo_param=3.5,angooh_param=30.0,verbose=True,optimize=None,memory=1):
### """ optimize=[None,Disk,RAM], memory=x*Gb"""
###
### if optimize in ['RAM','Disk']:
### l_frames=int((1073741824*float(memory))/(17*4*self.num_waters*1.0)) # 1Gb= 1073741824, 4 each integer
###
###
### if system==None or file_traj==None or begin==None or end==None:
### print 'Error: input variables needed'
### print 'kinetic_network(system=None,file_traj=None,begin=None,end=None)'
### return None
###
### # Setting up the hbond definition:
###
### f_water.hbonds.hb_def=hbonds_type(definition,verbose=False)
### if f_water.hbonds.hb_def == 0 : return
### if f_water.hbonds.hb_def == 1 : f_water.hbonds.sk_param=sk_param
### if f_water.hbonds.hb_def == 2 : f_water.hbonds.roh_param= roh_param
### if f_water.hbonds.hb_def == 3 : f_water.hbonds.roo_param, f_water.hbonds.cos_angooh_param= roo_param, cos(radians(angooh_param))
### if f_water.hbonds.hb_def == 4 : pass
### if f_water.hbonds.hb_def == 5 : pass
### if f_water.hbonds.hb_def == 6 : f_water.hbonds.cos_angooh_param= cos(radians(angooh_param))
### if f_water.hbonds.hb_def == 7 : pass
###
### # Frame to be analysed:
###
### system.last_frame=begin
###
### # Setting up the fortran variables:
###
### f_water.main.list_neighbours=0 # Optimization for hbonds=False for the first frame
###
### f_water.main.nw=system.num_waters
### f_water.main.initialize_coors_memory()
###
###
### ####### INITIALIZE NET#####
### nodes_ant=[0 for ii in range(system.num_waters)]
###
### num_nodes=-1
###
### self=network(verbose=False)
### self.file_traj=file_traj
###
### ####### INITIALIZE NET#####
###
### ###################################### first frame
### system.delete_coors()
### system.load_coors(file_traj)
###
### f_water.main.lbox[:,:]=system.frame[0].box[:,:]
###
### for jj in range(system.num_waters):
### f_water.main.xarr[jj,0,:]=system.frame[0].coors[system.water[jj].O.index,:]
### f_water.main.xarr[jj,1,:]=system.frame[0].coors[system.water[jj].H1.index,:]
### f_water.main.xarr[jj,2,:]=system.frame[0].coors[system.water[jj].H2.index,:]
###
###
### mss=f_water.microstates.microstates_box(system.num_waters)
###
### ###### NET: 1ST FRAME NODES ########
### for jj in range(system.num_waters):
### aa=str(mss[jj])
### try:
### nodes_ant[jj]=self.labels[aa]
### except:
### num_nodes+=1
### self.labels[aa]=num_nodes
### nodes_ant[jj]=num_nodes
### temp=cl_node()
### temp.label=aa
### self.node.append(temp)
###
### ###### NET: 1ST FRAME NODES ########
###
### system.delete_coors()
###
### ###################################### Remaining frames
###
### for ii in range(begin+1,end+1):
###
### system.load_coors(file_traj)
###
### f_water.main.lbox[:,:]=system.frame[0].box[:,:]
###
### for jj in range(system.num_waters):
### f_water.main.xarr[jj,0,:]=system.frame[0].coors[system.water[jj].O.index,:]
### f_water.main.xarr[jj,1,:]=system.frame[0].coors[system.water[jj].H1.index,:]
### f_water.main.xarr[jj,2,:]=system.frame[0].coors[system.water[jj].H2.index,:]
###
### mss=f_water.microstates.microstates_box(system.num_waters)
###
### ###### NET: FRAME NODES ########
### for jj in range(system.num_waters):
### bb=str(mss[jj])
### dd=nodes_ant[jj]
### try:
### cc=self.labels[bb]
### try:
### self.node[dd].link[cc]+=1
### except:
### self.node[dd].link[cc]=1
### nodes_ant[jj]=cc
### except:
### num_nodes+=1
### self.labels[bb]=num_nodes
### temp=cl_node()
### temp.label=bb
### self.node.append(temp)
### self.node[dd].link[num_nodes]=1
### nodes_ant[jj]=num_nodes
###
### ###### NET: FRAME NODES ########
###
### system.delete_coors()
###
###
###
### ################################################# END
###
### f_water.main.free_coors_memory()
###
### self.num_nodes=len(self.node)
### self.num_links=0
### self.weight=0
### self.k_max=0
### for ii in range(self.num_nodes):
### self.node[ii].k_out=len(self.node[ii].link)
### self.node[ii].weight=sum(self.node[ii].link.values())
### self.num_links+=self.node[ii].k_out
### self.weight+=self.node[ii].weight
### if (self.k_max<self.node[ii].k_out):
### self.k_max=self.node[ii].k_out
### self.k_total=self.num_links
###
### self.build_Ts()
###
### if verbose:
### self.info()
###
### return
class kinetic_network(network):
def __init__(self,system=None,file_traj=None,begin=None,end=None,definition='Skinner',sk_param=0.00850,roh_param=2.3000,roo_param=3.5,angooh_param=30.0,verbose=True,optimize=None,memory=1):
""" optimize=[None,Disk,RAM], memory=x*Gb"""
if optimize in ['RAM','Disk']:
l_frames=int((1073741824*float(memory))/(17*4*system.num_waters*1.0)) # 1Gb= 1073741824, 4 each integer
print l_frames
f_net.funcs.num_frames=l_frames
f_net.funcs.num_parts=1024
f_net.funcs.dim_mss=17
f_net.funcs.init_traj_mss_2_net()
return
if system==None or file_traj==None or begin==None or end==None:
print 'Error: input variables needed'
print 'kinetic_network(system=None,file_traj=None,begin=None,end=None)'
return None
# Setting up the hbond definition:
f_water.hbonds.hb_def=hbonds_type(definition,verbose=False)
if f_water.hbonds.hb_def == 0 : return
if f_water.hbonds.hb_def == 1 : f_water.hbonds.sk_param=sk_param
if f_water.hbonds.hb_def == 2 : f_water.hbonds.roh_param= roh_param
if f_water.hbonds.hb_def == 3 : f_water.hbonds.roo_param, f_water.hbonds.cos_angooh_param= roo_param, cos(radians(angooh_param))
if f_water.hbonds.hb_def == 4 : pass
if f_water.hbonds.hb_def == 5 : pass
if f_water.hbonds.hb_def == 6 : f_water.hbonds.cos_angooh_param= cos(radians(angooh_param))
if f_water.hbonds.hb_def == 7 : pass
# Frame to be analysed:
system.last_frame=begin
# Setting up the fortran variables:
f_water.main.list_neighbours=0 # Optimization for hbonds=False for the first frame
f_water.main.nw=system.num_waters
f_water.main.initialize_coors_memory()
####### INITIALIZE NET#####
nodes_ant=[0 for ii in range(system.num_waters)]
num_nodes=-1
self=network(verbose=False)
self.file_traj=file_traj
####### INITIALIZE NET#####
###################################### first frame
system.delete_coors()
system.load_coors(file_traj)
coors2fortran(system,frame=0)
mss=f_water.microstates.microstates_box(system.num_waters)
###### NET: 1ST FRAME NODES ########
for jj in range(system.num_waters):
aa=str(mss[jj])
try:
nodes_ant[jj]=self.labels[aa]
except:
nodes_ant[jj]=self.add_node(aa,iout=True)
system.delete_coors()
###################################### Remaining frames
for ii in range(begin+1,end+1):
system.load_coors(file_traj)
coors2fortran(system,frame=0)
mss=f_water.microstates.microstates_box(system.num_waters)
for jj in range(system.num_waters):
aa,nodes_ant[jj]=self.add_link(nodes_ant[jj],str(mss[jj]),weight=1,index_origin=True,iout=True)
system.delete_coors()
################################################# END
f_water.main.free_coors_memory()
# Computing weight nodes:
for ii in self.node:
ii.weight=sum(ii.link.values())
self.info(update=True,verbose=verbose)
return