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TooBBA
Commit 2fef443c authored by Stelios Karozis's avatar Stelios Karozis
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memory opt + debugging

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CHANGELOG
View file @ 2fef443c
......@@ -6,6 +6,17 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
## [Unreleased]
## [0.0.8] - 2020-07-16
### Added
- memory optimizations
- Add check of molecule existance in .ndx file
### Changed
- Update I/O to functions
### Removed
- Remove log message option
## [0.0.7] - 2020-07-03
### Added
- unified properties output
......@@ -18,7 +29,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
### Removed
- None
## [0.0.6] - 2020-07-02
### Added
- Initial support for gmx commands
......
main.py
View file @ 2fef443c
......@@ -7,10 +7,9 @@ import tooba_gmx as tbgmx
# in case of tail is the one closest to the head, hence
# the code is a good approximation
###################################################
LOG=0
SYSTEM_NAME='test'
DISCET=[6, 6, 6]
NUM_FR=1
DISCET=[3.5, 3.5, 3.5]
NUM_FR=100
TRAJ=SYSTEM_NAME+'/eq_traj.trr'
GRO=SYSTEM_NAME+'/eq_final.gro'
TPR=SYSTEM_NAME+'/eq_run.tpr'
......@@ -37,7 +36,7 @@ TPR=SYSTEM_NAME+'/eq_run.tpr'
###################################################
GROUPS={'ALL':['gmx_ndx','index',['save', ['pkl'],'index'],'density',['save', ['pkl'],'dens']],
'HD_GROUP':['surf',['save', ['pkl', 'json'],'time_domain_c-normal-cg']],
'TL_GROUP':['vector'],
'TL_GROUP':['vector',['save', ['pkl'],'vec']],
'COMBINE':[['HD_GROUP','surf'],['TL_GROUP','vector'],['COMB','tilt'],['save', ['pkl'],'tilt']]
}
ALL={'NS':['C6', 'Na', 'P4', 'P3', 'C7','C3', 'C4', 'C5', 'C8', 'C9', 'C10'], 'CHOL':['ROH','R1', 'R2', 'R3', 'R4', 'R5'], 'FFA':['AC','C1', 'C2', 'C3', 'C4']}
......@@ -56,6 +55,14 @@ _,data_num,_,res_num,res_type,atom_type,atom_num,_ = tbf.read_gro(GRO)
print(' ')
###################################################
#--------------------------------------------------
#Count frames & calculate time of calculations
cnt_fr,time_index=tbf.count_frames(TRAJ,True)
MAX_FR=list(time_index.keys())[-1]
#print(MAX_FR,time_index[MAX_FR])
ST_FR=MAX_FR-NUM_FR
#print(ST_FR,time_index[ST_FR])
###################################################
#--------------------------------------------------
#Read .itp files
#weights={}
#for MOL in ITP_DIC.keys():
......@@ -66,15 +73,12 @@ print(' ')
###################################################
#--------------------------------------------------
if os.path.isfile('./'+SYSTEM_NAME+'/'+SYSTEM_NAME+'_data.pkl'):
if LOG==1:
print('WARNING: Preprocessing files exist.')
print(' Erase data.pkl if the system is new.')
print('--------------------------------------------')
data_all=tbf.frompickle('./'+SYSTEM_NAME+'/'+SYSTEM_NAME+'_data.pkl')
pass
else:
#Read .trr file
data_all=tbf.fr_export(trajfile=TRAJ,num_frames=NUM_FR)
tbf.topickle(fl=data_all, sv_name='./'+SYSTEM_NAME+'/'+SYSTEM_NAME+'_data')
del data_all
###################################################
#--------------------------------------------------
#Check save files if exist in order to skip functions
......@@ -112,24 +116,18 @@ for i in GROUPS.keys():
#not COMBINE section
if i!='COMBINE':
if os.path.isfile('./'+SYSTEM_NAME+'/'+SYSTEM_NAME+'_'+i+'_ndx.pkl'):
if LOG==1:
print('WARNING: Preprocessing files exist.')
print(' Erase ndx_HEAD.pkl if the system is new.')
print('--------------------------------------------')
group_ndx=tbf.frompickle('./'+SYSTEM_NAME+'/'+SYSTEM_NAME+'_'+i+'_ndx.pkl')
pass
else:
#Find atom type index in lists created above
group_ndx=tbf.atomid_data(res_num, res_type, atom_type, atom_num, group=locals()[i])
tbf.topickle(fl=group_ndx, sv_name='./'+SYSTEM_NAME+'/'+SYSTEM_NAME+'_'+i+'_ndx')
del group_ndx
#--------------------------------------------------
if os.path.isfile('./'+SYSTEM_NAME+'/'+SYSTEM_NAME+'_'+i+'_box.pkl'):
if LOG==1:
print('WARNING: Preprocessing files exist.')
print(' Erase box.pkl if the system is new')
print(' or new grid is applied !')
print('--------------------------------------------')
box_res=tbf.frompickle('./'+SYSTEM_NAME+'/'+SYSTEM_NAME+'_'+i+'_box.pkl')
pass
else:
data_all=tbf.frompickle('./'+SYSTEM_NAME+'/'+SYSTEM_NAME+'_data.pkl')
group_ndx=tbf.frompickle('./'+SYSTEM_NAME+'/'+SYSTEM_NAME+'_'+i+'_ndx.pkl')
#Create subdomains coordinates
box_p=tbf.domain_decomposition(data=data_all,dx=DISCET[0],dy=DISCET[1],dz=DISCET[2])
#Assign desired atoms (from above function) to subdomains
......@@ -137,14 +135,32 @@ for i in GROUPS.keys():
##result2: {step:{res:{atom_type:{(subX,subYsubZ):[atom_num]}}}}
_,box_res=tbf.atom2grid(data_all,box_p, group_ndx)
tbf.topickle(fl=box_res, sv_name='./'+SYSTEM_NAME+'/'+SYSTEM_NAME+'_'+i+'_box')
del data_all
del group_ndx
del box_p
del box_res
###################################################
if os.path.isfile('./'+SYSTEM_NAME+'/'+SYSTEM_NAME+'_'+i+'_FR'+str(NUM_FR)+'.pkl'):
pass
else:
#Creates dictionary with coordinates per subdomain for each frame
data_all=tbf.frompickle('./'+SYSTEM_NAME+'/'+SYSTEM_NAME+'_data.pkl')
box_res=tbf.frompickle('./'+SYSTEM_NAME+'/'+SYSTEM_NAME+'_'+i+'_box.pkl')
_,coord_vector=tbf.sub_coord(box=box_res, data=data_all, res_num=res_num)
tbf.topickle(fl=coord_vector, sv_name='./'+SYSTEM_NAME+'/'+SYSTEM_NAME+'_'+i+'_FR'+str(NUM_FR))
del data_all
del box_res
del coord_vector
###################################################
#Creates dictionary with coordinates per subdomain for each frame
_,coord_vector=tbf.sub_coord(box=box_res, data=data_all, res_num=res_num)
for j in GROUPS[i]:
if len(j) > 1:
if j=='surf' and sv_index[j]['status']=='not exist':
if j not in locals():
surf={}
#Creates dictionary with c, normal per subdomain for each frame
coord_vector=tbf.frompickle('./'+SYSTEM_NAME+'/'+SYSTEM_NAME+'_'+i+'_FR'+str(NUM_FR)+'.pkl')
surf[i]=tbf.coord2norm2cg(coord_vector,img=False)
del coord_vector
sv_data=surf[i]
elif j=='surf' and sv_index[j]['status']=='exist':
if j not in locals():
......@@ -154,7 +170,9 @@ for i in GROUPS.keys():
if j=='vector' and sv_index[j]['status']=='not exist':
if j not in locals():
vector={}
coord_vector=tbf.frompickle('./'+SYSTEM_NAME+'/'+SYSTEM_NAME+'_'+i+'_FR'+str(NUM_FR)+'.pkl')
vector[i]=tbf.coord2vector(coord_vector)
del coord_vector
sv_data=vector[i]
elif j=='vector' and sv_index[j]['status']=='exist':
if j not in locals():
......@@ -171,12 +189,15 @@ for i in GROUPS.keys():
dens_df={}
for iidd in uniq_id.keys():
dens_df[iidd]={}
fl='./'+uniq_id[iidd]['system']+'/gmx_ndx/'+uniq_id[iidd]['ndx_file']
fl='./'+uniq_id[iidd]['system']+'/gmx_ndx/'+uniq_id[iidd]['ndx_file']
cnt=-1
for mol in locals()[i].keys():
ind=tbf.search_pattern(fl,mol)
if ind=='not exist':
break
cnt=cnt+1
for d in ('x','y','z'):
peaks = tbgmx.density_picks(TRR=TRAJ,TPR=TPR,IND=fl,SLC=400,ST=1000,EN=-1,normal=d,fld='./'+uniq_id[iidd]['system'],arg=cnt,dist_pk=20)
peaks = tbgmx.density_picks(TRR=TRAJ,TPR=TPR,IND=fl,SLC=400,ST=time_index[ST_FR],EN=-1,normal=d,fld='./'+uniq_id[iidd]['system'],arg=cnt,dist_pk=20)
if d=='x':
tmp=peaks
else:
......@@ -191,7 +212,9 @@ for i in GROUPS.keys():
dens_df=tbf.frompickle(sv_index[j]['name'])
#--------------------------------------------------
if j=='gmx_ndx':
box_res=tbf.frompickle('./'+SYSTEM_NAME+'/'+SYSTEM_NAME+'_'+i+'_box.pkl')
tbf.togmxndx(box_res, fld='./'+SYSTEM_NAME, sv_name=SYSTEM_NAME+'_'+i)
del box_res
#--------------------------------------------------
# Save module
if len(j)==3:
......@@ -214,16 +237,20 @@ for i in GROUPS.keys():
if j[0]!='COMB':
if j[1]=='surf':
surf=surf[j[0]]
#del surf[j[0]]
if j[1]=='vector':
vector=vector[j[0]]
#del vector[j[0]]
#Calculate COMBINE property
if j[0]=='COMB':
if j[1]=='tilt' and sv_index[str(j)]['status']=='not exist':
tilt=tbf.SurfVector_angle(surf,vector)
del surf
del vector
#Loop over timesteps and keep avgs tilts for each step
avg={}
ss=[]
for step in tilt.keys():
ss=[]
for sub in tilt[step].keys():
avgs=tilt[step][sub]['avg/frame']
if sub not in ss:
......@@ -231,6 +258,7 @@ for i in GROUPS.keys():
avg[sub]=avgs
else:
avg[sub].append(avgs)
del tilt
#Calculate total average
tot_avg={}
for sub in avg.keys():
......
tooba_f.py
View file @ 2fef443c
......@@ -5,6 +5,7 @@ import matplotlib.pyplot as plt
import scipy.optimize
import pickle as pkl
import json
import re
from progress.bar import Bar
from pytrr import (
......@@ -13,6 +14,18 @@ from pytrr import (
skip_trr_data,
)
def search_pattern(fl,pattern):
textfile = open(fl, 'r')
filetext = textfile.read()
textfile.close()
matches = re.findall(pattern, filetext)
if len(matches)==0:
ind='not exist'
else:
ind='exist'
return ind
def fitPlaneLTSQ(XYZ):
#Source: https://gist.github.com/RustingSword/e22a11e1d391f2ab1f2c
(rows, cols) = XYZ.shape
......@@ -123,23 +136,30 @@ def points2vector(data):
return vv[0]
def count_frames(trajfile='traj.trr'):
def count_frames(trajfile='traj.trr', pr_time=False):
"""
Count total frames of .trr file
parameters: trajfile = [.trr]
"""
time_index={}
cnt_fr=0
with open(trajfile, 'rb') as inputfile:
for i in range(1000):
for i in range(1000000):
try:
header = read_trr_header(inputfile)
#print('Step: {step}, time: {time}'.format(**header))
skip_trr_data(inputfile, header)
if pr_time==True:
#print('Step: {step}, time: {time}'.format(**header))
#print('Step: {step}, time: {time}'.format(**header))
time_index[cnt_fr]='{time}'.format(**header)
cnt_fr=cnt_fr+1
except EOFError:
pass
return cnt_fr
if pr_time==True:
return cnt_fr,time_index
else:
return cnt_fr
def fr_export(trajfile='traj.trr', num_frames=1):
"""
......@@ -616,10 +636,11 @@ def coord2norm2cg(coord_vector,img=True):
surf_points=coord_vector[step][subdomain][resid]
else:
surf_points=surf_points+coord_vector[step][subdomain][resid]
c,normal = fitPlaneLTSQ(np.array(surf_points))
surf[step][subdomain]={'c':c, 'normal':normal}
surf[step][subdomain].update(res_cg)
if img==True:
fl_save='png/'
save=fl_save+str(subdomain)
......@@ -643,7 +664,7 @@ def coord2vector(coord_vector):
output: dictionary = {step:{subdomain:{resid:[x, y, z]}}
"""
print(' ')
print('Finding surface progress:')
print('Finding vector progress:')
print('==============================')
vector={}
for step in coord_vector.keys():
......@@ -652,7 +673,10 @@ def coord2vector(coord_vector):
for subdomain in coord_vector[step].keys():
vector[step][subdomain]={}
for resid in coord_vector[step][subdomain].keys():
vv = points2vector(np.array(coord_vector[step][subdomain][resid]))
grp=[]
for ii in coord_vector[step][subdomain][resid]:
grp.append(ii)
vv = points2vector(np.array(grp))
vector[step][subdomain][resid]=vv
bar.next()
bar.finish()
......@@ -676,6 +700,11 @@ def SurfVector_angle(surf,vector):
angle[step]={}
bar = Bar('Step: '+step, max=len(surf[step].keys()))
for sudomain in surf[step].keys():
try:
vector[step][sudomain].keys()
except KeyError:
#print(step, sudomain)
continue
angle[step][sudomain]={}
tot=[]
for resid in vector[step][sudomain].keys():
......
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