New functions+debuging

.gitignore

@@ -8,4 +8,6 @@ __pycache__/
 *.pkl
 *.trr
 *.gro
-*.code-workspace
\ No newline at end of file
+*.code-workspace
+*.itp
+system/
\ No newline at end of file

CHANGELOG

@@ -6,6 +6,18 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+## [0.0.5] - 2020-05-20
+### Added
+- Add progress bar per function
+- Save preprocessing arrays to pickles and read them if exist for speed up whole process
+- new function to calculate surface per subdomain (different input) 
+
+### Changed
+- debug atomid_data function
+
+### Removed
+- None
+
 ## [0.0.4] - 2020-05-19
 ### Added
 - code for print data in json and pickle format

main.py

+import os
 import tooba_f as tbf
 ###################################################
 #NOTICE:    resids of head in each subdomain may differ in tail case
@@ -5,46 +6,75 @@ import tooba_f as tbf
 #           in case of tail is the one closest to the head, hence
 #           the code is a good approximation 
 ###################################################
-TRAJ='traj.trr'
+TRAJ='system/eq_traj.trr'
 NUM_FR=1
-GRO='initial.gro'
+GRO='system/eq_final.gro'
 HEAD=True
-HD_GROUP={'MMA':['C1', 'C2']}
+HD_GROUP={'NS':['C6', 'Na', 'P4', 'P3', 'C7'], 'CHOL':['ROH'], 'FFA':['AC']}
 TAIL=False
-TL_GROUP={'MMA':['C3', 'C4', 'C5']}
-DISCET=[1, 1, 1]
+TL_GROUP={'NS':['C3', 'C4', 'C5', 'C8', 'C9', 'C10'], 'CHOL':['R1', 'R2', 'R3', 'R4', 'R5'], 'FFA':['C1', 'C2', 'C3', 'C4']}
+DISCET=[3, 3, 3]
 RES_NAME='time_domain_c-normal-cg'
 ###################################################
-#Read .trr file
-data_all=tbf.fr_export(trajfile=TRAJ,num_frames=NUM_FR)
+###################################################
+print(' ')
+print('================')
+print('Starting process')
+print('================')
+###################################################
+###################################################
 #Read .gro file
 _,data_num,_,res_num,res_type,atom_type,atom_num,_ = tbf.read_gro(GRO)
-#Create subdomains coordinates
-box_p=tbf.domain_decomposition(data=data_all,dx=DISCET[0],dy=DISCET[1],dz=DISCET[2])
-
+print(' ')
+###################################################
+if os.path.isfile('./data.pkl'):
+    print('WARNING: Preprocessing files exist.')
+    print('         Erase data.pkl if the system is new.')
+    print('--------------------------------------------')
+    data_all=tbf.frompickle('./data.pkl')
+else:
+    #Read .trr file
+    data_all=tbf.fr_export(trajfile=TRAJ,num_frames=NUM_FR)
+    tbf.topickle(fl=data_all, sv_name='data')
 ###################################################
 if HEAD==True:
-    #Find atom type index in lists created above
-    group_ndx=tbf.atomid_data(res_num, atom_type, atom_num, group=HD_GROUP)
+    if os.path.isfile('./ndx_HEAD.pkl'): 
+        print('WARNING: Preprocessing files exist.')
+        print('         Erase ndx_HEAD.pkl if the system is new.')
+        print('--------------------------------------------')
+        group_ndx=tbf.frompickle('./ndx_HEAD.pkl')
+    else:
+        #Find atom type index in lists created above
+        group_ndx=tbf.atomid_data(res_num, res_type, atom_type, atom_num, group=HD_GROUP)
+        tbf.topickle(fl=group_ndx, sv_name='ndx_HEAD')
+###################################################
+if os.path.isfile('./box.pkl'):
+    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('./box.pkl')
+else:
+    #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
     ##result1: {step:{res:{atom_type:{atom_num:(subX,subYsubZ)}}}}
     ##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='box')
+###################################################
+###################################################
+if HEAD==True:
     #Creates dictionary with coordinates per subdomain for each frame
-    coord_norm,_=tbf.sub_coord(box=box_res, data=data_all, res_num=res_num)
+    coord_norm,coord_vector=tbf.sub_coord(box=box_res, data=data_all, res_num=res_num)
     #Creates dictionary with c, normal per subdomain for each frame
-    surf=tbf.coord2norm(coord_norm,img=True)
-
+    surf=tbf.coord2norm2cg(coord_vector,img=True)
+    print(surf)
+    exit()
     tbf.topickle(fl=surf, sv_name=RES_NAME)
     tbf.tojson(fl=surf, sv_name=RES_NAME)
 ###################################################
 if TAIL==True:
-    #Find atom type index in lists created above
-    group_ndx=tbf.atomid_data(res_num, atom_type, atom_num, group=TL_GROUP)
-    #Assign desired atoms (from above function) to subdomains
-    ##result1: {step:{res:{atom_type:{atom_num:(subX,subYsubZ)}}}}
-    ##result2: {step:{res:{atom_type:{(subX,subYsubZ):[atom_num]}}}}
-    _,box_res=tbf.atom2grid(data_all,box_p, group_ndx)
     #Creates dictionary with coordinates per subdomain for each frame
     _,coord_vector=tbf.sub_coord(box=box_res, data=data_all, res_num=res_num)
     vector=tbf.coord2vector(coord_vector)