diff --git a/.gitignore b/.gitignore index 51a08d73f0d66cac7783a9a8a3b693ec16a90f50..3b485632b1083f78911e68c64113b2e228526618 100644 --- a/.gitignore +++ b/.gitignore @@ -1,5 +1,4 @@ .gitignore -FORTRAN_vscode/ __pycache__/ .venv/ .vscode/ @@ -12,4 +11,4 @@ __pycache__/ *.code-workspace *.itp system/ -20190322_10 \ No newline at end of file +Case4_20190909_5 \ No newline at end of file diff --git a/main.py b/main.py index 0b2b1f26bec406acebf1c843abfe58a13070e18f..ce608f3ff01ee48ff558812f3e3225ab58d43256 100644 --- a/main.py +++ b/main.py @@ -1,4 +1,5 @@ import os +from collections import OrderedDict import pandas as pd import tooba_f as tbf import tooba_gmx as tbgmx @@ -8,7 +9,7 @@ import tooba_gmx as tbgmx # in case of tail is the one closest to the head, hence # the code is a good approximation ################################################### -SYSTEM_NAME='20190322_10' +SYSTEM_NAME='Case4_20190909_5' DISCET=[3.5, 3.5, 3.5] NUM_FR=750 TRAJ=SYSTEM_NAME+'/eq_traj.trr' @@ -39,6 +40,7 @@ TPR=SYSTEM_NAME+'/eq_run.tpr' # [save, [TYPE], SAVE_NAME]: Save result of previous function, type: pkl, json # ################################################### +GROUPS=OrderedDict() GROUPS={'ALL':['index+ALL_ndx',['save', ['pkl'],'index'],'density',['save', ['pkl'],'dens']], 'HD_GROUP':['surf',['save', ['pkl', 'json'],'surf'],'index+HD_ndx',['save', ['pkl'],'index'],'rdf',['save', ['pkl'],'rdf']], 'TL_GROUP':['vector',['save', ['pkl'],'vec']], @@ -48,12 +50,19 @@ GROUPS={'ALL':['index+ALL_ndx',['save', ['pkl'],'index'],'density',['save', ['pk 'ORDER_CHOL':['index_order+ORDER_CHOL_ndx',['save', ['pkl'],'index'],'order',['save',['pkl'], 'order']], 'COMBINE':[['HD_GROUP','surf'],['TL_GROUP','vector'],['COMB','tilt'],['save', ['pkl'],'tilt']] } +ALL=OrderedDict() ALL={'NS':['C1', 'C2', 'C3', 'C4', 'C5','C6', 'Na', 'P4', 'P3', 'C7','C3', 'C4', 'C5', 'C8', 'C9', 'C10'], 'CHOL':['ROH','R1', 'R2', 'R3', 'R4', 'R5'], 'FFA':['AC','C1', 'C2', 'C3', 'C4']} +HD_GROUP=OrderedDict() HD_GROUP={'NS':['C6', 'Na', 'P4', 'P3', 'C7'], 'CHOL':['ROH'], 'FFA':['AC']} +TL_GROUP=OrderedDict() TL_GROUP={'NS':['C3', 'C4', 'C5', 'C8', 'C9', 'C10'], 'CHOL':['R1', 'R2', 'R3', 'R4', 'R5'], 'FFA':['C1', 'C2', 'C3', 'C4']} +ORDER_NS_SPH=OrderedDict() ORDER_NS_SPH={'NS':['C1', 'C2', 'C3', 'C4', 'C5']} #propable problem with the same atomname of NS, FFA +ORDER_NS_ACYL=OrderedDict() ORDER_NS_ACYL={'NS':['C8', 'C9', 'C10']} +ORDER_FFA=OrderedDict() ORDER_FFA={'FFA':['C1', 'C2', 'C3', 'C4']} +ORDER_CHOL=OrderedDict() ORDER_CHOL={'CHOL':['R2', 'R3', 'R4', 'R5']} ################################################### ################################################### diff --git a/requirements.txt b/requirements.txt index 451c7be195235ccee9d5795f898d591bc10ae3c2..bb90f7a1604aeacb27f36eff5a4a0ce7ecfbc191 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,11 +1,11 @@ numpy scipy -mpl_toolkits +#mpl_toolkits matplotlib pytrr pandas -pickle -json +#pickle +#json progress.bar -subprocess -hashlib \ No newline at end of file +#subprocess +#hashlib \ No newline at end of file