Merge branch 'master' of github.com:dimonaks/siman

dimonaks · Aug 10, 2018 · 3c813d7 · 3c813d7
2 parents 64267df + 91a0b61
commit 3c813d7
Showing 1 changed file with 25 additions and 106 deletions.
diff --git a/project_template/project_conf.py b/project_template/project_conf.py
@@ -1,45 +1,38 @@
 # -*- coding: utf-8 -*-
 """
 Control of project
-
-TODO:
-cif2cell installation check or add to siman
 """
 from __future__ import division, unicode_literals, absolute_import 
 
-NEW_BATCH = True   # for testing new batch system based on set sequences 
-
-PBS_PROCS = True # if true than #PBS -l procs="+str(number_cores) is used
-WALLTIME_LIMIT = True
+"""General parameters"""
+PATH2POTENTIALS = '/home/aksenov/scientific_projects/PAW_PBE_VASP'
+pmgkey = "AWqKPyV8EmTRlf1t" # please get your own key from materials project for pymatgen
+PATH2DATABASE        = '/home/aksenov/Data/CEStorage/'
+PATH2JMOL  = 'jmol'
+PATH2NEBMAKE = '~/Simulation_wrapper/vts/nebmake.pl' # http://theory.cm.utexas.edu/vasp/scripts.html
+geo_folder           = './' # duplicate structures using .geo format files in this folder
 
-"""Cluster constants"""
-# cluster_address = '[email protected]' #
-# CLUSTER_ADDRESS = cluster_address
-# cluster_home    = '/home/aksenov/' # needed only for SLURM std out and std err
-# CLUSTER_PYTHONPATH = '/usr/lib64/python2.7/site-packages/numpy'
 
-# SCHEDULE_SYSTEM = 'SLURM' #see write_batch_header()
-# corenum = 16; #queue = ' -l cmmd '
-# CORENUM = corenum
 
-CLUSTERS = {}
-DEFAULT_CLUSTER = 'cee'
+"""Cluster parameters"""
 PATH2PROJECT = '' # path to project on cluster relative to home folder
-# project_path_cluster = '' 
-# PATH_TO_PROJECT_ON_CLUSTER = project_path_cluster
-
+DEFAULT_CLUSTER = 'cee'
+PBS_PROCS = True # if true than #PBS -l procs="+str(number_cores) is used
+WALLTIME_LIMIT = True
 
-CLUSTERS['cee'] = {'address':'[email protected]',
+#description of user clusters:
+CLUSTERS = {}
+CLUSTERS['cee'] = {
+'address':'[email protected]',
 'vasp_com':'prun /opt/vasp/bin/vasp5.4.1MPI_aksenov',
-# 'vasp_com':'prun /opt/vasp/bin/vasp5.4.1MPI_ncl',
-
 'homepath':'/home/aksenov/',
 'schedule':'SLURM',
 'corenum':16,
 'pythonpath':'/usr/lib64/python2.7/site-packages/numpy'
 }
 
-CLUSTERS['skol'] = {'address':'[email protected]',
+CLUSTERS['skol'] = {
+'address':'[email protected]',
 'vasp_com':'mpirun  vasp_std',
 'homepath':'/home/Dmitry.Aksenov/',
 'schedule':'PBS',
@@ -49,7 +42,8 @@
 'modules':'module load Compilers/Intel/psxe_2015.6; module load MPI/intel/5.1.3.258/intel; module load QCh/VASP/5.4.1p1/psxe2015.6; module load ScriptLang/python/2.7',
 }
 
-CLUSTERS['bsu'] = {'address':'[email protected]',
+CLUSTERS['bsu'] = {
+'address':'[email protected]',
 'vasp_com':'mpiexec --prefix /home/aleksenov_d/mpi/openmpi-1.6.3/installed vasp',
 'homepath':'/home/aleksenov_d',
 'schedule':'PBS',
@@ -60,96 +54,21 @@
 
 
 
-
-
-"""Local constants"""
-PATH2POTENTIALS = '/home/aksenov/scientific_projects/PAW_PBE_VASP'
-pmgkey = "AWqKPyV8EmTRlf1t"
-
-path_to_paper        = '/home/aksenov/Research/CEStorage/aksenov_report/'
-# PATH2DATABASE        = '/home/aksenov/Data/CEStorage/_aksenov'
-PATH2DATABASE        = '/home/aksenov/Data/CEStorage/'
-# gb4_geo_folder       = '/home/dim/Simulation_wrapper/gb4/out/'
-#we have gb5!
-PATH2JMOL  = 'jmol'
-PATH2NEBMAKE = '~/Simulation_wrapper/vts/nebmake.pl'
-
-geo_folder           = './'
-# path_to_images       = '/home/aksenov/ydisk/cathode_report/images/'
-path_to_images       = path_to_paper+'/fig/'
-# path_to_jmol         = '/home/dim/installed/jmol-14.2.12_2015.02.11/jmol.sh '
-path_to_wrapper      = '/home/aksenov/Simulation_wrapper/'
-
+"""Other parameters for developers, can be removed"""
+NEW_BATCH = True   # for testing new batch system based on set sequences 
 # RAMDISK              = '/mnt/ramdisk/'
 RAMDISK              = None
 EXCLUDE_NODES  = 1
-
-
-"""List of constants determined during installation"""
 CIF2CELL = True 
-
-
-
-
+path_to_wrapper      = '/home/aksenov/Simulation_wrapper/'
+path_to_images       = path_to_paper+'/fig/'
+path_to_paper        = '/home/aksenov/Research/CEStorage/aksenov_report/'
 
 
 """List of manually added calculations:"""
+#Deprecated, now not really needed
 MANUALLY_ADDED = [# calc name, calc folder, calc des  
     ( 'Li111'        ,"Li",        "2 Li"                                  ),
     ( 'Rb111'        ,"Rb/bcc",        "2 Rb"                                  ),
     ]
 
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-"""
-Naming conventions:
-
-endings:
-'_ml' - was used to show that this calculation uses manual equilibrium lattice determination and 
-contains several versions of identical structures with different
-lattice constants. Now not in use, because I always use this method. Usually 16 versions for hcp;
-
-'_r' - calculation with structure constructed for fitted lattice constants; 
-Now was replaced with '.f'; Usually one version.
-'.ur' - unrelaxed
-.r - relaxed atomic positions
-.o - optimised cell and volume and atomic positions automatically
-'.f'  - fitted
-'.fr' - means that current calculation based on the structure for which lattice constants were fitted and
-positions of atoms were relaxed. However see description to know for wich set they were fitted and relaxed.
-Calculations with '.f' and '.fr' can have different versions which are correspondig to different sets.
-
-.m - only matrix, all impurities were removed and matrix was freezed
-
-
-letters in name, wich are usually between didgits and element's names:
-b - stands for bulk, which denote ideal cells without boundaries.
-g - cells with grain boundary;
-v - means that impurity is in the volume of grain; far away from boundaries;
-i - means that impurity is close to interface plane (grain boundary)
-
-Versions:
-20 - usually means that lattice constatns was used from other calculation and this is very good assumtion.
-
-
-"""
-
-
-