Second revision edits for CrystEngComm

README.md

@@ -7,16 +7,25 @@ IPMOF uses Python 3.5.1 with required libraries listed in requirements.txt file.
 
 You can install IPMOF by cloning the repository and running setup.py as follows:
 
-`git clone https://github.com/kbsezginel/IPMOF.git`
+```python
+git clone https://github.com/kbsezginel/IPMOF.git
+cd IPMOF
+python setup.py install
+```
 
-`cd IPMOF`
+If you wish to use HPC capabilities you need to install other dependencies:
 
-`python setup.py install`
+```python
+pip install -r requirements_hpc.txt
+```
 
-If you wish to use HPC capabilities you need to install other dependencies:
+For mathutils python package (used in rotation operations), additional installation might be necessary.
 
-`pip install -r requirements_hpc.txt`
+In linux the following dependency for mathutils can be installed by:
 
+```python
+sudo apt-get install python3-dev
+```
 ## Usage
 IPMOF reads structure files from the mof folder in root directory.
 
@@ -47,7 +56,9 @@ fashion: _full_ > _uniq_ > _qnd_ > _dummy_. All list types except for _uniq_ all
 
 **To generate energy map type following in a command-line window:**
 
-`python ipmof_energymap.py`
+```python
+python ipmof_energymap.py
+```
 
 By default this will create energy maps for each MOF file in _~/mof_ directory. The atom list and energy map are stored as a numpy array. This can be changed to a human readable format (yaml) by changing the _energy_map_type_ simulation parameter to _yaml_.
 
@@ -59,7 +70,9 @@ Energy map is required only for the _passive_ MOF (should be in _~/energymap_) a
 
 **To test intepenetration type following in a command-line window:**
 
-`python ipmof_interpenetration.py`
+```python
+python ipmof_interpenetration.py
+```
 
 Simulation summary, simulation parameters, and information on discovered structures will be exported to _~/results/*Structure1_Structure2*/results.yaml_. Methods to analyze results are included in _~ipmof/analysis.py_ library. The structures discovered will be exported to _~/results/*Structure1_Structure2*_.
 

ipmof/interpenetration.py

@@ -5,6 +5,7 @@
 import shutil
 import time
 import math
+import yaml
 from random import random
 from glob import glob
 
@@ -377,7 +378,9 @@ def get_interpenetration_list(sim_par, sim_dir):
 
     Format: interpenetration_list = {'emap_path': [], 'emap_mof_path': [], 'ip_mof_path': []}
     """
-    if sim_par['core_database']:
+    if sim_par['interpenetration_list'] is not None:
+        interpenetration_list = yaml.load(open(sim_par['interpenetration_list'], 'r'))
+    elif sim_par['core_database']:
         if sim_par['core_limit'] is not None:
             interpenetration_list = core_interpenetration_list(sim_dir, limit=sim_par['core_limit'])
         else:

ipmof/parameters.py

@@ -21,6 +21,7 @@
                 'energy_map_atom_list': 'uniq',  # Atom list for energy map ('full', 'uniq', 'dummy', 'qnd')
                 'energy_map_type': 'numpy',      # Energy map file format ('numpy' or 'yaml')
                 'self_interpenetration': True,   # Test for homo-interpenetration or not
+                'interpenetration_list': None,  # Interpenetration list in yaml format
                 'report_structures': 10,         # Number of min. energy structures to report in results
                 'export_structures': 1,          # Number of min. energy structures to export
                 'export_format': 'cif',          # Export structure file format

settings/sim_par.sample.yaml

@@ -10,6 +10,7 @@ rotation_freedom: 30
 try_all_rotations: false
 force_field: uff
 self_interpenetration: true
+interpenetration_list: None
 energy_map_atom_list: uniq
 energy_map_type: numpy
 report_structures: 10