cleanup includes amat.tmp files (#9)

* cleanup_all removes amat.tmp files which can be quiet large (several Mb) * update README
grimme-lab · Mar 15, 2021 · 8eee434 · 8eee434
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diff --git a/README.rst b/README.rst
@@ -1,8 +1,12 @@
-|GitHub release|
+|GitHub release| |DOI|
 
 .. |GitHub release| image:: https://img.shields.io/github/v/release/grimme-lab/CENSO
    :target: https://github.com/grimme-lab/CENSO/releases/latest
 
+.. |DOI| image:: https://img.shields.io/badge/DOI-10.1021/acs.jpca.1c00971-blue
+    :target: https://doi.org/10.1021/acs.jpca.1c00971
+
+
 ====================================================================
 CENSO - Commandline ENergetic SOrting of Conformer Rotamer Ensembles
 ====================================================================
@@ -78,7 +82,7 @@ settings and provide paths to the external programs e.g. `xtb`, `crest`, `orca`
 Documentation:
 ==============
 
-Can be found following: https://fbohle.gitbook.io/censo/
+Can be found following: https://xtb-docs.readthedocs.io/en/latest/CENSO_docs/censo.html
 
 **Interactive Documentation can be accessed:**
 
@@ -205,6 +209,19 @@ a replacement solvent. E.g. if CCl4 is not available choose CHCl3.
 The solvent file is directly used in `CENSO` and typos will cause calculations to crash!
 Adding a new solvent is as easy as adding a new dictionary to the file.
 
+Cite
+----
+
+General reference:
+
+S. Grimme, F. Bohle, A. Hansen, P. Pracht, S. Spicher, and M. Stahn 
+*J. Phys. Chem. A* **2021**, XXXX, XXX, XXX-XXX.
+
+DOI: `10.1021/acs.jpca.1c00971 <https://doi.org/10.1021/acs.jpca.1c00971>`_. 
+
+Reference is available in `bibtex format <./docs/reference.bib>`_.
+
+
 License
 -------
 

diff --git a/censo_qm/censo.py b/censo_qm/censo.py
@@ -200,41 +200,41 @@ def main(argv=None):
     print(f"{'Input':20}: {ensembledata.nconfs_per_part['starting']:{conflength}}    -")
     if config.part0:
         print(
-            f"{'Part0_all':20}: {ensembledata.nconfs_per_part['part0']:{conflength}}    {ensembledata.part_info['part0']:.2f}s"
+            f"{'Part0_all':20}: {ensembledata.nconfs_per_part['part0']:{conflength}}    {ensembledata.part_info['part0']:.2f} s"
         )
         timings += ensembledata.part_info["part0"]
     if config.part1:
         print(
             f"{'Part1_initial_sort':20}: {ensembledata.nconfs_per_part['part1_firstsort']:{conflength}}    -"
         )
         print(
-            f"{'Part1_all':20}: {ensembledata.nconfs_per_part['part1_firstsort']:{conflength}}    {ensembledata.part_info['part1']:.2f}s"
+            f"{'Part1_all':20}: {ensembledata.nconfs_per_part['part1_firstsort']:{conflength}}    {ensembledata.part_info['part1']:.2f} s"
         )
         timings += ensembledata.part_info["part1"]
     if config.part2:
         print(
             f"{'Part2_opt':20}: {ensembledata.nconfs_per_part['part2_opt']:{conflength}}    -"
         )
         print(
-            f"{'Part2_all':20}: {ensembledata.nconfs_per_part['part2']:{conflength}}    {ensembledata.part_info['part2']:.2f}s"
+            f"{'Part2_all':20}: {ensembledata.nconfs_per_part['part2']:{conflength}}    {ensembledata.part_info['part2']:.2f} s"
         )
         timings += ensembledata.part_info["part2"]
     if config.part3:
         print(
-            f"{'Part3_all':20}: {ensembledata.nconfs_per_part['part3']:{conflength}}    {ensembledata.part_info['part3']:.2f}s"
+            f"{'Part3_all':20}: {ensembledata.nconfs_per_part['part3']:{conflength}}    {ensembledata.part_info['part3']:.2f} s"
         )
         timings += ensembledata.part_info["part3"]
     if config.part4:
         print(
-            f"{'Part4':20}: {'':{conflength}}    {ensembledata.part_info['part4']:.2f}s"
+            f"{'Part4':20}: {'':{conflength}}    {ensembledata.part_info['part4']:.2f} s"
         )
         timings += ensembledata.part_info["part4"]
     if config.optical_rotation:
         print(
-            f"{'Part5':20}: {'':{conflength}}    {ensembledata.part_info['part5']:.2f}s"
+            f"{'Part5':20}: {'':{conflength}}    {ensembledata.part_info['part5']:.2f} s"
         )
         timings += ensembledata.part_info["part5"]
     print("".ljust(int(PLENGTH / 2), "-"))
-    print(f"{'All parts':20}: {'':{conflength}}    {timings:.2f}s")
+    print(f"{'All parts':20}: {'':{conflength}}    {timings:.2f} s")
     print("\nCENSO all done!")
     return 0
diff --git a/censo_qm/cfg.py b/censo_qm/cfg.py
@@ -5,7 +5,7 @@
 """
 import os
 
-__version__ = "1.0.6"
+__version__ = "1.0.7"
 
 DESCR = f"""
          ______________________________________________________________
@@ -20,6 +20,11 @@
         |                     F. Bohle and S. Grimme                   |
         |                                                              |
         |______________________________________________________________|
+
+        Please cite: 
+        S. Grimme, F. Bohle, A. Hansen, P. Pracht, S. Spicher, and M. Stahn 
+        J. Phys. Chem. A 2021, XXXX, XXX, XXX-XXX.
+        DOI: https://doi.org/10.1021/acs.jpca.1c00971
         
         This program is distributed in the hope that it will be useful,
         but WITHOUT ANY WARRANTY; without even the implied warranty of

diff --git a/censo_qm/inputhandling.py b/censo_qm/inputhandling.py
@@ -10,6 +10,7 @@
 import time
 import math
 import sys
+import glob
 from copy import deepcopy
 from collections import OrderedDict
 from .cfg import (
@@ -1760,6 +1761,11 @@ def __init__(self):
             "func3":False,
             "basis3":False,
             # "consider_sym": False, # --> reset all rrho values!
+            # funcJ
+            # basisJ
+            # funcS
+            # basisS
+            # sm4_ j s
         }
 
 
@@ -1914,11 +1920,16 @@ def cleanup_run(self, complete=False):
             if os.path.isdir(os.path.join(self.cwd, "conformer_rotamer_check")):
                 print("Removing conformer_rotamer_check")
                 shutil.rmtree(os.path.join(self.cwd, "conformer_rotamer_check"))
-            # for file in files_in_cwd:
-            #     if 'mat.tmp' in file:
-            #             print(f"Removing: {file}")
-            #             os.remove(os.path.join(self.cwd,file))
-            # remove *mat.tmp files
+            # get files like amat.tmp from COSMO calculation (can be several Mb)
+            files_in_sub_cwd = glob.glob(self.cwd + '/**/**/**/*mat.tmp', recursive=True)
+            size = 0
+            for tmpfile in files_in_sub_cwd:
+                if any(x in tmpfile for x in ['a3mat.tmp', 'a2mat.tmp', 'amat.tmp']):
+                    if os.path.isfile(tmpfile):
+                        size += os.path.getsize(tmpfile)
+                        #print(f"Removing {tmpfile} {os.path.getsize(tmpfile)} byte")
+                        os.remove(tmpfile)
+            print(f"Removed {size/1024} Mb")
             # ask if CONF folders should be removed
 
     def get_method_name(

diff --git a/censo_qm/parallel.py b/censo_qm/parallel.py
@@ -102,10 +102,11 @@ def run_in_parallel(
             # put item on queue
             q.put(item)
             time.sleep(0.02)
+    njobs = q.qsize()
     time.sleep(0.02)
     if changed:
         ENVIRON['PARNODES'] = str(omp)
-    njobs = q.qsize()
+
     if instructdict.get("onlyread", False):
         print(f"\nReading data from {njobs} conformers calculated in previous run.")
     else:

diff --git a/docs/reference.bib b/docs/reference.bib
@@ -0,0 +1,13 @@
+@article{doi:10.1021/acs.jpca.1c00971,
+author = {Grimme, Stefan and Bohle, Fabian and Hansen, Andreas and Pracht, Philipp and Spicher, Sebastian and Stahn, Marcel},
+title = {Efficient Quantum Chemical Calculation of Structure Ensembles and Free Energies for Nonrigid Molecules},
+journal = {The Journal of Physical Chemistry A},
+volume = {0},
+number = {0},
+pages = {null},
+year = {0},
+doi = {10.1021/acs.jpca.1c00971},
+note ={PMID: 33688730},
+URL = {https://doi.org/10.1021/acs.jpca.1c00971},
+eprint = {https://doi.org/10.1021/acs.jpca.1c00971}
+}