Merge pull request #22 from calpolyccg/development

MD-SAPT 1.1.0

docs/conf.py

@@ -22,15 +22,15 @@
 
 # -- Project information -----------------------------------------------------
 
-project = 'mdsapt'
-copyright = ("2021, Alia Lescoulie. Project structure based on the "
+project = 'MD-SAPT'
+copyright = ("2021, Alia Lescoulie, Astrid Yu, and Ashley Ringer McDonald. Cal Poly Computational Chemistry Group. Project structure based on the "
              "Computational Molecular Science Python Cookiecutter version 1.6")
 author = 'Alia Lescoulie'
 
 # The short X.Y version
-version = ''
+version = '1.1'
 # The full version, including alpha/beta/rc tags
-release = ''
+release = '1.1.0'
 
 
 # -- General configuration ---------------------------------------------------
@@ -154,7 +154,7 @@
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
 man_pages = [
-    (master_doc, 'mdsapt', 'mdsapt Documentation',
+    (master_doc, 'MD-SAPT', 'mdsapt Documentation',
      [author], 1)
 ]
 

docs/index.rst

@@ -1,13 +1,15 @@
-MDSAPT Documentation
+MD-SAPT Documentation
 =========================================================
 
-**MDSAPT** is a Python package and `MDAnalysis <https://www.mdanalysis.org>`_ Kit for preforming
+**MD-SAPT** is a Python package and `MDAnalysis <https://www.mdanalysis.org>`_ Kit for preforming
 Symmetry Adapted Perturbation Theory (SAPT) calculations on molecular dynamics (MD) simulation
 trajectories using `Psi4 <https://psicode.org>`_.
 
-Currently MDSAPT is installable via GitHub and supports measuring interactions between ligands and
+Currently MD-SAPT is installable via GitHub and supports measuring interactions between ligands and
 standard amino acids.
 
+
+
 .. toctree::
    :maxdepth: 4
    :numbered:

docs/install.rst

@@ -1,9 +1,16 @@
 Installation
 ============
 
-Currently MD-SAPT is not available via any packaging system. It must be installed
-by cloning the GitHub repository.
+MD-SAPT can be installed by cloning the GitHub repository.
 
 .. code-block:: bash
-    git clone https://github.com/ALescoulie/MDSAPT.git
+
+    git clone https://github.com/calpolyccg/MDSAPT.git
     pip install ./MDSAPT
+
+MD-SAPT can also be installed from conda.
+
+.. code-block:: bash
+
+    conda install -c psi4 MDSAPT
+

docs/quick.rst

@@ -28,7 +28,7 @@ The following steps describe how to set up the input yaml file
 Running SAPT
 ____________
 
-With the input done MDSAPT is ready to be run. The settings are read using :class:`mdsapt.reader.InputReader`  which is then passed into :class:`mdsapt.reader.Optimizer` which handles preparing residues. Finally :class:`mdsapt.reader.TrajectorySAPT` is used to run SAPT over the MD data. The results are stored in a :class:`Pandas.DataFrame`.
+With the input done MD-SAPT is ready to be run. The settings are read using :class:`mdsapt.reader.InputReader`  which is then passed into :class:`mdsapt.reader.Optimizer` which handles preparing residues. Finally :class:`mdsapt.reader.TrajectorySAPT` is used to run SAPT over the MD data. The results are stored in a :class:`Pandas.DataFrame`.
 
 .. code-block:: Python
 

docs/scripts.rst

@@ -9,6 +9,7 @@ _____________________
 Usage
 
 .. code-block:: bash
+
     python mdsapt_get_runinput.py filename
 
 `mdsapt_run_sapt`
@@ -17,5 +18,6 @@ _________________
 Usage
 
 .. code-block:: bash
+
     python mdsapt_run_sapt.py input.yaml results.out
 

mdsapt/sapt.py

@@ -57,7 +57,7 @@ class TrajectorySAPT(AnalysisBase):
     _basis: str
     _settings: Dict[str, str]
     results: pd.DataFrame
-    _mht_to_kcalmol: float = 627529
+    _mht_to_kcalmol: float = 627.509
 
     def __init__(self, config: InputReader, optimizer: Optimizer, **universe_kwargs) -> None:
         """Sets up Trajectory and residue selections.
@@ -88,7 +88,8 @@ def __init__(self, config: InputReader, optimizer: Optimizer, **universe_kwargs)
         super(TrajectorySAPT, self).__init__(self._unv.trajectory)
 
     def _prepare(self) -> None:
-        self._col = ['residues', 'time', 'energy']
+        self._col = ['residues', 'time', 'total', 'electrostatic',
+                     'exchange', 'induction', 'dispersion']
         self.results = pd.DataFrame(columns=self._col)
         self._res_dict = {x: [] for x in self._col}
 
@@ -108,15 +109,24 @@ def _single_frame(self) -> None:
             dimer = psi4.geometry(coords)
             psi4.set_options(self._settings)
             psi4.set_memory(self._mem)
+            psi4.set_num_threads(self._cfg.ncpus)
 
             logger.info(f'Starting SAPT for {pair}')
 
             if self._save_psi_out:
                 psi4.set_output_file(f'sapt_{pair[0]}-{pair[1]}_{self._ts.time}.out')  # Saves output file
 
+            # Calculating SAPT
             psi4.energy(f'{self._method}/{self._basis}', molecule=dimer)
-            sapt = psi4.variable('SAPT TOTAL ENERGY')
-            result = [f'{pair[0]}-{pair[1]}', self._ts.time, sapt*self._mht_to_kcalmol]
+
+            # Getting results
+            sapt_tot = psi4.variable('SAPT TOTAL ENERGY')*self._mht_to_kcalmol
+            sapt_col = psi4.variable('SAPT ELST ENERGY')*self._mht_to_kcalmol
+            sapt_exh = psi4.variable('SAPT EXCH ENERGY')*self._mht_to_kcalmol
+            sapt_ind = psi4.variable('SAPT IND ENERGY')*self._mht_to_kcalmol
+            sapt_dsp = psi4.variable('SAPT DISP ENERGY')*self._mht_to_kcalmol
+
+            result = [f'{pair[0]}-{pair[1]}', self._ts.time, sapt_tot, sapt_col, sapt_exh, sapt_ind, sapt_dsp]
             for r in range(len(result)):
                 self._res_dict[self._col[r]].append(result[r])
 

mdsapt/tests/test_reader.py

@@ -19,8 +19,8 @@ class TestInputReader(object):
             'step': 1
         },
         'system_settings': {
-            'ncpus': 4,
-            'memory': '12GB',
+            'ncpus': 16,
+            'memory': '48GB',
             'time': '24:00:00'
         },
         'opt_settings': {

mdsapt/tests/test_sapt.py

@@ -25,4 +25,9 @@ def setup(self):
 
     def test_run_sapt(self):
         SAPT12 = TrajectorySAPT(self.settings, self.opt)
-        SAPT12.run(self.settings.trj_settings['start'], self.settings.trj_settings['stop'], self.settings.trj_settings['step'])
+        SAPT12.run(self.settings.trj_settings['start'], self.settings.trj_settings['stop'], self.settings.trj_settings['step'])
+        cols_act = SAPT12.results.columns
+        cols_exp = ['residues', 'time', 'total', 'electrostatic', 'exchange', 'induction', 'dispersion']
+        assert (len(cols_act) == len(cols_exp))
+        assert all([cols_act[i] == cols_exp[i] for i in range(len(cols_act))])
+        SAPT12.results.to_csv('sapt_test.csv')

mdsapt/tests/testing_resources/test_input.yaml

@@ -12,8 +12,8 @@ trajectory_settings:
   stop: 2
   step: 1
 system_settings:
-  ncpus: 4
-  memory: 12GB
+  ncpus: 16
+  memory: 48GB
   time: '24:00:00'
 opt_settings:
   pH: 7.0