Merge pull request #45 from bc118/rename_variables

rename function variables

docs/getting_started/quick_start/fit_a_dihedral_with_Gaussian_and_write_all_files.rst

@@ -22,24 +22,25 @@ Import the required packages.
 
     import unyt as u
     from mosdef_dihedral_fit.dihedral_fit.fit_dihedral_with_gomc import fit_dihedral_with_gomc
+    import os
 
 Select the desired variables, file, and set the temperature.
 
 .. code:: ipython3
 
     # The MoSDeF force field (FF) XML file which will be used.
-    FF_XML_file = 'path_to_file/oplsaa_ethane_HC_CT_CT_HC.xml'
+    forcefield_file = 'path_to_file/oplsaa_ethane_HC_CT_CT_HC.xml'
 
     # The mol2 file which is used.
     mol2_file = 'path_to_file/ethane_aa.mol2'
 
     # The temperature of the Molecular Mechanics (MM) simulation.
     temperature_in_unyt_units = 298.15 * u.Kelvin
 
-    # Choose mixing rule (VDWGeometricSigma_bool) to override the value (True or False)
-    # that was chosen in the force field (FF) XML file.  This variable is not required and will be
-    # selected automatically; however, you should override it if you are unsure of the setting.
-    VDWGeometricSigma_bool = True
+    # Override the chosen mixing rule (combining_rule), 'geometric' or 'lorentz'), 
+    # which was set in the force field (FF) XML file.  This variable is not required and will be
+    # selected automatically; however, you can override it if you are unsure of the setting.
+    combining_rule = 'geometric'
 
     # Atom type naming convention ( str, optional, default=’all_unique’, (‘general’ or ‘all_unique’) )
     # General is safe and recommended since we are using a single FF XML file.
@@ -53,15 +54,15 @@ Select the desired variables, file, and set the temperature.
     # More than 1 Gaussian file can be loaded, allowing the user to run multiple dihedral angles in separate file,
     # minimizing the time required to run the simulations
     # (i.e., the user can split them up into many simulations to obtain the full dihedral rotation).
-    log_files_and_removed_points = {
+    qm_log_file_dict = {
         'path_to_file/HC_CT_CT_HC_multiplicity_1.log': [0],
     }
 
     # The dihedral which is being fit.
     fit_dihedral_atom_types = ['HC', 'CT', 'CT', 'HC']
 
     # All the other dihedrals which can be zeroed in the fitting process, in a nested list
-    zeroed_dihedrals = None
+    zero_dihedral_atom_types = None
 
 
 Run the dihedral fit to fit to the MM simulations:
@@ -72,27 +73,52 @@ Run the dihedral fit to fit to the MM simulations:
     fit_dihedral_with_gomc(
         fit_dihedral_atom_types,
         mol2_file,
-        FF_XML_file,
+        forcefield_file,
         temperature_in_unyt_units,
         gomc_binary_directory,
-        log_files_and_removed_points,
-        zeroed_dihedral_atom_types=zeroed_dihedrals,
+        qm_log_file_dict,
+        zero_dihedral_atom_types=zero_dihedral_atom_types,
         qm_engine="gaussian",
-        VDWGeometricSigma=VDWGeometricSigma_bool,
+        combining_rule=combining_rule,
         atom_type_naming_style='general',
         gomc_cpu_cores=1,
-        fit_min_validated_r_squared=0.99,
-        fit_validation_r_squared_rtol=1e-03
+        r_squared_min=0.99,
+        r_squared_rtol=1e-03
     )
 
+The most important output files:
+
+.. code:: ipython3
+
+    # The OPLS dihedral fit constants
+    print('The OPLS dihedral fit constants:\n')
+    os.system("cat opls_dihedral_k_constants_fit_energy.txt")
+
+    # The converted OPLS to periodic dihedral fit constants
+    print('The converted OPLS to periodic dihedral fit constants:\n')
+    os.system("cat periodic_dihedral_k_constants_fit_energy.txt")
+
+    # The converted OPLS to RB-torsions dihedral fit constants
+    print('The converted OPLS to RB-torsions dihedral fit constants:\n')
+    os.system("cat RB_torsion_k_constants_fit_energy.txt")
+
+    # This file contains the raw points used in the fits (QM - MM_less_dihedral(s)_energy being fit)
+    print('This file contains the raw points used in the fits (QM - MM_less_dihedral(s)_energy being fit):\n')
+    os.system("cat all_normalized_energies_in_kcal_per_mol.txt")
+
+
+The plotted dihedral fits:
+   #. opls_all_single_fit_dihedral_k_constants_figure.pdf
+   #. opls_all_summed_dihedrals_k_constants_figure.pdf
+
 
 Fit a dihedral for propionic acid using Gaussian-style output files
 -------------------------------------------------------------------
 The propionic acid CT-CT-C-OH dihedral fit example is provided below. This is an example where the CT-CT-C-OH is fit for both
 CT-CT-C-OH and CT-CT-C-O, by fitting the CT-CT-C-OH and zeroing the CT-CT-C-O, which makes it easier to fit.
 
 Additionally, one can perform the dihedral fit with QM calculations with any QM engine as long as they are in the
-`Gaussian style output files format <https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/tree/main/mosdef_dihedral_fit/utils/files/gaussian_style_output_files>`_
+`Gaussian style output files format <https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/tree/main/mosdef_dihedral_fit/tests/files/gaussian_style_output_files>`_
 together with the GOMC Molecular Mechanics (MM) engine, and write out all the viable dihedral fits via the standard
 OPLS equation.  It also outputs the periodic dihedral format and the RB torsions format,
 which are analytically converted from the standard OPLS dihedral fit.
@@ -106,24 +132,26 @@ Import the required packages.
 
     import unyt as u
     from mosdef_dihedral_fit.dihedral_fit.fit_dihedral_with_gomc import fit_dihedral_with_gomc
+    import os
 
 Select the desired variables, file, and set the temperature.
 
 .. code:: ipython3
 
     # The MoSDeF force field (FF) XML file which will be used.
-    FF_XML_file = 'path_to_file/oplsaa_CT_CT_C_OH_in_COOH.xml'
+    forcefield_file = 'path_to_file/gmso_oplsaa_CT_CT_C_OH_in_COOH.xml'
 
     # The mol2 file which is used.
     mol2_file = 'path_to_file/CT_CT_C_3_OH.mol2'
 
     # The temperature of the Molecular Mechanics (MM) simulation.
-    temperature_in_unyt_units = 298.15 * u.Kelvin
+    temperature_in_unyt_units = 25 * u.Celcius
 
-    # Choose mixing rule (VDWGeometricSigma_bool) to override the value (True or False)
-    # that was chosen in the force field (FF) XML file.  This variable is not required and will be
-    # selected automatically; however, you should override it if you are unsure of the setting.
-    VDWGeometricSigma_bool = True
+
+    # Override the chosen mixing rule (combining_rule), 'geometric' or 'lorentz'), 
+    # which was set in the force field (FF) XML file.  This variable is not required and will be
+    # selected automatically; however, you can override it if you are unsure of the setting.
+    combining_rule = 'geometric'
 
     # Atom type naming convention ( str, optional, default=’all_unique’, (‘general’ or ‘all_unique’) )
     # General is safe and recommended since we are using a single FF XML file.
@@ -137,7 +165,7 @@ Select the desired variables, file, and set the temperature.
     # More than 1 Gaussian file can be loaded, allowing the user to run multiple dihedral angles in separate file,
     # minimizing the time required to run the simulations
     # (i.e., the user can split them up into many simulations to obtain the full dihedral rotation).
-    log_files_and_removed_points = {
+    qm_log_file_dict = {
         'path_to_file/output_folder_part_1': [],
 	'path_to_file/output_folder_part_2': [],
     }
@@ -146,7 +174,7 @@ Select the desired variables, file, and set the temperature.
     fit_dihedral_atom_types = ['CT', 'CT', 'C', 'OH']
 
     # All the other dihedrals which can be zeroed in the fitting process, in a nested list
-    zeroed_dihedrals = [['CT', 'CT', 'C', 'O_3']]
+    zero_dihedral_atom_types = [['CT', 'CT', 'C', 'O_3']]
 
 Run the dihedral fit to fit to the MM simulations:
 
@@ -156,16 +184,41 @@ Run the dihedral fit to fit to the MM simulations:
     fit_dihedral_with_gomc(
         fit_dihedral_atom_types,
         mol2_file,
-        FF_XML_file,
+        forcefield_file,
         temperature_in_unyt_units,
         gomc_binary_directory,
-        log_files_and_removed_points,
+        qm_log_file_dict,
 	manual_dihedral_atom_numbers_list=[3, 2, 1, 4],
-        zeroed_dihedral_atom_types=zeroed_dihedrals,
+        zero_dihedral_atom_types=zero_dihedral_atom_types,
         qm_engine="gaussian_style_final_files",
-        VDWGeometricSigma=VDWGeometricSigma_bool,
+        combining_rule=combining_rule,
         atom_type_naming_style='general',
         gomc_cpu_cores=1,
-    	fit_min_validated_r_squared=0.99,
-    	fit_validation_r_squared_rtol=5e-03
+    	r_squared_min=0.99,
+    	r_squared_rtol=5e-03
     )
+
+The most important output files:
+
+.. code:: ipython3
+
+    # The OPLS dihedral fit constants
+    print('The OPLS dihedral fit constants:\n')
+    os.system("cat opls_dihedral_k_constants_fit_energy.txt")
+
+    # The converted OPLS to periodic dihedral fit constants
+    print('The converted OPLS to periodic dihedral fit constants:\n')
+    os.system("cat periodic_dihedral_k_constants_fit_energy.txt")
+
+    # The converted OPLS to RB-torsions dihedral fit constants
+    print('The converted OPLS to RB-torsions dihedral fit constants:\n')
+    os.system("cat RB_torsion_k_constants_fit_energy.txt")
+
+    # This file contains the raw points used in the fits (QM - MM_less_dihedral(s)_energy being fit)
+    print('This file contains the raw points used in the fits (QM - MM_less_dihedral(s)_energy being fit):\n')
+    os.system("cat all_normalized_energies_in_kcal_per_mol.txt")
+
+
+The plotted dihedral fits:
+   #. opls_all_single_fit_dihedral_k_constants_figure.pdf
+   #. opls_all_summed_dihedrals_k_constants_figure.pdf

docs/index.rst

@@ -11,7 +11,7 @@ Ryckaert-Bellemans (RB) torsion.
 The **MoSDeF-dihedral-fit** software produces dihedral fits for existing force fields, compatible with
 `GPU Optimized Monte Carlo (GOMC) >= v2.75 <http://gomc.eng.wayne.edu>`_ and
 `Molecular Simulation Design Framework (MoSDeF) <https://mosdef.org>`_, with only tens of lines of python code,
-the `Gaussian 16 <https://www.gaussin.com>`_ log files, and a **mol2** file.
+the `Gaussian 16 <https://gaussian.com>`_ log files, and a **mol2** file.
 
 .. note::
     Currently, this means that only the fourth (4th) cosine multiple or power is utilized in the dihedral fit.

docs/overview/general_info.rst

@@ -14,7 +14,7 @@ Ryckaert-Bellemans (RB) torsion.
 The **MoSDeF-dihedral-fit** software produces dihedral fits for existing force fields, compatible with
 `GPU Optimized Monte Carlo (GOMC) >= v2.75 <http://gomc.eng.wayne.edu>`_ and
 `Molecular Simulation Design Framework (MoSDeF) <https://mosdef.org>`_, with only tens of lines of python code,
-the `Gaussian 16 <https://www.gaussin.com>`_ log files, and a **mol2** file.
+the `Gaussian 16 <https://gaussian.com>`_ log files, and a **mol2** file.
 
 .. note::
     Currently, this means that only the fourth (4th) cosine multiple or power is utilized in the dihedral fit.

docs/reference/citing_mosdef_dihedral_fit_python.rst

@@ -4,7 +4,7 @@ Citing
 
 If you use this code for your research, please cite for following sources:
 
-`The GitHub repository <https://github.com/GOMC-WSU/MoSDeF-GOMC>`_:
+`The GitHub repository <https://github.com/GOMC-WSU/MoSDeF-dihedral-fit>`_:
 
 **ACS**