Added the path to the FF, psf, and pdb file to be selected by the user. Moved restart variables to the required variables, and added the ability to use new restart input files. (#937)

* Added functionallity and tests to select any desired path to be written for the gomc_controlfile_writer.  This include a default check to see if the FF, psf, and pdb files exist in the specified path, but this can also be overridden.  This will allow may simulation to be run from 1 existing system build and FF file.

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* Fixed some spacing issues int the gomc_conf_writer.py docstrings.

* Fixed some spacing issues int the gomc_conf_writer.py docstrings rev 1

* Fixed some spacing issues int the gomc_conf_writer.py docstrings rev 2

* Fixed some spacing issues int the gomc_conf_writer.py docstrings rev 3

* Fixed some spacing issues int the gomc_conf_writer.py docstrings rev 4

* Fixed some spacing issues int the gomc_conf_writer.py docstrings rev 4

* Fixed some spacing issues int the gomc_conf_writer.py docstrings rev 5

* added gomc file input directory changes, full path changes, and checking if files exist.  Before, the gomc input file had to be in the same directory.

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* reformated restart and restartcheckpoint to required variables. Added binCoordinates, extendedSystem, and binVelocities as options to restart the simulations. Added overrides for Coordinates_box and Structure_box in the required variables. Renamed alot of the new required variables. This is in the gomc_conf_writer.py

* reformated restart and restartcheckpoint to required variables. Added binCoordinates, extendedSystem, and binVelocities as options to restart the simulations. Added overrides for Coordinates_box and Structure_box in the required variables. Renamed alot of the new required variables. This is in the gomc_conf_writer.py

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* removed extra coordinate and structure descriptions in the attributes of the gomc_conf_writer.py

* added more tests for the gomc_conf_writer.

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* added more test cases to the gomc_conf_writer.py, specificly the new input file path and file overrides and new restart variable moved to the required variables.

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* improved variable text descriptions

* Fixed an few errors.  One which didnt allow the structure paths to be changed without the coordinate paths, so now either or can be overridden.  Second, allows only the pdb and psf files to be used to restart the simulation, but these will need to be the GOMC output files.

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* Fixed areas of the code to accept .par files for the FF files along with the current .inp files.

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* added test for the parameters for .inp and .par files fo rthe gomc_conf_writer.py

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* added check_input_files_exist check int eh test_gomc_conf_writer.py file.

* added the default file name and directory to the docstrings for the parameter, coordinate, and structure files in the gomc_conf_writer.py file.

* fixed a mislabed variable in place for the charmm_writer.py file (residue_id_list to structure_box_0_and_1_ff), which likely got autochanged by accident

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* added line to fix potenial bug in unique atom name writers (unique_atom_naming function)

* The OutMolNumber variable is wrong and changed to the correct OutMolNum variable.

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* fixed typo and removed a few undeeded if statements per the review comments.

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* fixed typo

* added a sorting function for the input_variables_dict gomc_writer input, which removes checking variables that are set as none. Therefore, these variables are just set to the defaults, like they were never entered. Otherwise, they are checked and dont match the required input varible formats and will not provide informative errors for the users.

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Co-authored-by: bc118 <crawfordb118@gmail.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Author: bc118

mbuild/formats/charmm_writer.py

@@ -49,7 +49,6 @@ def _get_bond_type_key(
         bond_atom_2_residue_name : str
             The residue name for atom 2 in the bond.
     """
-
     bond_k_constant = round(
         bond.type.k
         * (sigma_conversion_factor ** 2 / epsilon_conversion_factor),
@@ -947,6 +946,7 @@ def unique_atom_naming(
             elif len(str(atom.name)) > 2:
                 if len(str(atom.name)) == 3:
                     no_digits_atom_name = 1
+                    atom_name_value = atom.name
                 else:
                     text_to_write = (
                         "ERROR: atom numbering will not work propery at"
@@ -1800,7 +1800,7 @@ def __init__(
                 boxes_for_simulation=self.boxes_for_simulation,
             )
 
-            self.residue_id_list = (
+            self.structure_box_0_and_1_ff = (
                 self.structure_box_0_ff + self.structure_box_1_ff
             )
             self.combined_1_4_lj_dict_per_residue.update(
@@ -1865,7 +1865,9 @@ def __init__(
                     "Total charge is {}.".format(total_charge)
                 )
 
-            total_charge = sum([atom.charge for atom in self.residue_id_list])
+            total_charge = sum(
+                [atom.charge for atom in self.structure_box_0_and_1_ff]
+            )
             if round(total_charge, 4) != 0.0:
                 warn(
                     "System is not charge neutral for structure_0_and_1. "
@@ -1962,7 +1964,7 @@ def __init__(
             self.types = np.array(
                 [
                     atom.type + "_" + str(atom.residue.name)
-                    for atom in self.residue_id_list.atoms
+                    for atom in self.structure_box_0_and_1_ff.atoms
                 ]
             )
 
@@ -1979,7 +1981,9 @@ def __init__(
 
         if self.structure_box_1:
             self.masses = (
-                np.array([atom.mass for atom in self.residue_id_list.atoms])
+                np.array(
+                    [atom.mass for atom in self.structure_box_0_and_1_ff.atoms]
+                )
                 / self.mass_conversion_factor
             )
             self.mass_dict = dict(
@@ -2060,7 +2064,7 @@ def __init__(
 
         # if self.structure_box_1 != None:
         if self.structure_box_1:
-            self.structure_selection = self.residue_id_list
+            self.structure_selection = self.structure_box_0_and_1_ff
         else:
             self.structure_selection = self.structure_box_0_ff