Add packmol_args parameter to packing fucntions. Allows user to give additional commands to PACKMOL.

mbuild/packing.py

@@ -27,21 +27,25 @@
 output {1}
 seed {2}
 sidemax {3}
+{4}
 """
+
 PACKMOL_SOLUTE = """
 structure {0}
     number 1
     center
     fixed {1:.3f} {2:.3f} {3:.3f} 0. 0. 0.
 end structure
 """
+
 PACKMOL_BOX = """
 structure {0}
     number {1:d}
     inside box {2:.3f} {3:.3f} {4:.3f} {5:.3f} {6:.3f} {7:.3f}
     {8}
 end structure
 """
+
 PACKMOL_SPHERE = """
 structure {0}
     number {1:d}
@@ -56,6 +60,20 @@
 constrain_rotation z 0. 0.
 """
 
+packmol_default_args = {"tolerance": 0.2, "seed": 12345}
+
+
+def combine_packmol_args(default_args, custom_args):
+
+    # List of all available packmol_inputs
+    packmol_inputs = []
+
+    #
+
+    # Parse through custom args first
+
+    # Combine into single dict
+
 
 def fill_box(
     compound,
@@ -71,6 +89,7 @@
     fix_orientation=False,
     temp_file=None,
     update_port_locations=False,
+    packmol_args=None,
 ):
     """Fill a box with an `mbuild.compound` or `Compound` s using PACKMOL.
 
@@ -130,8 +149,19 @@
     temp_file : str, default=None
         File name to write PACKMOL raw output to.
     update_port_locations : bool, default=False
-        After packing, port locations can be updated, but since compounds can be
-        rotated, port orientation may be incorrect.
+        After packing, port locations can be updated, but since compounds
+        can be rotated, port orientation may be incorrect.
+    packmol_args : dict
+        Dictionary where the key, value pairs are options and their
+        corresponding keyword arguments for PACKMOL. Some PACKMOL options
+        do not require a specified keyword. In this case, the value in
+        the dictionary should be an empty string e.g. {'movebadrandom':""}
+        These commands are placed at the header of the PACKMOL input file
+        and therefore applied to all structures. NOTE: The PACKMOL options
+        for seed and tolerance are specified by the function parameters
+        seed and overlap.
+        Other command options can be found in the PACKMOL userguide:
+        http://www.ime.unicamp.br/~martinez/packmol/userguide.shtml
 
     Returns
     -------
@@ -231,14 +261,20 @@
     box_maxs = [a_max - (edge * 10) for a_max in box_maxs]
     box_mins = [a_min + (edge * 10) for a_min in box_mins]
 
+    # generate string of addl. packmol inputs given in packmol_args
+    packmol_commands = ""
+    if packmol_args:
+        for arg in packmol_args:
+            packmol_commands += "{} {} \n".format(arg, packmol_args[arg])
+
     # Build the input file for each compound and call packmol.
     filled_xyz = _new_xyz_file()
 
     # create a list to contain the file handles for the compound temp files
     compound_xyz_list = list()
     try:
         input_text = PACKMOL_HEADER.format(
-            overlap, filled_xyz.name, seed, sidemax * 10
+            overlap, filled_xyz.name, seed, sidemax * 10, packmol_commands
         )
         for comp, m_compounds, rotate in zip(
             compound, n_compounds, fix_orientation
@@ -291,6 +327,7 @@
     fix_orientation=False,
     temp_file=None,
     update_port_locations=False,
+    packmol_args=None,
 ):
     """Fill a region of a box with `mbuild.Compound` (s) using PACKMOL.
 
@@ -327,8 +364,19 @@
     temp_file : str, default=None
         File name to write PACKMOL raw output to.
     update_port_locations : bool, default=False
-        After packing, port locations can be updated, but since compounds can be
-        rotated, port orientation may be incorrect.
+        After packing, port locations can be updated, but since compounds
+        can be rotated, port orientation may be incorrect.
+    packmol_args : dict
+        Dictionary where the key, value pairs are options and their
+        corresponding keyword arguments for PACKMOL. Some PACKMOL options
+        do not require a specified keyword. In this case, the value in
+        the dictionary should be an empty string e.g. {'movebadrandom':""}
+        These commands are placed at the header of the PACKMOL input file
+        and therefore applied to all structures. NOTE: The PACKMOL options
+        for seed and tolerance are specified by the function parameters
+        seed and overlap.
+        Other command options can be found in the PACKMOL userguide:
+        http://www.ime.unicamp.br/~martinez/packmol/userguide.shtml
 
     Returns
     -------
@@ -407,14 +455,20 @@
     # In angstroms for packmol.
     overlap *= 10
 
+    # generate string of addl. packmol inputs given in packmol_args
+    packmol_commands = ""
+    if packmol_args:
+        for arg in packmol_args:
+            packmol_commands += "{} {} \n".format(arg, packmol_args[arg])
+
     # Build the input file and call packmol.
     filled_xyz = _new_xyz_file()
 
     # List to hold file handles for the temporary compounds
     compound_xyz_list = list()
     try:
         input_text = PACKMOL_HEADER.format(
-            overlap, filled_xyz.name, seed, sidemax * 10
+            overlap, filled_xyz.name, seed, sidemax * 10, packmol_commands
         )
         for comp, m_compounds, rotate, items_n in zip(
             compound, n_compounds, fix_orientation, container
@@ -475,6 +529,7 @@
     fix_orientation=False,
     temp_file=None,
     update_port_locations=False,
+    packmol_args=None,
 ):
     """Fill a sphere with a compound using PACKMOL.
 
@@ -518,8 +573,19 @@
     temp_file : str, default=None
         File name to write PACKMOL raw output to.
     update_port_locations : bool, default=False
-        After packing, port locations can be updated, but since compounds can be
-        rotated, port orientation may be incorrect.
+        After packing, port locations can be updated, but since compounds
+        can be rotated, port orientation may be incorrect.
+    packmol_args : dict
+        Dictionary where the key, value pairs are options and their
+        corresponding keyword arguments for PACKMOL. Some PACKMOL options
+        do not require a specified keyword. In this case, the value in
+        the dictionary should be an empty string e.g. {'movebadrandom':""}
+        These commands are placed at the header of the PACKMOL input file
+        and therefore applied to all structures. NOTE: The PACKMOL options
+        for seed and tolerance are specified by the function parameters
+        seed and overlap.
+        Other command options can be found in the PACKMOL userguide:
+        http://www.ime.unicamp.br/~martinez/packmol/userguide.shtml
 
     Returns
     -------
@@ -613,14 +679,20 @@
     radius *= 10
     overlap *= 10
 
+    # generate string of addl. packmol inputs given in packmol_args
+    packmol_commands = ""
+    if packmol_args:
+        for arg in packmol_args:
+            packmol_commands += "{} {} \n".format(arg, packmol_args[arg])
+
     # Build the input file for each compound and call packmol.
     filled_xyz = _new_xyz_file()
 
     # List to hold file handles for the temporary compounds
     compound_xyz_list = list()
     try:
         input_text = PACKMOL_HEADER.format(
-            overlap, filled_xyz.name, seed, sidemax * 10
+            overlap, filled_xyz.name, seed, sidemax * 10, packmol_commands
         )
         for comp, m_compounds, rotate in zip(
             compound, n_compounds, fix_orientation
@@ -670,6 +742,7 @@
     temp_file=None,
     update_port_locations=False,
     center_solute=True,
+    packmol_args=None,
 ):
     """Solvate a compound in a box of solvent using PACKMOL.
 
@@ -701,10 +774,21 @@
     temp_file : str, default=None
         File name to write PACKMOL raw output to.
     update_port_locations : bool, default=False
-        After packing, port locations can be updated, but since compounds can be
-        rotated, port orientation may be incorrect.
+        After packing, port locations can be updated, but since compounds
+        can be rotated, port orientation may be incorrect.
     center_solute : bool, optional, default=True
         Move solute center of mass to the center of the `mb.Box` used.
+    packmol_args : dict
+        Dictionary where the key, value pairs are options and their
+        corresponding keyword arguments for PACKMOL. Some PACKMOL options
+        do not require a specified keyword. In this case, the value in
+        the dictionary should be an empty string e.g. {'movebadrandom':""}
+        These commands are placed at the header of the PACKMOL input file
+        and therefore applied to all structures. NOTE: The PACKMOL options
+        for seed and tolerance are specified by the function parameters
+        seed and overlap.
+        Other command options can be found in the PACKMOL userguide:
+        http://www.ime.unicamp.br/~martinez/packmol/userguide.shtml
 
     Returns
     -------
@@ -735,6 +819,13 @@
     # Apply edge buffer
     box_maxs = np.subtract(box_maxs, edge * 10)
     box_mins = np.add(box_mins, edge * 10)
+
+    # generate string of addl. packmol inputs given in packmol_args
+    packmol_commands = ""
+    if packmol_args:
+        for arg in packmol_args:
+            packmol_commands += "{} {} \n".format(arg, packmol_args[arg])
+
     # Build the input file for each compound and call packmol.
     solvated_xyz = _new_xyz_file()
     solute_xyz = _new_xyz_file()
@@ -744,7 +835,7 @@
     try:
         solute.save(solute_xyz.name, overwrite=True)
         input_text = PACKMOL_HEADER.format(
-            overlap, solvated_xyz.name, seed, sidemax * 10
+            overlap, solvated_xyz.name, seed, sidemax * 10, packmol_commands
         ) + PACKMOL_SOLUTE.format(solute_xyz.name, *center_solute.tolist())
 
         for solv, m_solvent, rotate in zip(solvent, n_solvent, fix_orientation):

mbuild/tests/test_packing.py

@@ -305,6 +305,72 @@
         with pytest.warns(UserWarning):
             mb.fill_box(h2o, n_compounds=10, box=[1, 1, 1], overlap=10)
 
+    def test_packmol_args(self, h2o):
+        try:
+            filled = mb.fill_box(
+                h2o,
+                n_compounds=2,
+                box=[0.1, 0.1, 0.1],
+                packmol_args={"maxit": 10, "movebadrandom": "", "nloop": 100},
+            )
+        except RuntimeError:
+            with open("log.txt", "r") as logfile:
+                assert "(movebadrandom)" in logfile.read()
+                logfile.seek(0)
+                assert (
+                    "User defined GENCAN number of iterations:           10"
+                    in logfile.read()
+                )
+
+        try:
+            mb.fill_region(
+                h2o,
+                10,
+                [[2, 2, 2, 4, 4, 4]],
+                bounds=[[2, 2, 2, 4, 4, 4]],
+                packmol_args={"maxit": 10, "movebadrandom": "", "nloop": 100},
+            )
+        except RuntimeError:
+            with open("log.txt", "r") as logfile:
+                assert "(movebadrandom)" in logfile.read()
+                logfile.seek(0)
+                assert (
+                    "User defined GENCAN number of iterations:           10"
+                    in logfile.read()
+                )
+
+        try:
+            filled = mb.fill_sphere(
+                h2o,
+                n_compounds=2,
+                sphere=[3, 3, 3, 1.5],
+                packmol_args={"maxit": 10, "movebadrandom": "", "nloop": 100},
+            )
+        except RuntimeError:
+            with open("log.txt", "r") as logfile:
+                assert "(movebadrandom)" in logfile.read()
+                logfile.seek(0)
+                assert (
+                    "User defined GENCAN number of iterations:           10"
+                    in logfile.read()
+                )
+        try:
+            mb.solvate(
+                solute=h2o,
+                solvent=[h2o],
+                n_solvent=[10],
+                box=[2, 2, 2],
+                packmol_args={"maxit": 15, "movebadrandom": "", "nloop": 100},
+            )
+        except RuntimeError:
+            with open("log.txt", "r") as logfile:
+                assert "(movebadrandom)" in logfile.read()
+                logfile.seek(0)
+                assert (
+                    "User defined GENCAN number of iterations:           15"
+                    in logfile.read()
+                )
+
     def test_rotate(self, h2o):
         filled = mb.fill_box(h2o, 2, box=[1, 1, 1], fix_orientation=True)
         w0 = filled.xyz[:3]