Merge branch 'forced-swap' of github.com:wehs7661/ensemble_md into forced-swap

Author: ajfriedman22

README.md

@@ -1,7 +1,7 @@
 Ensemble Molecular Dynamics
 ==============================
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ensemble_md/replica_exchange_EE.py

@@ -164,7 +164,7 @@ def set_params(self, analysis):
             "resname_transform": None,
             "resname_list": None,
             "swap_rep_pattern": None,
-            "allow_virtual_V": False,  # Allow use of V to indicate virtual atoms in topology
+            "allow_virtual_V": True,  # Allow use of V to indicate virtual atoms in topology
             "nst_sim": None,
             "proposal": 'exhaustive',
             "w_combine": False,

ensemble_md/utils/coordinate_swap.py

@@ -1252,7 +1252,7 @@ def _read_gro(side, resname_list, gro_list):
     return name, num
 
 
-def create_atom_map(gro_list, resname_list, swap_patterns, allow_virtual_V=False):
+def create_atom_map(gro_list, resname_list, swap_patterns, allow_virtual_V=True):
     """
     If you generate your hybrid topologies in a way that the
     same atom has the same name in each molecule then this

ensemble_md/utils/gmx_parser.py

@@ -335,14 +335,18 @@ def compare_MDPs(mdp_list, print_diff=False):
                     # the parameter is not in all MDP files
                     diff_params[p] = [d[p] if p in d else None for d in params_dicts]
                 else:
-                    # the parameter is in all MDP files (Note that "set([1, 1, 1]={1}.)")
-                    if isinstance(params_dicts[0][p], list):
-                        # the parameter is a list, which is unhashable
-                        if len(set([tuple(d[p]) for d in params_dicts])) > 1:
-                            diff_params[p] = [d[p] for d in params_dicts]
+                    if type(params_dicts[0][p]) is not type(params_dicts[1][p]):
+                        # e.g., tau_t = 1.0 1.0 1.0 v.s. tau_t = 1.0 (list v.s. float)
+                        diff_params[p] = [d[p] for d in params_dicts]
                     else:
-                        if len(set([d[p] for d in params_dicts])) > 1:
-                            diff_params[p] = [d[p] for d in params_dicts]
+                        # the parameter is in all MDP files (Note that "set([1, 1, 1]={1}.)")
+                        if isinstance(params_dicts[0][p], list):
+                            # the parameter is a list, which is unhashable
+                            if len(set([tuple(d[p]) for d in params_dicts])) > 1:
+                                diff_params[p] = [d[p] for d in params_dicts]
+                        else:
+                            if len(set([d[p] for d in params_dicts])) > 1:
+                                diff_params[p] = [d[p] for d in params_dicts]
 
     if print_diff:
         print("The following parameters are different among the MDP files:")

readthedocs.yml

@@ -1,5 +1,8 @@
 version: 2
 
+sphinx:
+  configuration: docs/conf.py
+
 build:
   os: "ubuntu-22.04"
   tools: