Minor bugfixes; Modified expanded.mdp for tutorial 1

wehs7661 · May 16, 2024 · c283c57 · c283c57
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Showing 5 changed files with 7 additions and 11 deletions.
diff --git a/docs/examples/tutorial_1/expanded.mdp b/docs/examples/tutorial_1/expanded.mdp
@@ -2,7 +2,7 @@
 integrator = md-vv
 tinit = 0
 dt = 0.002
-nsteps = 500
+nsteps = 50000000
 comm_mode = Linear
 nstcomm = 1
 nstfout = 0
@@ -93,18 +93,13 @@ lmc_gibbsdelta = -1
 lmc_forced_nstart = 0
 symmetrized_transition_matrix = yes
 nst_transition_matrix = 100000
-wl_scale = 0.8
-wl_ratio = 0.8
-init_wl_delta = 0.5
 
 ; expanded ensemble variables
 nstexpanded = 10
-lmc_stats = wang-landau
+lmc_stats = no
 lmc_move = metropolized-gibbs
-lmc_weights_equil = wl-delta
-weight_equil_wl_delta = 0.001
 
 ; lambda-states          = 1      2      3      4      5      6      7      8      9
 coul_lambdas = 0.0 0.25 0.5 0.75 1.0 1.0 1.0 1.0 1.0
 vdw_lambdas = 0.0 0.0 0.0 0.0 0.0 0.25 0.5 0.75 1.0
-init_lambda_weights = 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
+init_lambda_weights = 0.00000 1.61343 2.71400 3.40859 3.60446 4.78543 5.37983 3.29843 0.36336
diff --git a/docs/examples/tutorial_1/params.yaml b/docs/examples/tutorial_1/params.yaml
@@ -7,3 +7,4 @@ n_sim: 4
 n_iter: 5         
 s: 1                         
 nst_sim: 500
+runtime_args: {'-nt': '1', '-ntmpi': '1'}
diff --git a/docs/simulations.rst b/docs/simulations.rst
@@ -303,7 +303,7 @@ include parameters for data analysis here.
   - :code:`w_mean_type`: (Optional, Default: :code:`'simple'`)
       The type of mean to use when combining weights. Available options include :code:`simple` and :code:`weighted`.
       For the latter case, inverse-variance weighted means are used. For more details about, please refer to :ref:`doc_w_schemes`.
-  - :code:`N_cutoff`: (Optional, Default: 1000)
+  - :code:`N_cutoff`: (Optional, Default: -1)
       The histogram cutoff for weight corrections. A cutoff of 1000 means that weight corrections will be applied only if
       the counts of the involved states are both larger than 1000. A value of -1 means that no weight correction will be performed.
       For more details, please please refer to :ref:`doc_weight_correction`.

diff --git a/ensemble_md/cli/run_REXEE.py b/ensemble_md/cli/run_REXEE.py
@@ -235,7 +235,7 @@ def main():
                         print('Performing weight correction ...')
                     else:
                         print('Performing weight correction ...', end='')
-                    weights = REXEE.weights_correction(weights_avg, counts)
+                    weights = REXEE.weight_correction(weights_avg, counts)
                     _ = REXEE.combine_weights(weights, print_values=False)[1]  # just to print the combined weights  # noqa: E501
                 else:
                     print('Note: No weight correction will be performed.')

diff --git a/ensemble_md/replica_exchange_EE.py b/ensemble_md/replica_exchange_EE.py
@@ -161,7 +161,7 @@ def set_params(self, analysis):
             "proposal": 'exhaustive',
             "w_combine": False,
             "w_mean_type": 'simple',
-            "N_cutoff": 1000,
+            "N_cutoff": -1,
             "hist_corr": False,
             "verbose": True,
             "mdp_args": None,