update MWs in MCCCS-MN log file generation

reproducibility_project/clear_folder.py

@@ -38,7 +38,7 @@ def main():
     ):
         print("-----------------------------------------------------")
 
-        if molecule == "waterSPCE" and engine == "mcccs":
+        if molecule == "benzeneUA" and engine == "mcccs":
             print(
                 molecule,
                 ensemble,

reproducibility_project/find_job.py

@@ -38,7 +38,9 @@ def main():
     ):
         print("-----------------------------------------------------")
 
-        if molecule == "ethanolAA" and engine == "mcccs":
+        jobs = []
+
+        if molecule == "benzeneUA" and engine == "mcccs":
             print(
                 molecule,
                 ensemble,
@@ -50,7 +52,15 @@ def main():
             )
 
             for job in group:
-                print(job.sp.replica, job)
+                jobs.append(
+                    [
+                        job.sp.replica,
+                        str(job),
+                    ]
+                )
+            jobs.sort()
+            for job in jobs:
+                print(job)
 
 
 if __name__ == "__main__":

reproducibility_project/src/engine_input/mcccs/benzeneUA/NPT/fort.4.cool

@@ -108,7 +108,6 @@
 
 
  &mc_simple
-     pm_atom_tra= 0.05
      armtra=  1.000000000000000E-002
      rmtra=  0.300000000000000
      rmrot=  0.400000000000000

reproducibility_project/src/engine_input/mcccs/benzeneUA/NPT/fort.4.equil

@@ -108,7 +108,6 @@
 
 
  &mc_simple
-     pm_atom_tra= 0.05
      armtra=  1.000000000000000E-002
      rmtra=  0.300000000000000
      rmrot=  0.400000000000000

reproducibility_project/src/engine_input/mcccs/benzeneUA/NPT/fort.4.melt

@@ -108,7 +108,6 @@
 
 
  &mc_simple
-     pm_atom_tra= 0.05
      armtra=  1.000000000000000E-002
      rmtra=  0.300000000000000
      rmrot=  0.400000000000000

reproducibility_project/src/engine_input/mcccs/benzeneUA/NPT/fort.4.prod

@@ -108,7 +108,6 @@
 
 
  &mc_simple
-     pm_atom_tra= 0.05
      armtra=  1.000000000000000E-002
      rmtra=  0.300000000000000
      rmrot=  0.400000000000000

reproducibility_project/src/engines/mcccs/analysis.py

@@ -85,6 +85,7 @@ def main():
         base_dir = os.getcwd()
         if ensemble == "NPT":
             density_list = []
+            density_list_logfile = []
             for job in group:
                 os.chdir(job.ws)
                 # print(job)
@@ -103,15 +104,25 @@ def main():
                         )
                     )
                 density_list.append(avg_one_seed_density_box1(prod_run_files))
-
+                density_list_logfile.append(density_avg_logfile("log-npt.txt"))
                 # print(density_list)
             filtered_density_list = list(filter(None, density_list))
-            output_string = "The average density is {} g/ml with SEM {} from {} samples".format(
+            filtered_density_list_logfile = list(
+                filter(None, density_list_logfile)
+            )
+            output_string = "For NpT cases, the first line is runfile avg and second line is logfile avg\nThe average density is {} g/ml with SEM {} from {} samples\n".format(
                 np.mean(filtered_density_list),
                 np.std(filtered_density_list)
                 / np.sqrt(len(filtered_density_list)),
                 len(filtered_density_list),
             )
+            output_string += "The average density is {} g/ml with SEM {} from {} samples".format(
+                np.mean(filtered_density_list_logfile),
+                np.std(filtered_density_list_logfile)
+                / np.sqrt(len(filtered_density_list_logfile)),
+                len(filtered_density_list_logfile),
+            )
+
             print(output_string)
             os.chdir(base_dir)
             with open("density_results.txt", "w") as text_file:
@@ -171,6 +182,16 @@ def main():
         os.chdir("..")
 
 
+def density_avg_logfile(logfile):
+    """Calc average for log files."""
+    data = np.loadtxt("log-npt.txt", skiprows=1)
+
+    # Calculate the average of the third from last column (density)
+    density_column_index = -3  # Third from last column
+    average_density = np.mean(data[:, density_column_index])
+    return average_density
+
+
 def avg_one_seed_density_box1(prod_run_files):
     """For a one particular seed, read all the prod run files and provide the average density (g/ml) for one seed."""
     if len(prod_run_files) == 0:

reproducibility_project/src/engines/mcccs/analysis_data/benzeneUA_NPT_450.0K_2260.0kPa_cutoff_hard_lrc_energy_pressure/density_results.txt

@@ -1 +1,3 @@
-The average density is 0.698325046875 g/ml with SEM 0.00019497573995066978 from 16 samples
+For NpT cases, the first line is runfile avg and second line is logfile avg
+The average density is 0.6980418125000001 g/ml with SEM 0.00023460065439170633 from 16 samples
+The average density is 0.698041913994141 g/ml with SEM 0.0002348979377991116 from 16 samples

reproducibility_project/src/engines/mcccs/analysis_data/ethanolAA_NPT_280.0K_101.325kPa_cutoff_hard_lrc_energy_pressure/density_results.txt

@@ -1 +1,3 @@
-The average density is 0.8132740781250001 g/ml with SEM 0.00022710556005862753 from 16 samples
+For NpT cases, the first line is runfile avg and second line is logfile avg
+The average density is 0.8127313437499999 g/ml with SEM 0.0002470408075268068 from 16 samples
+The average density is 0.8127309012571694 g/ml with SEM 0.00024699982340980933 from 16 samples

reproducibility_project/src/engines/mcccs/analysis_data/ethanolAA_NPT_300.0K_101.325kPa_cutoff_hard_lrc_energy_pressure/density_results.txt

@@ -1 +1,3 @@
-The average density is 0.7915156250000001 g/ml with SEM 0.00022247973156454715 from 16 samples
+For NpT cases, the first line is runfile avg and second line is logfile avg
+The average density is 0.7914194531250001 g/ml with SEM 0.00021111305682752364 from 16 samples
+The average density is 0.7914208917911247 g/ml with SEM 0.00021123437103423662 from 16 samples

reproducibility_project/src/engines/mcccs/analysis_data/ethanolAA_NPT_320.0K_101.325kPa_cutoff_hard_lrc_energy_pressure/density_results.txt

@@ -1 +1,3 @@
-The average density is 0.76872575 g/ml with SEM 0.00020045779758662987 from 16 samples
+For NpT cases, the first line is runfile avg and second line is logfile avg
+The average density is 0.76839096875 g/ml with SEM 0.00020634974964182785 from 16 samples
+The average density is 0.7683913005838312 g/ml with SEM 0.0002062944575966398 from 16 samples

reproducibility_project/src/engines/mcccs/analysis_data/methaneUA_GEMC-NVT_140.0K_1318.0kPa_cutoff_hard_lrc_energy_pressure/density_results.txt

@@ -1,2 +1,2 @@
-Box1 The average density is 0.374604859375 g/ml with SEM 3.351215358442761e-05 from 16 samples
+Box1 The average density is 0.374604859375 g/ml with SEM 3.3512153584427606e-05 from 16 samples
 Box2 The average density is 0.010456921875 g/ml with SEM 1.4941499182717499e-05 from 16 samples

reproducibility_project/src/engines/mcccs/analysis_data/methaneUA_NPT_140.0K_1318.0kPa_cutoff_hard_lrc_energy_pressure/density_results.txt

@@ -1 +1,3 @@
-The average density is 0.375760578125 g/ml with SEM 4.58862635118307e-05 from 16 samples
+For NpT cases, the first line is runfile avg and second line is logfile avg
+The average density is 0.375760578125 g/ml with SEM 4.588626351183069e-05 from 16 samples
+The average density is 0.3757593605773165 g/ml with SEM 4.592843462569958e-05 from 16 samples

reproducibility_project/src/engines/mcccs/analysis_data/pentaneUA-constrain_bonds_GEMC-NVT_372.0K_1402.0kPa_cutoff_hard_lrc_energy_pressure/density_results.txt

@@ -1,2 +1,2 @@
-Box1 The average density is 0.538999234375 g/ml with SEM 7.901658581811365e-05 from 16 samples
-Box2 The average density is 0.02035428125 g/ml with SEM 3.284094656059866e-05 from 16 samples
+Box1 The average density is 0.5389992343750001 g/ml with SEM 7.901658581811365e-05 from 16 samples
+Box2 The average density is 0.02035428125 g/ml with SEM 3.284094656059865e-05 from 16 samples

reproducibility_project/src/engines/mcccs/analysis_data/pentaneUA-constrain_bonds_NPT_372.0K_1402.0kPa_cutoff_hard_lrc_energy_pressure/density_results.txt

@@ -1 +1,3 @@
-The average density is 0.5410875312499999 g/ml with SEM 8.71734668226038e-05 from 16 samples
+For NpT cases, the first line is runfile avg and second line is logfile avg
+The average density is 0.54108753125 g/ml with SEM 8.71734668226038e-05 from 16 samples
+The average density is 0.5410886453415662 g/ml with SEM 8.653017097453927e-05 from 16 samples

reproducibility_project/src/engines/mcccs/analysis_data/waterSPCE_NPT_280.0K_101.325kPa_cutoff_hard_lrc_energy_pressure/density_results.txt

@@ -1 +1,3 @@
-The average density is 1.0072252343750001 g/ml with SEM 0.00047373785257594106 from 16 samples
+For NpT cases, the first line is runfile avg and second line is logfile avg
+The average density is 1.00705103125 g/ml with SEM 0.0003472372551509214 from 16 samples
+The average density is 1.0070531403810825 g/ml with SEM 0.00034683889433465964 from 16 samples

reproducibility_project/src/engines/mcccs/analysis_data/waterSPCE_NPT_300.0K_101.325kPa_cutoff_hard_lrc_energy_pressure/density_results.txt

@@ -1 +1,3 @@
-The average density is 0.9977669062499999 g/ml with SEM 0.0003959896293592313 from 16 samples
+For NpT cases, the first line is runfile avg and second line is logfile avg
+The average density is 0.99770809375 g/ml with SEM 0.0003722279679110896 from 16 samples
+The average density is 0.9977080406908347 g/ml with SEM 0.00037210745263542696 from 16 samples

reproducibility_project/src/engines/mcccs/analysis_data/waterSPCE_NPT_320.0K_101.325kPa_cutoff_hard_lrc_energy_pressure/density_results.txt

@@ -1 +1,3 @@
-The average density is 0.9861051249999999 g/ml with SEM 0.00017870171851222096 from 16 samples
+For NpT cases, the first line is runfile avg and second line is logfile avg
+The average density is 0.986137296875 g/ml with SEM 0.0002256395199824372 from 16 samples
+The average density is 0.9861366533115048 g/ml with SEM 0.0002257823152641847 from 16 samples

reproducibility_project/src/engines/mcccs/project.py

@@ -287,7 +287,17 @@ def sanitize_npt_log(step, job):
     """Sanitize the output logs for NPT simulations."""
     import numpy as np
 
-    mw = job.sp.mass
+    masses = {
+        "methaneUA": 16.043,
+        "pentaneUA-flexible_bonds": 72.151,
+        "pentaneUA-constrain_bonds": 72.151,
+        "benzeneUA": 78.114,
+        "waterSPCE": 18.015324,
+        "ethanolAA": 46.068672,
+    }
+
+    mw = masses[job.sp.molecule]
+    print("sanitizing for", job, "molecule =", job.sp.molecule, "mw=", mw)
     temp = job.sp.temperature
     files = sorted(glob("fort*12*{}*".format(step)))
     arrays = []