diff --git a/reproducibility_project/spe_subproject/SPE.ipynb b/reproducibility_project/spe_subproject/SPE.ipynb
index d92cb9a6..be2d4383 100644
--- a/reproducibility_project/spe_subproject/SPE.ipynb
+++ b/reproducibility_project/spe_subproject/SPE.ipynb
@@ -32,17 +32,17 @@
"source": [
"pretty_names = {\n",
" \"cassandra\": \"Cassandra\",\n",
- " \"mcccs\": \"MCCCS-MN\", \n",
+ " \"mcccs\": \"MCCCS-MN\",\n",
" \"gomc\": \"GOMC\",\n",
- " \"gromacs\": \"GROMACS\", \n",
- " \"hoomd\": \"HOOMD-blue\", \n",
+ " \"gromacs\": \"GROMACS\",\n",
+ " \"hoomd\": \"HOOMD-blue\",\n",
" \"lammps-VU\": \"LAMMPS\",\n",
"}\n",
"pretty_molecules = {\n",
- " \"methaneUA\": \"TraPPE Methane\", \n",
- " \"pentaneUA\": \"TraPPE Pentane\", \n",
- " \"benzeneUA\": \"TraPPE Benzene\", \n",
- " \"ethanolAA\": \"OPLS-AA Ethanol\", \n",
+ " \"methaneUA\": \"TraPPE Methane\",\n",
+ " \"pentaneUA\": \"TraPPE Pentane\",\n",
+ " \"benzeneUA\": \"TraPPE Benzene\",\n",
+ " \"ethanolAA\": \"OPLS-AA Ethanol\",\n",
" \"waterSPCE\": \"SPC/E Water\"}"
]
},
@@ -55,17 +55,17 @@
},
"outputs": [],
"source": [
- "engines = [\"lammps-VU\", \n",
- " \"hoomd\", \n",
+ "engines = [\"lammps-VU\",\n",
+ " \"hoomd\",\n",
" \"gromacs\",\n",
" \"mcccs\",\n",
- " \"gomc\", \n",
+ " \"gomc\",\n",
" \"cassandra\"]\n",
"\n",
"molecules = [\"methaneUA\", \"pentaneUA\", \"benzeneUA\", \"waterSPCE\", \"ethanolAA\"]\n",
- "properties = ['potential_energy', \n",
- " 'tot_vdw_energy', \n",
- " 'tail_energy', \n",
+ "properties = ['potential_energy',\n",
+ " 'tot_vdw_energy',\n",
+ " 'tail_energy',\n",
" 'tot_electrostatics',\n",
" 'short_range_electrostatics',\n",
" 'long_range_electrostatics',\n",
@@ -74,7 +74,7 @@
" 'angles_energy',\n",
" 'dihedrals_energy',\n",
" 'tot_bonded_energy',\n",
- " 'intramolecular_energy', \n",
+ " 'intramolecular_energy',\n",
" 'intermolecular_energy',]"
]
},
@@ -87,9 +87,9 @@
"source": [
"spe_data = dict()\n",
"for molecule in molecules:\n",
- " spe_data[molecule] = dict() \n",
+ " spe_data[molecule] = dict()\n",
" for engine in engines:\n",
- " spe_data[molecule][engine] = dict() \n",
+ " spe_data[molecule][engine] = dict()\n",
" for property in properties:\n",
" spe_data[molecule][engine][property] = 0"
]
@@ -109,15 +109,15 @@
"metadata": {},
"outputs": [],
"source": [
- "lmp_map = {\"potential_energy\": \"potential_energy\", \n",
- " \"tot_vdw_energy\": \"tot_vdw_energy\", \n",
+ "lmp_map = {\"potential_energy\": \"potential_energy\",\n",
+ " \"tot_vdw_energy\": \"tot_vdw_energy\",\n",
" \"short_range_electrostatics\": \"tot_electrostatics\",\n",
" \"tot_electrostatics\": \"tot_electrostatics\",\n",
- " \"pair_energy\": \"tot_pair_energy\", \n",
- " \"bonds_energy\": \"bonds_energy\", \n",
- " \"angles_energy\": \"angles_energy\", \n",
+ " \"pair_energy\": \"tot_pair_energy\",\n",
+ " \"bonds_energy\": \"bonds_energy\",\n",
+ " \"angles_energy\": \"angles_energy\",\n",
" \"dihedrals_energy\": \"dihedrals_energy\",\n",
- " \"tail_energy\": \"tail_energy\", \n",
+ " \"tail_energy\": \"tail_energy\",\n",
" \"long_range_electrostatics\": \"long_range_electrostatics\",}"
]
},
@@ -131,11 +131,11 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "Not included methaneUA pair_energy\n",
"Not included ethanolAA pair_energy\n",
+ "Not included pentaneUA pair_energy\n",
"Not included benzeneUA pair_energy\n",
- "Not included waterSPCE pair_energy\n",
- "Not included pentaneUA pair_energy\n"
+ "Not included methaneUA pair_energy\n",
+ "Not included waterSPCE pair_energy\n"
]
}
],
@@ -177,9 +177,9 @@
"metadata": {},
"outputs": [],
"source": [
- "properties = ['potential_energy', \n",
- " 'tot_vdw_energy', \n",
- " 'tail_energy', \n",
+ "properties = ['potential_energy',\n",
+ " 'tot_vdw_energy',\n",
+ " 'tail_energy',\n",
" 'tot_electrostatics',\n",
" 'short_range_electrostatics',\n",
" 'long_range_electrostatics',\n",
@@ -188,7 +188,7 @@
" 'angles_energy',\n",
" 'dihedrals_energy',\n",
" 'tot_bonded_energy',\n",
- " 'intramolecular_energy', \n",
+ " 'intramolecular_energy',\n",
" 'intermolecular_energy',]"
]
},
@@ -199,15 +199,15 @@
"metadata": {},
"outputs": [],
"source": [
- "hoomd_map = {\"pair_LJ\": (\"tot_pair_energy\", \"tot_vdw_energy\",), \n",
- " \"pair_LJ_tail\": \"tail_energy\", \n",
+ "hoomd_map = {\"pair_LJ\": (\"tot_pair_energy\", \"tot_vdw_energy\",),\n",
+ " \"pair_LJ_tail\": \"tail_energy\",\n",
" \"pair_Ewald\": (\"short_range_electrostatics\", \"tot_electrostatics\",),\n",
" \"pppm_Coulomb\": (\"long_range_electrostatics\", \"tot_electrostatics\",),\n",
" \"special_pair_LJ\": \"tot_pair_energy\",\n",
- " \"special_pair_Coulomb\": (\"short_range_electrostatics\", \"tot_electrostatics\"), \n",
- " \"bond_Harmonic\": \"bonds_energy\", \n",
- " \"angle_Harmonic\": \"angles_energy\", \n",
- " \"dihedral_OPLS\": \"dihedrals_energy\", \n",
+ " \"special_pair_Coulomb\": (\"short_range_electrostatics\", \"tot_electrostatics\"),\n",
+ " \"bond_Harmonic\": \"bonds_energy\",\n",
+ " \"angle_Harmonic\": \"angles_energy\",\n",
+ " \"dihedral_OPLS\": \"dihedrals_energy\",\n",
" \"potential_energy\": \"potential_energy\"}"
]
},
@@ -246,14 +246,14 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "Not included methaneUA lj14\n",
- "Not included methaneUA coulomb14\n",
- "Not included pentaneUA lj14\n",
- "Not included pentaneUA coulomb14\n",
"Not included benzeneUA lj14\n",
"Not included benzeneUA coulomb14\n",
+ "Not included methaneUA lj14\n",
+ "Not included methaneUA coulomb14\n",
"Not included waterSPCE lj14\n",
"Not included waterSPCE coulomb14\n",
+ "Not included pentaneUA lj14\n",
+ "Not included pentaneUA coulomb14\n",
"Not included ethanolAA lj14\n",
"Not included ethanolAA coulomb14\n"
]
@@ -362,13 +362,13 @@
"source": [
"gomc_map = {\n",
" \"TOTAL\": \"potential_energy\",\n",
- " \"INTRA(B)\": \"intramolecular_energy\", \n",
+ " \"INTRA(B)\": \"intramolecular_energy\",\n",
" \"INTRA(NB)\": (\"intramolecular_energy\", \"tot_vdw_energy\", \"tot_pair_energy\"),\n",
- " \"BOND(B)\": \"bonds_energy\", \n",
- " \"ANGLE(B)\": \"angles_energy\", \n",
+ " \"BOND(B)\": \"bonds_energy\",\n",
+ " \"ANGLE(B)\": \"angles_energy\",\n",
" \"DIHEDRAL(B)\": \"dihedrals_energy\",\n",
" \"INTER(LJ)\": (\"intermolecular_energy\", \"tot_vdw_energy\", \"tot_pair_energy\"),\n",
- " \"LRC\": \"tail_energy\",\n",
+ " \"LRC\": (\"tail_energy\", \"tot_vdw_energy\"),\n",
" \"TOTAL_ELECT\": \"tot_electrostatics\",\n",
"}"
]
@@ -383,6 +383,12 @@
"name": "stdout",
"output_type": "stream",
"text": [
+ "Not included benzeneUA ETITLE:\n",
+ "Not included benzeneUA STEP\n",
+ "Not included benzeneUA REAL\n",
+ "Not included benzeneUA RECIP\n",
+ "Not included benzeneUA SELF\n",
+ "Not included benzeneUA CORR\n",
"Not included ethanolAA ETITLE:\n",
"Not included ethanolAA STEP\n",
"Not included ethanolAA REAL\n",
@@ -395,31 +401,25 @@
"Not included waterSPCE RECIP\n",
"Not included waterSPCE SELF\n",
"Not included waterSPCE CORR\n",
- "Not included benzeneUA ETITLE:\n",
- "Not included benzeneUA STEP\n",
- "Not included benzeneUA REAL\n",
- "Not included benzeneUA RECIP\n",
- "Not included benzeneUA SELF\n",
- "Not included benzeneUA CORR\n",
- "Not included pentaneUA ETITLE:\n",
- "Not included pentaneUA STEP\n",
- "Not included pentaneUA REAL\n",
- "Not included pentaneUA RECIP\n",
- "Not included pentaneUA SELF\n",
- "Not included pentaneUA CORR\n",
"Not included methaneUA ETITLE:\n",
"Not included methaneUA STEP\n",
"Not included methaneUA REAL\n",
"Not included methaneUA RECIP\n",
"Not included methaneUA SELF\n",
- "Not included methaneUA CORR\n"
+ "Not included methaneUA CORR\n",
+ "Not included pentaneUA ETITLE:\n",
+ "Not included pentaneUA STEP\n",
+ "Not included pentaneUA REAL\n",
+ "Not included pentaneUA RECIP\n",
+ "Not included pentaneUA SELF\n",
+ "Not included pentaneUA CORR\n"
]
}
],
"source": [
"for job in project.find_jobs({\"engine\": \"gomc\"}):\n",
" with open(f\"{job.ws}/out_production_run.dat\") as f:\n",
- " data = f.readlines() \n",
+ " data = f.readlines()\n",
" for i, line in enumerate(data):\n",
" if \"INITIAL SIMULATION ENERGY\" in line:\n",
" for title, value in zip(data[i+2].split(), data[i+4].split()):\n",
@@ -431,7 +431,7 @@
" for key in gomc_map[title]:\n",
" spe_data[job.sp.molecule][job.sp.engine][key] += K_to_kj_per_mol_conversion(float(value))\n",
" else:\n",
- " print(f\"Not included {job.sp.molecule} {title}\") "
+ " print(f\"Not included {job.sp.molecule} {title}\")"
]
},
{
@@ -559,7 +559,7 @@
" \n",
" | gomc | \n",
" 536736.554367 | \n",
- " 536864.783328 | \n",
+ " 536736.553776 | \n",
" -128.229552 | \n",
" 0.0 | \n",
" 0.0 | \n",
@@ -593,24 +593,24 @@
""
],
"text/plain": [
- " potential_energy tot_vdw_energy tail_energy tot_electrostatics \\\n",
- "lammps-VU 536743.553773 536743.553773 -128.231235 0.0 \n",
+ " potential_energy tot_vdw_energy tail_energy tot_electrostatics \n",
+ "lammps-VU 536743.553773 536743.553773 -128.231235 0.0 \\\n",
"hoomd 536736.470216 536736.470216 -128.229542 0.0 \n",
"gromacs 536736.437500 536736.442657 -128.244843 0.0 \n",
"mcccs 536736.674114 536736.674114 -128.229591 0.0 \n",
- "gomc 536736.554367 536864.783328 -128.229552 0.0 \n",
+ "gomc 536736.554367 536736.553776 -128.229552 0.0 \n",
"cassandra 536737.280000 536737.280260 -128.229740 0.0 \n",
"\n",
- " short_range_electrostatics long_range_electrostatics \\\n",
- "lammps-VU 0.0 0.0 \n",
+ " short_range_electrostatics long_range_electrostatics \n",
+ "lammps-VU 0.0 0.0 \\\n",
"hoomd 0.0 0.0 \n",
"gromacs 0.0 0.0 \n",
"mcccs NaN NaN \n",
"gomc 0.0 0.0 \n",
"cassandra 0.0 0.0 \n",
"\n",
- " tot_pair_energy bonds_energy angles_energy dihedrals_energy \\\n",
- "lammps-VU 536743.553773 0.0 0.0 0.0 \n",
+ " tot_pair_energy bonds_energy angles_energy dihedrals_energy \n",
+ "lammps-VU 536743.553773 0.0 0.0 0.0 \\\n",
"hoomd 536736.470216 0.0 0.0 0.0 \n",
"gromacs 536736.442657 0.0 0.0 0.0 \n",
"mcccs 536736.674114 0.0 0.0 0.0 \n",
@@ -740,7 +740,7 @@
"
\n",
" | gomc | \n",
" 537737.391951 | \n",
- " 537918.489298 | \n",
+ " 537737.381481 | \n",
" -181.107817 | \n",
" 0.0 | \n",
" 0.0 | \n",
@@ -774,24 +774,24 @@
""
],
"text/plain": [
- " potential_energy tot_vdw_energy tail_energy tot_electrostatics \\\n",
- "lammps-VU 537739.120141 537739.120141 -181.108084 0.0 \n",
+ " potential_energy tot_vdw_energy tail_energy tot_electrostatics \n",
+ "lammps-VU 537739.120141 537739.120141 -181.108084 0.0 \\\n",
"hoomd 537737.484007 537737.484000 -181.107804 0.0 \n",
"gromacs 537737.187500 537737.164017 -181.148483 0.0 \n",
"mcccs 537737.792781 537737.792781 -181.107910 0.0 \n",
- "gomc 537737.391951 537918.489298 -181.107817 0.0 \n",
+ "gomc 537737.391951 537737.381481 -181.107817 0.0 \n",
"cassandra 537738.400000 537738.401390 -181.108110 0.0 \n",
"\n",
- " short_range_electrostatics long_range_electrostatics \\\n",
- "lammps-VU 0.0 0.0 \n",
+ " short_range_electrostatics long_range_electrostatics \n",
+ "lammps-VU 0.0 0.0 \\\n",
"hoomd 0.0 0.0 \n",
"gromacs 0.0 0.0 \n",
"mcccs NaN NaN \n",
"gomc 0.0 0.0 \n",
"cassandra 0.0 0.0 \n",
"\n",
- " tot_pair_energy bonds_energy angles_energy dihedrals_energy \\\n",
- "lammps-VU 537739.120141 5.538203e-07 6.262974e-08 2.922458e-09 \n",
+ " tot_pair_energy bonds_energy angles_energy dihedrals_energy \n",
+ "lammps-VU 537739.120141 5.538203e-07 6.262974e-08 2.922458e-09 \\\n",
"hoomd 537737.484000 5.538199e-07 6.686200e-06 2.921942e-09 \n",
"gromacs 537737.164017 2.275352e-06 6.813034e-06 5.722046e-03 \n",
"mcccs 537737.792781 0.000000e+00 6.262988e-08 2.921697e-09 \n",
@@ -880,7 +880,7 @@
" 0.0 | \n",
" 388939.009526 | \n",
" 1.536153e-22 | \n",
- " 2.887668e-10 | \n",
+ " 2.882556e-10 | \n",
" 0.000000e+00 | \n",
" 0.000000e+00 | \n",
" 0.000000e+00 | \n",
@@ -921,7 +921,7 @@
"
\n",
" | gomc | \n",
" 388939.051080 | \n",
- " 389189.609891 | \n",
+ " 388939.051186 | \n",
" -250.558706 | \n",
" 0.0 | \n",
" 0.0 | \n",
@@ -955,25 +955,25 @@
""
],
"text/plain": [
- " potential_energy tot_vdw_energy tail_energy tot_electrostatics \\\n",
- "lammps-VU 388924.223641 388924.223579 -250.549162 0.0 \n",
+ " potential_energy tot_vdw_energy tail_energy tot_electrostatics \n",
+ "lammps-VU 388924.223641 388924.223579 -250.549162 0.0 \\\n",
"hoomd 388939.009526 388939.009526 -250.558687 0.0 \n",
"gromacs 388939.125000 388939.131805 -250.586945 0.0 \n",
"mcccs 388939.009581 388939.009519 -250.558687 0.0 \n",
- "gomc 388939.051080 389189.609891 -250.558706 0.0 \n",
+ "gomc 388939.051080 388939.051186 -250.558706 0.0 \n",
"cassandra 388939.820000 388939.821030 -250.558970 0.0 \n",
"\n",
- " short_range_electrostatics long_range_electrostatics \\\n",
- "lammps-VU 0.0 0.0 \n",
+ " short_range_electrostatics long_range_electrostatics \n",
+ "lammps-VU 0.0 0.0 \\\n",
"hoomd 0.0 0.0 \n",
"gromacs 0.0 0.0 \n",
"mcccs NaN NaN \n",
"gomc 0.0 0.0 \n",
"cassandra 0.0 0.0 \n",
"\n",
- " tot_pair_energy bonds_energy angles_energy dihedrals_energy \\\n",
- "lammps-VU 388924.223579 6.028773e-05 1.522308e-06 3.992398e-08 \n",
- "hoomd 388939.009526 1.536153e-22 2.887668e-10 0.000000e+00 \n",
+ " tot_pair_energy bonds_energy angles_energy dihedrals_energy \n",
+ "lammps-VU 388924.223579 6.028773e-05 1.522308e-06 3.992398e-08 \\\n",
+ "hoomd 388939.009526 1.536153e-22 2.882556e-10 0.000000e+00 \n",
"gromacs 388939.131805 0.000000e+00 3.852421e-10 0.000000e+00 \n",
"mcccs 388939.009519 6.028811e-05 1.522316e-06 3.992194e-08 \n",
"gomc 389189.609891 0.000000e+00 0.000000e+00 0.000000e+00 \n",
@@ -1053,12 +1053,12 @@
"
\n",
" \n",
" | hoomd | \n",
- " 57176.161037 | \n",
+ " 57176.472998 | \n",
" 76663.760676 | \n",
" -275.651183 | \n",
- " -19487.599639 | \n",
- " -14304.716189 | \n",
- " -5182.883450 | \n",
+ " -19487.287483 | \n",
+ " -18732.078823 | \n",
+ " -755.208660 | \n",
" 76663.760676 | \n",
" 0.0 | \n",
" 0.000000e+00 | \n",
@@ -1102,7 +1102,7 @@
"
\n",
" | gomc | \n",
" 57175.433264 | \n",
- " 76939.418379 | \n",
+ " 76663.767176 | \n",
" -275.651204 | \n",
" -19488.333923 | \n",
" 0.000000 | \n",
@@ -1136,24 +1136,24 @@
""
],
"text/plain": [
- " potential_energy tot_vdw_energy tail_energy tot_electrostatics \\\n",
- "lammps-VU 57176.385301 76663.713512 -275.651013 -19487.328212 \n",
- "hoomd 57176.161037 76663.760676 -275.651183 -19487.599639 \n",
+ " potential_energy tot_vdw_energy tail_energy tot_electrostatics \n",
+ "lammps-VU 57176.385301 76663.713512 -275.651013 -19487.328212 \\\n",
+ "hoomd 57176.472998 76663.760676 -275.651183 -19487.287483 \n",
"gromacs 57175.917969 76663.549835 -275.825165 -19487.629883 \n",
"mcccs 57175.422752 76664.198289 -275.652756 -19488.775537 \n",
- "gomc 57175.433264 76939.418379 -275.651204 -19488.333923 \n",
+ "gomc 57175.433264 76663.767176 -275.651204 -19488.333923 \n",
"cassandra 57175.778000 76663.843520 -275.651480 -19488.070300 \n",
"\n",
- " short_range_electrostatics long_range_electrostatics \\\n",
- "lammps-VU 292697.838098 -312185.166310 \n",
- "hoomd -14304.716189 -5182.883450 \n",
+ " short_range_electrostatics long_range_electrostatics \n",
+ "lammps-VU 292697.838098 -312185.166310 \\\n",
+ "hoomd -18732.078823 -755.208660 \n",
"gromacs 0.000000 4493.100586 \n",
"mcccs NaN NaN \n",
"gomc 0.000000 0.000000 \n",
"cassandra 324948.580000 -344436.650300 \n",
"\n",
- " tot_pair_energy bonds_energy angles_energy dihedrals_energy \\\n",
- "lammps-VU 57176.385301 0.0 0.000000e+00 0.0 \n",
+ " tot_pair_energy bonds_energy angles_energy dihedrals_energy \n",
+ "lammps-VU 57176.385301 0.0 0.000000e+00 0.0 \\\n",
"hoomd 76663.760676 0.0 0.000000e+00 0.0 \n",
"gromacs 57175.919952 0.0 0.000000e+00 0.0 \n",
"mcccs 57175.422752 0.0 0.000000e+00 0.0 \n",
@@ -1234,12 +1234,12 @@
"
\n",
" \n",
" | hoomd | \n",
- " 31409.638975 | \n",
+ " 31409.638694 | \n",
" 19363.949308 | \n",
" -417.875752 | \n",
- " 3575.467242 | \n",
+ " 3575.466991 | \n",
" -12484.323747 | \n",
- " 16059.790990 | \n",
+ " 16059.790738 | \n",
" 19408.270670 | \n",
" 0.000060 | \n",
" 7233.270511 | \n",
@@ -1283,7 +1283,7 @@
"
\n",
" | gomc | \n",
" 31409.560443 | \n",
- " 22825.758862 | \n",
+ " 22407.883079 | \n",
" -417.875783 | \n",
" 575.785432 | \n",
" 0.000000 | \n",
@@ -1317,24 +1317,24 @@
""
],
"text/plain": [
- " potential_energy tot_vdw_energy tail_energy tot_electrostatics \\\n",
- "lammps-VU 31409.503929 19408.270670 -417.875752 3575.331283 \n",
- "hoomd 31409.638975 19363.949308 -417.875752 3575.467242 \n",
+ " potential_energy tot_vdw_energy tail_energy tot_electrostatics \n",
+ "lammps-VU 31409.503929 19408.270670 -417.875752 3575.331283 \\\n",
+ "hoomd 31409.638694 19363.949308 -417.875752 3575.466991 \n",
"gromacs 31409.148438 19408.189564 -417.956024 3575.072021 \n",
"mcccs 31409.519803 19408.405387 -417.878592 3575.159662 \n",
- "gomc 31409.560443 22825.758862 -417.875783 575.785432 \n",
+ "gomc 31409.560443 22407.883079 -417.875783 575.785432 \n",
"cassandra 31409.469000 19408.114324 -417.876220 3575.341600 \n",
"\n",
- " short_range_electrostatics long_range_electrostatics \\\n",
- "lammps-VU 81265.612659 -77690.281376 \n",
- "hoomd -12484.323747 16059.790990 \n",
+ " short_range_electrostatics long_range_electrostatics \n",
+ "lammps-VU 81265.612659 -77690.281376 \\\n",
+ "hoomd -12484.323747 16059.790738 \n",
"gromacs -14791.646484 1403.370850 \n",
"mcccs NaN NaN \n",
"gomc 0.000000 0.000000 \n",
"cassandra 95647.914200 -92072.572600 \n",
"\n",
- " tot_pair_energy bonds_energy angles_energy dihedrals_energy \\\n",
- "lammps-VU 22983.601953 0.000060 7233.270516 1192.631400 \n",
+ " tot_pair_energy bonds_energy angles_energy dihedrals_energy \n",
+ "lammps-VU 22983.601953 0.000060 7233.270516 1192.631400 \\\n",
"hoomd 19408.270670 0.000060 7233.270511 1192.630492 \n",
"gromacs 22983.261585 0.000063 7233.265625 1192.620605 \n",
"mcccs 22983.565049 0.000000 7233.316278 1192.638475 \n",
@@ -1355,9 +1355,9 @@
}
],
"source": [
- "import pandas as pd \n",
+ "import pandas as pd\n",
"\n",
- "summarize_dfs = dict() \n",
+ "summarize_dfs = dict()\n",
"for molecule in spe_data:\n",
" print(molecule)\n",
" df = pd.DataFrame.from_dict(spe_data[molecule]).transpose()\n",
@@ -1366,38 +1366,13 @@
]
},
{
- "cell_type": "code",
- "execution_count": 20,
- "id": "1412a0e2-9297-4bce-af26-6a8d80567906",
- "metadata": {
- "tags": []
- },
- "outputs": [
- {
- "data": {
- "text/plain": [
- "{'potential_energy': 536736.4375,\n",
- " 'tot_vdw_energy': 536736.4426574707,\n",
- " 'tail_energy': -128.24484252929688,\n",
- " 'tot_electrostatics': 0.0,\n",
- " 'short_range_electrostatics': 0.0,\n",
- " 'long_range_electrostatics': 0.0,\n",
- " 'tot_pair_energy': 536736.4426574707,\n",
- " 'bonds_energy': 0.0,\n",
- " 'angles_energy': 0.0,\n",
- " 'dihedrals_energy': 0.0,\n",
- " 'tot_bonded_energy': 0.0,\n",
- " 'intramolecular_energy': nan,\n",
- " 'intermolecular_energy': nan}"
- ]
- },
- "execution_count": 20,
- "metadata": {},
- "output_type": "execute_result"
- }
- ],
+ "cell_type": "markdown",
+ "id": "63790c5f",
+ "metadata": {},
"source": [
- "spe_data[\"methaneUA\"][\"gromacs\"]"
+ "### Note for GOMC energy\n",
+ "- `INTRA (NB)` include short range electrostatic --> got included in `tot_vdw_energy`\n",
+ "- Short range electrostatic is not part of `tot_electrostatics` "
]
},
{
@@ -1409,21 +1384,21 @@
"source": [
"potential_energy_table = dict()\n",
"\n",
- "engines = (\"lammps-VU\", \"hoomd\", \"gromacs\", \n",
+ "engines = (\"lammps-VU\", \"hoomd\", \"gromacs\",\n",
" \"mcccs\", \"gomc\", \"cassandra\")\n",
"molecules = (\"methaneUA\", \"pentaneUA\", \"benzeneUA\", \"ethanolAA\", \"waterSPCE\")\n",
"\n",
- "for engine in engines: \n",
+ "for engine in engines:\n",
" potential_energy_table[pretty_names[engine]] = list()\n",
" for molecule in molecules:\n",
" potential_energy_table[pretty_names[engine]].append(\n",
" spe_data[molecule][engine][\"potential_energy\"])\n",
- " \n",
- "potential_energy_df = pd.DataFrame.from_dict(potential_energy_table, \n",
- " orient=\"index\", \n",
+ "\n",
+ "potential_energy_df = pd.DataFrame.from_dict(potential_energy_table,\n",
+ " orient=\"index\",\n",
" columns=[pretty_molecules[molecule] for molecule in molecules])\n",
"\n",
- "potential_energy_df.to_csv(\"csvs/potential_energy.csv\") \n"
+ "potential_energy_df.to_csv(\"csvs/potential_energy.csv\")\n"
]
},
{
@@ -1435,21 +1410,21 @@
"source": [
"electrostatics_table = dict()\n",
"\n",
- "engines = (\"lammps-VU\", \"hoomd\", \"gromacs\", \n",
+ "engines = (\"lammps-VU\", \"hoomd\", \"gromacs\",\n",
" \"mcccs\", \"gomc\", \"cassandra\")\n",
"molecules = (\"methaneUA\", \"pentaneUA\", \"benzeneUA\", \"ethanolAA\", \"waterSPCE\")\n",
"\n",
- "for engine in engines: \n",
+ "for engine in engines:\n",
" electrostatics_table[pretty_names[engine]] = list()\n",
" for molecule in molecules:\n",
" electrostatics_table[pretty_names[engine]].append(\n",
" spe_data[molecule][engine][\"tot_electrostatics\"])\n",
- " \n",
- "electrostatics_df = pd.DataFrame.from_dict(electrostatics_table, \n",
- " orient=\"index\", \n",
+ "\n",
+ "electrostatics_df = pd.DataFrame.from_dict(electrostatics_table,\n",
+ " orient=\"index\",\n",
" columns=[pretty_molecules[molecule] for molecule in molecules])\n",
"\n",
- "electrostatics_df.to_csv(\"csvs/electrostatics_energy.csv\") \n"
+ "electrostatics_df.to_csv(\"csvs/electrostatics_energy.csv\")\n"
]
},
{
@@ -1461,30 +1436,22 @@
"source": [
"vdw_table = dict()\n",
"\n",
- "engines = (\"lammps-VU\", \"hoomd\", \"gromacs\", \n",
+ "engines = (\"lammps-VU\", \"hoomd\", \"gromacs\",\n",
" \"mcccs\", \"gomc\", \"cassandra\")\n",
"molecules = (\"methaneUA\", \"pentaneUA\", \"benzeneUA\", \"ethanolAA\", \"waterSPCE\")\n",
"\n",
- "for engine in engines: \n",
+ "for engine in engines:\n",
" vdw_table[pretty_names[engine]] = list()\n",
" for molecule in molecules:\n",
" vdw_table[pretty_names[engine]].append(\n",
" spe_data[molecule][engine][\"tot_vdw_energy\"])\n",
- " \n",
- "vdw_df = pd.DataFrame.from_dict(vdw_table, \n",
- " orient=\"index\", \n",
+ "\n",
+ "vdw_df = pd.DataFrame.from_dict(vdw_table,\n",
+ " orient=\"index\",\n",
" columns=[pretty_molecules[molecule] for molecule in molecules])\n",
"\n",
- "vdw_df.to_csv(\"csvs/vdw_energy.csv\") \n"
+ "vdw_df.to_csv(\"csvs/vdw_energy.csv\")\n"
]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "id": "3d089dda-d33b-4f73-a8b0-95b36be74d87",
- "metadata": {},
- "outputs": [],
- "source": []
}
],
"metadata": {
@@ -1503,7 +1470,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
- "version": "3.10.13"
+ "version": "3.10.11"
}
},
"nbformat": 4,
diff --git a/reproducibility_project/spe_subproject/csvs/benzeneUA_spe.csv b/reproducibility_project/spe_subproject/csvs/benzeneUA_spe.csv
index 679cbc4b..0fcaab66 100644
--- a/reproducibility_project/spe_subproject/csvs/benzeneUA_spe.csv
+++ b/reproducibility_project/spe_subproject/csvs/benzeneUA_spe.csv
@@ -1,7 +1,7 @@
-,potential_energy,tot_vdw_energy,tail_energy,tot_electrostatics,short_range_electrostatics,long_range_electrostatics,tot_pair_energy,bonds_energy,angles_energy,dihedrals_energy,tot_bonded_energy,intramolecular_energy,intermolecular_energy,total_electrostatics
-lammps-VU,388924.22364089265,388924.2235790427,-250.54916165210687,0.0,0.0,0.0,388924.2235790427,6.02877287576594e-05,1.522308140204045e-06,3.9923977221445445e-08,0.0,0.0,0.0,
-hoomd,388939.009526007,0.0,-250.558686917935,0.0,0.0,0.0,388939.009526006,1.53615277086747e-22,2.88255557109613e-10,0.0,0.0,0.0,0.0,
-gromacs,388939.125,388939.1318054199,-250.58694458007812,0.0,0.0,0.0,388939.1318054199,0.0,3.8524208822998673e-10,0.0,3.8524208822998673e-10,,,
-mcccs,388939.0095806981,388939.0095188476,-250.55868691331776,0.0,,,388939.0095188476,6.028810906180086e-05,1.5223164286319892e-06,3.9921937021332453e-08,6.185034742745418e-05,,,
-gomc,388939.0510802308,0.0,-250.5587055035384,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,389189.60989132803,0.0
-cassandra,388939.82,388939.82103,-250.55897,0.0,0.0,0.0,388939.82103,,3.3068365e-07,7.6991505e-08,,4.07675155e-07,389190.38,
+,potential_energy,tot_vdw_energy,tail_energy,tot_electrostatics,short_range_electrostatics,long_range_electrostatics,tot_pair_energy,bonds_energy,angles_energy,dihedrals_energy,tot_bonded_energy,intramolecular_energy,intermolecular_energy
+lammps-VU,388924.22364089265,388924.2235790427,-250.54916165210687,0.0,0.0,0.0,388924.2235790427,6.02877287576594e-05,1.522308140204045e-06,3.9923977221445445e-08,6.184996087508489e-05,,
+hoomd,388939.009526007,388939.009526006,-250.558686917935,0.0,0.0,0.0,388939.009526006,1.53615277086747e-22,2.88255557109613e-10,0.0,0.0,0.0,0.0
+gromacs,388939.125,388939.1318054199,-250.58694458007812,0.0,0.0,0.0,388939.1318054199,0.0,3.8524208822998673e-10,0.0,3.8524208822998673e-10,,
+mcccs,388939.0095806981,388939.0095188476,-250.55868691331776,0.0,,,388939.0095188476,6.028810906180086e-05,1.5223164286319892e-06,3.9921937021332453e-08,6.185034742745418e-05,,
+gomc,388939.0510802308,388939.0511858245,-250.5587055035384,0.0,0.0,0.0,389189.60989132803,0.0,0.0,0.0,0.0,0.0,389189.60989132803
+cassandra,388939.82,388939.82103,-250.55897,0.0,0.0,0.0,388939.82103,,3.3068365e-07,7.6991505e-08,,4.07675155e-07,389190.38
diff --git a/reproducibility_project/spe_subproject/csvs/electrostatics_energy.csv b/reproducibility_project/spe_subproject/csvs/electrostatics_energy.csv
index 566e6748..2daa7078 100644
--- a/reproducibility_project/spe_subproject/csvs/electrostatics_energy.csv
+++ b/reproducibility_project/spe_subproject/csvs/electrostatics_energy.csv
@@ -1,6 +1,6 @@
,TraPPE Methane,TraPPE Pentane,TraPPE Benzene,OPLS-AA Ethanol,SPC/E Water
LAMMPS,0.0,0.0,0.0,3575.331282583502,-19487.328211568238
-HOOMD-blue,0.0,0.0,0.0,3575.4672422771982,-19487.599638683998
+HOOMD-blue,0.0,0.0,0.0,3575.466990784098,-19487.28748265558
GROMACS,0.0,0.0,0.0,3575.072021484375,-19487.6298828125
MCCCS-MN,0.0,0.0,0.0,3575.1596619394923,-19488.77553704541
GOMC,0.0,0.0,0.0,575.7854324857847,-19488.33392311652
diff --git a/reproducibility_project/spe_subproject/csvs/ethanolAA_spe.csv b/reproducibility_project/spe_subproject/csvs/ethanolAA_spe.csv
index b5189111..cb01a792 100644
--- a/reproducibility_project/spe_subproject/csvs/ethanolAA_spe.csv
+++ b/reproducibility_project/spe_subproject/csvs/ethanolAA_spe.csv
@@ -1,7 +1,7 @@
-,potential_energy,tot_vdw_energy,tail_energy,tot_electrostatics,short_range_electrostatics,long_range_electrostatics,tot_pair_energy,bonds_energy,angles_energy,dihedrals_energy,tot_bonded_energy,intramolecular_energy,intermolecular_energy,total_electrostatics
-lammps-VU,31409.503929307408,19408.270670300964,-417.8757523306034,3575.331282583502,81265.61265888733,-77690.28137630383,22983.601952884466,5.9652454519500356e-05,7233.270516470011,1192.6314003007387,0.0,0.0,0.0,
-hoomd,31409.6386935969,0.0,-417.875752330603,0.0,-12484.3237474291,16059.7907382132,19408.27067030094,5.96524545191986e-05,7233.27051100042,1192.63049177032,0.0,0.0,0.0,
-gromacs,31409.1484375,19408.18956375122,-417.9560241699219,3575.072021484375,-14791.646484375,1403.370849609375,22983.261585235596,6.286923598963767e-05,7233.265625,1192.62060546875,8425.886293337986,,,
-mcccs,31409.519802548064,19408.405387095594,-417.8785923630039,3575.1596619394923,,,22983.565049035085,0.0,7233.316278303621,1192.6384752094077,8425.95475351303,,,
-gomc,31409.560442760474,0.0,-417.87578305803,0.0,0.0,0.0,0.0,6.225275294415543e-05,7233.2713718767545,1192.6204803853652,0.0,3043.937811510002,19781.821050573206,575.7854324857847
-cassandra,31409.469,19408.114324000002,-417.87622,3575.3415999999957,95647.9142,-92072.5726,22983.455923999998,,7233.2478,1192.7656,,11469.911144,20357.434399999995,
+,potential_energy,tot_vdw_energy,tail_energy,tot_electrostatics,short_range_electrostatics,long_range_electrostatics,tot_pair_energy,bonds_energy,angles_energy,dihedrals_energy,tot_bonded_energy,intramolecular_energy,intermolecular_energy
+lammps-VU,31409.503929307408,19408.270670300964,-417.8757523306034,3575.331282583502,81265.61265888733,-77690.28137630383,22983.601952884466,5.9652454519500356e-05,7233.270516470011,1192.6314003007387,8425.901976423203,,
+hoomd,31409.6386935969,19363.9493078645,-417.875752330603,3575.466990784098,-12484.3237474291,16059.7907382132,19408.27067030094,5.96524545191986e-05,7233.27051100042,1192.63049177032,0.0,0.0,0.0
+gromacs,31409.1484375,19408.18956375122,-417.9560241699219,3575.072021484375,-14791.646484375,1403.370849609375,22983.261585235596,6.286923598963767e-05,7233.265625,1192.62060546875,8425.886293337986,,
+mcccs,31409.519802548064,19408.405387095594,-417.8785923630039,3575.1596619394923,,,22983.565049035085,0.0,7233.316278303621,1192.6384752094077,8425.95475351303,,
+gomc,31409.560442760474,22407.883079025178,-417.87578305803,575.7854324857847,0.0,0.0,22825.758862083207,6.225275294415543e-05,7233.2713718767545,1192.6204803853652,0.0,11469.829713658895,19781.821050573206
+cassandra,31409.469,19408.114324000002,-417.87622,3575.3415999999957,95647.9142,-92072.5726,22983.455923999998,,7233.2478,1192.7656,,11469.911144,20357.434399999995
diff --git a/reproducibility_project/spe_subproject/csvs/methaneUA_spe.csv b/reproducibility_project/spe_subproject/csvs/methaneUA_spe.csv
index a9148c64..dea2892c 100644
--- a/reproducibility_project/spe_subproject/csvs/methaneUA_spe.csv
+++ b/reproducibility_project/spe_subproject/csvs/methaneUA_spe.csv
@@ -1,7 +1,7 @@
-,potential_energy,tot_vdw_energy,tail_energy,tot_electrostatics,short_range_electrostatics,long_range_electrostatics,tot_pair_energy,bonds_energy,angles_energy,dihedrals_energy,tot_bonded_energy,intramolecular_energy,intermolecular_energy,total_electrostatics
-lammps-VU,536743.5537731947,536743.5537731947,-128.23123468785766,0.0,0.0,0.0,536743.5537731947,0.0,0.0,0.0,0.0,0.0,0.0,
-hoomd,536736.470216157,0.0,-128.229542383854,0.0,0.0,0.0,536736.470216156,0.0,0.0,0.0,0.0,0.0,0.0,
-gromacs,536736.4375,536736.4426574707,-128.24484252929688,0.0,0.0,0.0,536736.4426574707,0.0,0.0,0.0,0.0,,,
-mcccs,536736.674114428,536736.674114428,-128.22959109636633,0.0,,,536736.674114428,0.0,0.0,0.0,0.0,,,
-gomc,536736.5543672631,0.0,-128.22955215302466,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,536864.7833282579,0.0
-cassandra,536737.28,536737.28026,-128.22974,0.0,0.0,0.0,536737.28026,,0.0,0.0,,0.0,536865.51,
+,potential_energy,tot_vdw_energy,tail_energy,tot_electrostatics,short_range_electrostatics,long_range_electrostatics,tot_pair_energy,bonds_energy,angles_energy,dihedrals_energy,tot_bonded_energy,intramolecular_energy,intermolecular_energy
+lammps-VU,536743.5537731947,536743.5537731947,-128.23123468785766,0.0,0.0,0.0,536743.5537731947,0.0,0.0,0.0,0.0,,
+hoomd,536736.470216157,536736.470216156,-128.229542383854,0.0,0.0,0.0,536736.470216156,0.0,0.0,0.0,0.0,0.0,0.0
+gromacs,536736.4375,536736.4426574707,-128.24484252929688,0.0,0.0,0.0,536736.4426574707,0.0,0.0,0.0,0.0,,
+mcccs,536736.674114428,536736.674114428,-128.22959109636633,0.0,,,536736.674114428,0.0,0.0,0.0,0.0,,
+gomc,536736.5543672631,536736.5537761048,-128.22955215302466,0.0,0.0,0.0,536864.7833282579,0.0,0.0,0.0,0.0,0.0,536864.7833282579
+cassandra,536737.28,536737.28026,-128.22974,0.0,0.0,0.0,536737.28026,,0.0,0.0,,0.0,536865.51
diff --git a/reproducibility_project/spe_subproject/csvs/pentaneUA_spe.csv b/reproducibility_project/spe_subproject/csvs/pentaneUA_spe.csv
index 85679c85..049a34fc 100644
--- a/reproducibility_project/spe_subproject/csvs/pentaneUA_spe.csv
+++ b/reproducibility_project/spe_subproject/csvs/pentaneUA_spe.csv
@@ -1,7 +1,7 @@
-,potential_energy,tot_vdw_energy,tail_energy,tot_electrostatics,short_range_electrostatics,long_range_electrostatics,tot_pair_energy,bonds_energy,angles_energy,dihedrals_energy,tot_bonded_energy,intramolecular_energy,intermolecular_energy,total_electrostatics
-lammps-VU,537739.1201412209,537739.1201406015,-181.1080840640345,0.0,0.0,0.0,537739.1201406015,5.538203280251401e-07,6.262974415313544e-08,2.922457877532078e-09,0.0,0.0,0.0,
-hoomd,537737.484007284,0.0,-181.107803669136,0.0,0.0,0.0,537737.484000041,5.53819893825059e-07,6.68619961920037e-06,2.92194221925724e-09,0.0,0.0,0.0,
-gromacs,537737.1875,537737.1640167236,-181.1484832763672,0.0,0.0,0.0,537737.1640167236,2.275351789648994e-06,6.813033905928023e-06,0.0057220458984375,0.005731134284133077,,,
-mcccs,537737.7927811133,537737.7927810473,-181.10791011303985,0.0,,,537737.7927810473,0.0,6.262987838449455e-08,2.9216973545551533e-09,6.55515757390497e-08,,,
-gomc,537737.3919505652,0.0,-181.10781695713783,0.0,0.0,0.0,0.0,2.4486286741319637e-06,7.013628549639668e-06,0.010041617717836702,0.0,-122.1003235547879,538040.5896215064,0.0
-cassandra,537738.4,537738.40139,-181.10811,0.0,0.0,0.0,537738.40139,,6.3702885e-08,2.9359072e-09,,-122.1004999333612,538041.61,
+,potential_energy,tot_vdw_energy,tail_energy,tot_electrostatics,short_range_electrostatics,long_range_electrostatics,tot_pair_energy,bonds_energy,angles_energy,dihedrals_energy,tot_bonded_energy,intramolecular_energy,intermolecular_energy
+lammps-VU,537739.1201412209,537739.1201406015,-181.1080840640345,0.0,0.0,0.0,537739.1201406015,5.538203280251401e-07,6.262974415313544e-08,2.922457877532078e-09,6.193725300558077e-07,,
+hoomd,537737.484007284,537737.484000041,-181.107803669136,0.0,0.0,0.0,537737.484000041,5.53819893825059e-07,6.68619961920037e-06,2.92194221925724e-09,0.0,0.0,0.0
+gromacs,537737.1875,537737.1640167236,-181.1484832763672,0.0,0.0,0.0,537737.1640167236,2.275351789648994e-06,6.813033905928023e-06,0.0057220458984375,0.005731134284133077,,
+mcccs,537737.7927811133,537737.7927810473,-181.10791011303985,0.0,,,537737.7927810473,0.0,6.262987838449455e-08,2.9216973545551533e-09,6.55515757390497e-08,,
+gomc,537737.3919505652,537737.3814809944,-181.10781695713783,0.0,0.0,0.0,537918.4892979516,2.4486286741319637e-06,7.013628549639668e-06,0.010041617717836702,0.0,-122.09027247479642,538040.5896215064
+cassandra,537738.4,537738.40139,-181.10811,0.0,0.0,0.0,537738.40139,,6.3702885e-08,2.9359072e-09,,-122.1004999333612,538041.61
diff --git a/reproducibility_project/spe_subproject/csvs/potential_energy.csv b/reproducibility_project/spe_subproject/csvs/potential_energy.csv
index ebf86776..e10532b8 100644
--- a/reproducibility_project/spe_subproject/csvs/potential_energy.csv
+++ b/reproducibility_project/spe_subproject/csvs/potential_energy.csv
@@ -1,6 +1,6 @@
,TraPPE Methane,TraPPE Pentane,TraPPE Benzene,OPLS-AA Ethanol,SPC/E Water
LAMMPS,536743.5537731947,537739.1201412209,388924.22364089265,31409.503929307408,57176.38530082049
-HOOMD-blue,536736.470216157,537737.484007284,388939.009526007,31409.6389750015,57176.1610373271
+HOOMD-blue,536736.470216157,537737.484007284,388939.009526007,31409.6386935969,57176.4729980335
GROMACS,536736.4375,537737.1875,388939.125,31409.1484375,57175.91796875
MCCCS-MN,536736.674114428,537737.7927811133,388939.0095806981,31409.519802548064,57175.42275162585
GOMC,536736.5543672631,537737.3919505652,388939.0510802308,31409.560442760474,57175.433263516505
diff --git a/reproducibility_project/spe_subproject/csvs/vdw_energy.csv b/reproducibility_project/spe_subproject/csvs/vdw_energy.csv
index ae025e21..db9cac62 100644
--- a/reproducibility_project/spe_subproject/csvs/vdw_energy.csv
+++ b/reproducibility_project/spe_subproject/csvs/vdw_energy.csv
@@ -1,7 +1,7 @@
,TraPPE Methane,TraPPE Pentane,TraPPE Benzene,OPLS-AA Ethanol,SPC/E Water
LAMMPS,536743.5537731947,537739.1201406015,388924.2235790427,19408.270670300964,76663.71351238873
-HOOMD-blue,536736.470216156,537737.484000041,388939.009526007,19363.9493078645,76663.7606760111
+HOOMD-blue,536736.470216156,537737.484000041,388939.009526006,19363.9493078645,76663.7606760111
GROMACS,536736.4426574707,537737.1640167236,388939.1318054199,19408.18956375122,76663.54983520508
MCCCS-MN,536736.674114428,537737.7927810473,388939.0095188476,19408.405387095594,76664.19828867125
-GOMC,536864.7833282579,537918.4892979516,389189.60989132803,22825.758862083207,76939.41837932877
+GOMC,536736.5537761048,537737.3814809944,388939.0511858245,22407.883079025178,76663.76717582422
Cassandra,536737.28026,537738.40139,388939.82103,19408.114324000002,76663.84352
diff --git a/reproducibility_project/spe_subproject/csvs/waterSPCE_spe.csv b/reproducibility_project/spe_subproject/csvs/waterSPCE_spe.csv
index c1676d36..8cb1ddd3 100644
--- a/reproducibility_project/spe_subproject/csvs/waterSPCE_spe.csv
+++ b/reproducibility_project/spe_subproject/csvs/waterSPCE_spe.csv
@@ -1,7 +1,7 @@
-,potential_energy,tot_vdw_energy,tail_energy,tot_electrostatics,short_range_electrostatics,long_range_electrostatics,tot_pair_energy,bonds_energy,angles_energy,dihedrals_energy,tot_bonded_energy,intramolecular_energy,intermolecular_energy,total_electrostatics
-lammps-VU,57176.38530082049,76663.71351238873,-275.65101326646686,-19487.328211568238,292697.83809846675,-312185.166310035,57176.38530082049,0.0,0.0,0.0,0.0,0.0,0.0,
-hoomd,57176.4729980335,0.0,-275.65118284735,0.0,-18732.0788230695,-755.208659586083,76663.7606760111,0.0,0.0,0.0,0.0,0.0,0.0,
-gromacs,57175.91796875,76663.54983520508,-275.8251647949219,-19487.6298828125,0.0,4493.1005859375,57175.91995239258,0.0,0.0,0.0,0.0,,,
-mcccs,57175.42275162585,76664.19828867125,-275.65275632152225,-19488.77553704541,,,57175.42275162584,0.0,0.0,0.0,0.0,,,
-gomc,57175.433263516505,0.0,-275.6512035045485,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,76939.41837932877,-19488.33392311652
-cassandra,57175.778,76663.84352,-275.65148,-19488.070299999996,324948.58,-344436.65030000004,57175.77322,,7.2745889e-09,0.0,,7.2745889e-09,57451.4247,
+,potential_energy,tot_vdw_energy,tail_energy,tot_electrostatics,short_range_electrostatics,long_range_electrostatics,tot_pair_energy,bonds_energy,angles_energy,dihedrals_energy,tot_bonded_energy,intramolecular_energy,intermolecular_energy
+lammps-VU,57176.38530082049,76663.71351238873,-275.65101326646686,-19487.328211568238,292697.83809846675,-312185.166310035,57176.38530082049,0.0,0.0,0.0,0.0,,
+hoomd,57176.4729980335,76663.7606760111,-275.65118284735,-19487.28748265558,-18732.0788230695,-755.208659586083,76663.7606760111,0.0,0.0,0.0,0.0,0.0,0.0
+gromacs,57175.91796875,76663.54983520508,-275.8251647949219,-19487.6298828125,0.0,4493.1005859375,57175.91995239258,0.0,0.0,0.0,0.0,,
+mcccs,57175.42275162585,76664.19828867125,-275.65275632152225,-19488.77553704541,,,57175.42275162584,0.0,0.0,0.0,0.0,,
+gomc,57175.433263516505,76663.76717582422,-275.6512035045485,-19488.33392311652,0.0,0.0,76939.41837932877,0.0,0.0,0.0,0.0,0.0,76939.41837932877
+cassandra,57175.778,76663.84352,-275.65148,-19488.070299999996,324948.58,-344436.65030000004,57175.77322,,7.2745889e-09,0.0,,7.2745889e-09,57451.4247