{ "cells": [ { "cell_type": "markdown", "id": "e4e1e412", "metadata": {}, "source": [ "## Initial Imports" ] }, { "cell_type": "code", "execution_count": 1, "id": "29df709e", "metadata": {}, "outputs": [], "source": [ "from scm.plams import read_molecules, Settings, AMSJob, init, config, JobRunner, view" ] }, { "cell_type": "markdown", "id": "e26bd035", "metadata": {}, "source": [ "## Summary Text File" ] }, { "cell_type": "markdown", "id": "f6c3c741", "metadata": {}, "source": [ "Set up a results file, `summary.txt`, which will hold a table with reaction energies." ] }, { "cell_type": "code", "execution_count": 2, "id": "72874d95", "metadata": {}, "outputs": [], "source": [ "summary_fname = \"summary.txt\"\n", "with open(summary_fname, \"w\", buffering=1) as summary_file:\n", " summary_file.write(\n", " \"#Method HC7_1 HC7_2 HC7_3 HC7_4 HC7_5 HC7_6 HC7_7 ISOL6_1 ISOL6_2 ISOL6_3 ISOL6_4 ISOL6_5 (kcal/mol)\\n\"\n", " )\n", " summary_file.write(\n", " \"Truhlar_ref 14.34 25.02 1.90 9.81 14.84 193.99 127.22 9.77 21.76 6.82 33.52 5.30\\n\"\n", " )\n", " summary_file.write(\n", " \"Smith_wB97X_ref 28.77 41.09 1.75 6.26 9.30 238.83 157.65 9.32 20.80 1.03 26.43 0.40\\n\"\n", " )" ] }, { "cell_type": "markdown", "id": "00410e3b", "metadata": { "tags": [] }, "source": [ "## Benchmark Calculation Setup" ] }, { "cell_type": "markdown", "id": "8fbabb5f", "metadata": {}, "source": [ "The molecules used in the benchmark calculations are loaded, and the settings for each engine created. " ] }, { "cell_type": "code", "execution_count": 3, "id": "e03b31bc", "metadata": {}, "outputs": [], "source": [ "from pathlib import Path\n", "import zipfile\n", "\n", "# dependency: {} molecules_ReactionEnergyBenchmark.zip\n", "\n", "archive = Path(\"molecules_ReactionEnergyBenchmark.zip\")\n", "if archive.exists() and not Path(\"HC7-11\").exists():\n", " with zipfile.ZipFile(archive) as zf:\n", " zf.extractall(Path.cwd())\n", "\n", "mol_dict = read_molecules(\"HC7-11\")\n", "mol_dict.update(read_molecules(\"ISOL6\"))" ] }, { "cell_type": "code", "execution_count": 4, "id": "b4fd01b0", "metadata": {}, "outputs": [], "source": [ "s_reaxff = Settings()\n", "s_reaxff.input.ReaxFF.ForceField = \"CHON-2019.ff\"\n", "\n", "s_ani2x = Settings()\n", "s_ani2x.input.MLPotential.Backend = \"TorchANI\"\n", "s_ani2x.input.MLPotential.Model = \"ANI-2x\"\n", "\n", "s_ani1ccx = Settings()\n", "s_ani1ccx.input.MLPotential.Backend = \"TorchANI\"\n", "s_ani1ccx.input.MLPotential.Model = \"ANI-1ccx\"\n", "\n", "s_dftb = Settings()\n", "s_dftb.input.DFTB.Model = \"SCC-DFTB\"\n", "s_dftb.input.DFTB.ResourcesDir = \"DFTB.org/mio-1-1\"\n", "\n", "s_band = Settings()\n", "s_band.input.BAND.XC.libxc = \"wb97x\"\n", "s_band.input.BAND.Basis.Type = \"TZP\"\n", "s_band.input.BAND.Basis.Core = \"None\"\n", "\n", "s_adf = Settings()\n", "s_adf.input.ADF.Basis.Type = \"TZP\"\n", "s_adf.input.ADF.Basis.Core = \"None\"\n", "s_adf.input.ADF.XC.libxc = \"WB97X\"\n", "\n", "s_mp2 = Settings()\n", "s_mp2.input.ADF.Basis.Type = \"TZ2P\"\n", "s_mp2.input.ADF.Basis.Core = \"None\"\n", "s_mp2.input.ADF.XC.MP2 = \"\"" ] }, { "cell_type": "markdown", "id": "9a1d21e8", "metadata": {}, "source": [ "The engines in `s_engine_dict` below will be used for the calculation - you can remove the engines that you would not like to run (for example, if you do not have the necessary license)." ] }, { "cell_type": "code", "execution_count": 5, "id": "123ead3a", "metadata": {}, "outputs": [], "source": [ "s_engine_dict = {\n", " \"ANI-1ccx\": s_ani1ccx,\n", " \"ANI-2x\": s_ani2x,\n", " \"DFTB\": s_dftb,\n", " \"ReaxFF\": s_reaxff,\n", " \"ADF\": s_adf,\n", " \"MP2\": s_mp2,\n", " \"BAND\": s_band,\n", "}" ] }, { "cell_type": "code", "execution_count": 6, "id": "40806dcf", "metadata": {}, "outputs": [], "source": [ "s_ams = Settings()\n", "s_ams.input.ams.Task = \"SinglePoint\"\n", "# s_ams.input.ams.Task = 'GeometryOptimization'\n", "# s_ams.input.ams.GeometryOptimization.CoordinateType = 'Cartesian'\n", "\n", "jobs = dict()" ] }, { "cell_type": "markdown", "id": "81817cb5", "metadata": {}, "source": [ "## Running Benchmark Calculations" ] }, { "cell_type": "markdown", "id": "5721af70", "metadata": {}, "source": [ "Benchmark calculations are configured to run in parallel with one core per job." ] }, { "cell_type": "code", "execution_count": 7, "id": "9ba200ab", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Running up to 12 jobs in parallel\n" ] } ], "source": [ "import multiprocessing\n", "\n", "maxjobs = multiprocessing.cpu_count()\n", "config.default_jobrunner = JobRunner(parallel=True, maxjobs=maxjobs)\n", "config.job.runscript.nproc = 1\n", "\n", "print(f\"Running up to {maxjobs} jobs in parallel\")" ] }, { "cell_type": "markdown", "id": "06407460", "metadata": {}, "source": [ "Note: calculations will take some time to run, around 1-2 hours on a modern laptop." ] }, { "cell_type": "code", "execution_count": 8, "id": "e075c4e0", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "[23.03|12:29:26] JOB ANI-1ccx_ethylene STARTED\n", "[23.03|12:29:26] JOB ANI-1ccx_hexane STARTED\n", "[23.03|12:29:26] JOB ANI-1ccx_methane STARTED\n", "[23.03|12:29:26] JOB ANI-1ccx_2233tetramethylbutane STARTED\n", "[23.03|12:29:26] JOB ANI-1ccx_bicyclo222octane STARTED\n", "[23.03|12:29:26] JOB ANI-1ccx_31 STARTED\n", "[23.03|12:29:26] JOB ANI-1ccx_adamantane STARTED\n", "[23.03|12:29:26] JOB ANI-1ccx_ethyne STARTED\n", "[23.03|12:29:26] JOB ANI-1ccx_22 STARTED\n", "[23.03|12:29:26] JOB ANI-1ccx_ethylene RUNNING\n", "[23.03|12:29:26] JOB ANI-1ccx_1 STARTED\n", "[23.03|12:29:26] JOB ANI-1ccx_ethane STARTED\n", "[23.03|12:29:26] JOB ANI-1ccx_octane STARTED\n", "[23.03|12:29:26] JOB ANI-1ccx_e_14 STARTED\n", "[23.03|12:29:26] JOB ANI-1ccx_hexane RUNNING\n", "[23.03|12:29:26] JOB ANI-1ccx_p_9 STARTED\n", "[23.03|12:29:26] JOB ANI-1ccx_e_3 STARTED\n", "[23.03|12:29:26] JOB ANI-1ccx_e_13 STARTED\n", "[23.03|12:29:26] JOB ANI-1ccx_e_10 STARTED\n", "[23.03|12:29:26] JOB ANI-1ccx_p_14 STARTED\n", "[23.03|12:29:26] JOB ANI-1ccx_p_10 STARTED\n", "[23.03|12:29:26] JOB ANI-1ccx_methane RUNNING\n", "[23.03|12:29:26] JOB ANI-1ccx_p_13 STARTED\n", "[23.03|12:29:26] JOB ANI-1ccx_p_3 STARTED\n", "[23.03|12:29:26] JOB ANI-1ccx_e_9 STARTED\n", "[23.03|12:29:26] JOB ANI-2x_ethylene STARTED\n", "[23.03|12:29:26] JOB ANI-2x_hexane STARTED\n", "[23.03|12:29:26] JOB ANI-2x_methane STARTED\n", "[23.03|12:29:26] JOB ANI-2x_2233tetramethylbutane STARTED\n", "[23.03|12:29:26] JOB ANI-2x_bicyclo222octane STARTED\n", "[23.03|12:29:26] JOB ANI-1ccx_2233tetramethylbutane RUNNING\n", "[23.03|12:29:26] JOB ANI-1ccx_bicyclo222octane RUNNING\n", "[23.03|12:29:26] JOB ANI-2x_31 STARTED\n", "[23.03|12:29:26] JOB ANI-2x_adamantane STARTED\n", "[23.03|12:29:26] JOB ANI-2x_ethyne STARTED\n", "[23.03|12:29:26] JOB ANI-2x_22 STARTED\n", "[23.03|12:29:26] JOB ANI-2x_1 STARTED\n", "[23.03|12:29:26] JOB ANI-1ccx_31 RUNNING\n", "[23.03|12:29:26] JOB ANI-1ccx_adamantane RUNNING\n", "[23.03|12:29:26] JOB ANI-2x_ethane STARTED\n", "[23.03|12:29:26] JOB ANI-2x_octane STARTED\n", "[23.03|12:29:26] JOB ANI-2x_e_14 STARTED\n", "[23.03|12:29:26] JOB ANI-2x_p_9 STARTED\n", "[23.03|12:29:26] JOB ANI-2x_e_3 STARTED\n", "[23.03|12:29:26] JOB ANI-2x_e_13 STARTED\n", "[23.03|12:29:26] JOB ANI-2x_e_10 STARTED\n", "[23.03|12:29:26] JOB ANI-2x_p_14 STARTED\n", "[23.03|12:29:26] JOB ANI-2x_p_10 STARTED\n", "[23.03|12:29:26] JOB ANI-2x_p_13 STARTED\n", "[23.03|12:29:26] JOB ANI-2x_p_3 STARTED\n", "[23.03|12:29:26] JOB ANI-2x_e_9 STARTED\n", "[23.03|12:29:26] JOB DFTB_ethylene STARTED\n", "[23.03|12:29:26] JOB DFTB_hexane STARTED\n", "[23.03|12:29:26] JOB DFTB_methane STARTED\n", "[23.03|12:29:26] JOB DFTB_2233tetramethylbutane STARTED\n", "[23.03|12:29:26] JOB ANI-1ccx_ethyne RUNNING\n", "[23.03|12:29:26] JOB DFTB_bicyclo222octane STARTED\n", "[23.03|12:29:26] JOB DFTB_31 STARTED\n", "[23.03|12:29:26] JOB DFTB_adamantane STARTED\n", "[23.03|12:29:26] JOB DFTB_ethyne STARTED\n", "[23.03|12:29:26] JOB DFTB_22 STARTED\n", "[23.03|12:29:26] JOB DFTB_1 STARTED\n", "[23.03|12:29:26] JOB ANI-1ccx_22 RUNNING\n", "[23.03|12:29:26] JOB DFTB_ethane STARTED\n", "[23.03|12:29:26] JOB DFTB_octane STARTED\n", "[23.03|12:29:26] JOB DFTB_e_14 STARTED\n", "[23.03|12:29:26] JOB DFTB_p_9 STARTED\n", "[23.03|12:29:26] JOB DFTB_e_3 STARTED\n", "[23.03|12:29:26] JOB ANI-1ccx_1 RUNNING\n", "[23.03|12:29:26] JOB DFTB_e_13 STARTED\n", "[23.03|12:29:26] JOB ANI-1ccx_ethane RUNNING\n", "[23.03|12:29:26] JOB DFTB_e_10 STARTED\n", "[23.03|12:29:26] JOB DFTB_p_14 STARTED\n", "[23.03|12:29:26] JOB DFTB_p_10 STARTED\n", "[23.03|12:29:26] JOB DFTB_p_13 STARTED\n", "[23.03|12:29:26] JOB DFTB_p_3 STARTED\n", "[23.03|12:29:27] JOB DFTB_e_9 STARTED\n", "[23.03|12:29:27] JOB ReaxFF_ethylene STARTED\n", "[23.03|12:29:27] JOB ANI-1ccx_octane RUNNING\n", "[23.03|12:29:27] JOB ANI-1ccx_e_14 RUNNING\n", "[23.03|12:29:27] JOB ReaxFF_hexane STARTED\n", "[23.03|12:29:27] JOB ANI-1ccx_p_9 RUNNING\n", "[23.03|12:29:27] JOB ReaxFF_methane STARTED\n", "[23.03|12:29:27] JOB ANI-1ccx_p_14 RUNNING\n", "[23.03|12:29:27] JOB ANI-1ccx_e_3 RUNNING\n", "[23.03|12:29:27] JOB ReaxFF_2233tetramethylbutane STARTED\n", "[23.03|12:29:27] JOB ReaxFF_bicyclo222octane STARTED\n", "[23.03|12:29:27] JOB ReaxFF_31 STARTED\n", "[23.03|12:29:27] JOB ReaxFF_adamantane STARTED\n", "[23.03|12:29:27] JOB ReaxFF_ethyne STARTED\n", "[23.03|12:29:27] JOB ReaxFF_22 STARTED\n", "[23.03|12:29:27] JOB ReaxFF_1 STARTED\n", "[23.03|12:29:27] JOB ReaxFF_ethane STARTED\n", "[23.03|12:29:27] JOB ReaxFF_octane STARTED\n", "[23.03|12:29:27] JOB ReaxFF_e_14 STARTED\n", "[23.03|12:29:27] JOB ReaxFF_p_9 STARTED\n", "[23.03|12:29:27] JOB ReaxFF_e_3 STARTED\n", "[23.03|12:29:27] JOB ReaxFF_e_13 STARTED\n", "[23.03|12:29:27] JOB ReaxFF_e_10 STARTED\n", "[23.03|12:29:27] JOB ANI-1ccx_e_10 RUNNING\n", "[23.03|12:29:27] JOB ANI-1ccx_e_13 RUNNING\n", "[23.03|12:29:27] JOB ANI-1ccx_p_10 RUNNING\n", "[23.03|12:29:27] JOB ANI-1ccx_p_13 RUNNING\n", "[23.03|12:29:27] JOB ANI-1ccx_p_3 RUNNING\n", "[23.03|12:29:27] JOB ANI-1ccx_e_9 RUNNING\n", "[23.03|12:29:27] JOB ANI-2x_ethylene RUNNING\n", "[23.03|12:29:27] JOB ReaxFF_p_14 STARTED\n", "[23.03|12:29:27] JOB ReaxFF_p_10 STARTED\n", "[23.03|12:29:27] JOB ReaxFF_p_13 STARTED\n", "[23.03|12:29:27] JOB ReaxFF_p_3 STARTED\n", "[23.03|12:29:27] JOB ReaxFF_e_9 STARTED\n", "[23.03|12:29:27] JOB ANI-2x_methane RUNNING\n", "[23.03|12:29:27] JOB ANI-2x_hexane RUNNING\n", "[23.03|12:29:27] JOB ADF_ethylene STARTED\n", "[23.03|12:29:27] JOB ADF_hexane STARTED\n", "[23.03|12:29:27] JOB ANI-2x_31 RUNNING\n", "[23.03|12:29:27] JOB ADF_methane STARTED\n", "[23.03|12:29:27] JOB ADF_2233tetramethylbutane STARTED\n", "[23.03|12:29:27] JOB ANI-2x_2233tetramethylbutane RUNNING\n", "[23.03|12:29:27] JOB ADF_bicyclo222octane STARTED\n", "[23.03|12:29:27] JOB ANI-2x_bicyclo222octane RUNNING\n", "[23.03|12:29:27] JOB ADF_31 STARTED\n", "[23.03|12:29:27] JOB ADF_adamantane STARTED\n", "[23.03|12:29:27] JOB ANI-2x_adamantane RUNNING\n", "[23.03|12:29:27] JOB ADF_ethyne STARTED\n", "[23.03|12:29:27] JOB ADF_22 STARTED\n", "[23.03|12:29:27] JOB ANI-2x_ethyne RUNNING\n", "[23.03|12:29:27] JOB ADF_1 STARTED\n", "[23.03|12:29:27] JOB ADF_ethane STARTED\n", "[23.03|12:29:27] JOB ANI-2x_22 RUNNING\n", "[23.03|12:29:27] JOB ANI-2x_octane RUNNING\n", "[23.03|12:29:27] JOB ADF_octane STARTED\n", "[23.03|12:29:27] JOB ANI-2x_1 RUNNING\n", "[23.03|12:29:27] JOB ANI-2x_e_14 RUNNING\n", "[23.03|12:29:27] JOB ADF_e_14 STARTED\n", "[23.03|12:29:27] JOB ADF_p_9 STARTED\n", "[23.03|12:29:27] JOB ADF_e_3 STARTED\n", "[23.03|12:29:27] JOB ANI-2x_ethane RUNNING\n", "[23.03|12:29:27] JOB ANI-2x_p_9 RUNNING\n", "[23.03|12:29:27] JOB ANI-2x_e_3 RUNNING\n", "[23.03|12:29:27] JOB ADF_e_13 STARTED\n", "[23.03|12:29:27] JOB ADF_e_10 STARTED\n", "[23.03|12:29:27] JOB ANI-2x_e_10 RUNNING\n", "[23.03|12:29:27] JOB ADF_p_14 STARTED\n", "[23.03|12:29:27] JOB ADF_p_10 STARTED\n", "[23.03|12:29:27] JOB ADF_p_13 STARTED\n", "[23.03|12:29:27] JOB ADF_p_3 STARTED\n", "[23.03|12:29:27] JOB ANI-2x_e_13 RUNNING\n", "[23.03|12:29:27] JOB ADF_e_9 STARTED\n", "[23.03|12:29:27] JOB ANI-2x_p_14 RUNNING\n", "[23.03|12:29:27] JOB ANI-2x_p_10 RUNNING\n", "[23.03|12:29:27] JOB MP2_ethylene STARTED\n", "[23.03|12:29:27] JOB ANI-2x_p_13 RUNNING\n", "[23.03|12:29:27] JOB MP2_hexane STARTED\n", "[23.03|12:29:27] JOB DFTB_ethylene RUNNING\n", "[23.03|12:29:27] JOB DFTB_bicyclo222octane RUNNING\n", "[23.03|12:29:27] JOB DFTB_ethane RUNNING\n", "[23.03|12:29:27] JOB DFTB_ethyne RUNNING\n", "[23.03|12:29:27] JOB DFTB_adamantane RUNNING\n", "[23.03|12:29:27] JOB DFTB_methane RUNNING\n", "[23.03|12:29:27] JOB ANI-2x_e_9 RUNNING\n", "[23.03|12:29:27] JOB DFTB_1 RUNNING\n", "[23.03|12:29:27] JOB DFTB_2233tetramethylbutane RUNNING\n", "[23.03|12:29:27] JOB DFTB_22 RUNNING\n", "[23.03|12:29:27] JOB MP2_methane STARTED\n", "[23.03|12:29:27] JOB DFTB_31 RUNNING\n", "[23.03|12:29:27] JOB DFTB_octane RUNNING\n", "[23.03|12:29:27] JOB MP2_2233tetramethylbutane STARTED\n", "[23.03|12:29:27] JOB ANI-2x_p_3 RUNNING\n", "[23.03|12:29:27] JOB MP2_bicyclo222octane STARTED\n", "[23.03|12:29:27] JOB DFTB_e_14 RUNNING\n", "[23.03|12:29:27] JOB MP2_31 STARTED\n", "[23.03|12:29:27] JOB DFTB_p_9 RUNNING\n", "[23.03|12:29:27] JOB DFTB_hexane RUNNING\n", "[23.03|12:29:27] JOB MP2_adamantane STARTED\n", "[23.03|12:29:27] JOB DFTB_e_3 RUNNING\n", "[23.03|12:29:27] JOB MP2_ethyne STARTED\n", "[23.03|12:29:27] JOB DFTB_e_10 RUNNING\n", "[23.03|12:29:27] JOB MP2_22 STARTED\n", "[23.03|12:29:27] JOB MP2_1 STARTED\n", "[23.03|12:29:27] JOB DFTB_e_13 RUNNING\n", "[23.03|12:29:27] JOB MP2_ethane STARTED\n", "[23.03|12:29:27] JOB DFTB_p_14 RUNNING\n", "[23.03|12:29:27] JOB MP2_octane STARTED\n", "[23.03|12:29:27] JOB MP2_e_14 STARTED\n", "[23.03|12:29:27] JOB DFTB_p_10 RUNNING\n", "[23.03|12:29:27] JOB DFTB_p_3 RUNNING\n", "[23.03|12:29:27] JOB MP2_p_9 STARTED\n", "[23.03|12:29:27] JOB MP2_e_3 STARTED\n", "[23.03|12:29:27] JOB DFTB_p_13 RUNNING\n", "[23.03|12:29:27] JOB MP2_e_13 STARTED\n", "[23.03|12:29:27] JOB MP2_e_10 STARTED\n", "[23.03|12:29:27] JOB DFTB_e_9 RUNNING\n", "[23.03|12:29:27] JOB MP2_p_14 STARTED\n", "[23.03|12:29:27] JOB ReaxFF_ethylene RUNNING\n", "[23.03|12:29:27] JOB ReaxFF_hexane RUNNING\n", "[23.03|12:29:27] JOB ADF_22 RUNNING\n", "[23.03|12:29:27] JOB ReaxFF_methane RUNNING\n", "[23.03|12:29:27] JOB MP2_p_10 STARTED\n", "[23.03|12:29:27] JOB MP2_p_13 STARTED\n", "[23.03|12:29:27] JOB ReaxFF_bicyclo222octane RUNNING\n", "[23.03|12:29:27] JOB ReaxFF_2233tetramethylbutane RUNNING\n", "[23.03|12:29:27] JOB MP2_p_3 STARTED\n", "[23.03|12:29:28] JOB MP2_e_9 STARTED\n", "[23.03|12:29:28] JOB BAND_ethylene STARTED\n", "[23.03|12:29:28] JOB ReaxFF_31 RUNNING\n", "[23.03|12:29:28] JOB BAND_hexane STARTED\n", "[23.03|12:29:28] JOB BAND_methane STARTED\n", "[23.03|12:29:28] JOB ReaxFF_adamantane RUNNING\n", "[23.03|12:29:28] JOB BAND_2233tetramethylbutane STARTED\n", "[23.03|12:29:28] JOB ReaxFF_ethyne RUNNING\n", "[23.03|12:29:28] JOB ReaxFF_1 RUNNING\n", "[23.03|12:29:28] JOB BAND_bicyclo222octane STARTED\n", "[23.03|12:29:28] JOB BAND_31 STARTED\n", "[23.03|12:29:28] JOB BAND_adamantane STARTED\n", "[23.03|12:29:28] JOB ReaxFF_22 RUNNING\n", "[23.03|12:29:28] JOB BAND_ethyne STARTED\n", "[23.03|12:29:28] JOB BAND_22 STARTED\n", "[23.03|12:29:28] JOB ReaxFF_ethane RUNNING\n", "[23.03|12:29:28] JOB BAND_1 STARTED\n", "[23.03|12:29:28] JOB BAND_ethane STARTED\n", "[23.03|12:29:28] JOB BAND_octane STARTED\n", "[23.03|12:29:28] JOB ReaxFF_octane RUNNING\n", "[23.03|12:29:28] JOB BAND_e_14 STARTED\n", "[23.03|12:29:28] JOB ReaxFF_e_14 RUNNING\n", "[23.03|12:29:28] JOB BAND_p_9 STARTED\n", "[23.03|12:29:28] JOB ReaxFF_p_9 RUNNING\n", "[23.03|12:29:28] JOB BAND_e_3 STARTED\n", "[23.03|12:29:28] JOB ReaxFF_e_3 RUNNING\n", "[23.03|12:29:28] JOB BAND_e_13 STARTED\n", "[23.03|12:29:28] JOB ReaxFF_e_10 RUNNING\n", "[23.03|12:29:28] JOB BAND_e_10 STARTED\n", "[23.03|12:29:28] JOB BAND_p_14 STARTED\n", "[23.03|12:29:28] JOB ReaxFF_p_3 RUNNING\n", "[23.03|12:29:28] JOB ReaxFF_e_13 RUNNING\n", "[23.03|12:29:28] JOB ReaxFF_p_10 RUNNING\n", "[23.03|12:29:28] JOB ReaxFF_p_14 RUNNING\n", "[23.03|12:29:28] JOB ReaxFF_p_13 RUNNING\n", "[23.03|12:29:28] JOB ReaxFF_e_9 RUNNING\n", "[23.03|12:29:28] JOB ADF_ethylene RUNNING\n", "[23.03|12:29:28] JOB ADF_hexane RUNNING\n", "[23.03|12:29:28] JOB ADF_2233tetramethylbutane RUNNING\n", "[23.03|12:29:28] JOB ADF_methane RUNNING\n", "[23.03|12:29:28] JOB ADF_bicyclo222octane RUNNING\n", "[23.03|12:29:28] JOB BAND_p_10 STARTED\n", "[23.03|12:29:28] JOB ADF_31 RUNNING\n", "[23.03|12:29:28] JOB BAND_p_13 STARTED\n", "[23.03|12:29:28] JOB ADF_adamantane RUNNING\n", "[23.03|12:29:28] JOB BAND_p_3 STARTED\n", "[23.03|12:29:28] JOB ADF_1 RUNNING\n", "[23.03|12:29:28] JOB BAND_e_9 STARTED\n", "[23.03|12:29:28] Waiting for job ANI-1ccx_ethylene to finish\n", "[23.03|12:29:28] JOB ADF_ethane RUNNING\n", "[23.03|12:29:28] JOB ADF_octane RUNNING\n", "[23.03|12:29:28] JOB ADF_e_14 RUNNING\n", "[23.03|12:29:28] JOB ADF_e_3 RUNNING\n", "[23.03|12:29:28] JOB ADF_p_9 RUNNING\n", "[23.03|12:29:28] JOB ADF_e_13 RUNNING\n", "[23.03|12:29:28] JOB ADF_e_10 RUNNING\n", "[23.03|12:29:28] JOB ADF_p_14 RUNNING\n", "[23.03|12:29:28] JOB ADF_p_10 RUNNING\n", "[23.03|12:29:28] JOB ADF_p_13 RUNNING\n", "[23.03|12:29:28] JOB ADF_p_3 RUNNING\n", "[23.03|12:29:28] JOB ADF_e_9 RUNNING\n", "[23.03|12:29:28] JOB MP2_ethylene RUNNING\n", "[23.03|12:29:28] JOB MP2_methane RUNNING\n", "[23.03|12:29:28] JOB MP2_2233tetramethylbutane RUNNING\n", "[23.03|12:29:28] JOB MP2_adamantane RUNNING\n", "[23.03|12:29:28] JOB MP2_hexane RUNNING\n", "[23.03|12:29:28] JOB MP2_e_14 RUNNING\n", "[23.03|12:29:28] JOB MP2_31 RUNNING\n", "[23.03|12:29:28] JOB MP2_bicyclo222octane RUNNING\n", "[23.03|12:29:28] JOB MP2_ethyne RUNNING\n", "[23.03|12:29:28] JOB MP2_e_3 RUNNING\n", "[23.03|12:29:28] JOB MP2_22 RUNNING\n", "[23.03|12:29:28] JOB MP2_e_13 RUNNING\n", "[23.03|12:29:28] JOB MP2_ethane RUNNING\n", "[23.03|12:29:28] JOB MP2_p_9 RUNNING\n", "[23.03|12:29:28] JOB MP2_octane RUNNING\n", "[23.03|12:29:28] JOB MP2_e_10 RUNNING\n", "[23.03|12:29:28] JOB MP2_p_14 RUNNING\n", "[23.03|12:29:28] JOB MP2_1 RUNNING\n", "[23.03|12:29:28] JOB ADF_ethyne RUNNING\n", "[23.03|12:29:28] JOB MP2_p_13 RUNNING\n", "[23.03|12:29:28] JOB BAND_bicyclo222octane RUNNING\n", "[23.03|12:29:28] JOB MP2_p_10 RUNNING\n", "[23.03|12:29:28] JOB BAND_2233tetramethylbutane RUNNING\n", "[23.03|12:29:28] JOB MP2_p_3 RUNNING\n", "[23.03|12:29:28] JOB BAND_1 RUNNING\n", "[23.03|12:29:28] JOB BAND_22 RUNNING\n", "[23.03|12:29:28] JOB MP2_e_9 RUNNING\n", "[23.03|12:29:28] JOB BAND_31 RUNNING\n", "[23.03|12:29:28] JOB BAND_ethane RUNNING\n", "[23.03|12:29:28] JOB BAND_p_14 RUNNING\n", "[23.03|12:29:28] JOB BAND_e_13 RUNNING\n", "[23.03|12:29:28] JOB BAND_adamantane RUNNING\n", "[23.03|12:29:28] JOB BAND_ethylene RUNNING\n", "[23.03|12:29:28] JOB BAND_e_3 RUNNING\n", "[23.03|12:29:28] JOB BAND_methane RUNNING\n", "[23.03|12:29:28] JOB BAND_p_13 RUNNING\n", "[23.03|12:29:28] JOB BAND_p_3 RUNNING\n", "[23.03|12:29:28] JOB BAND_e_14 RUNNING\n", "[23.03|12:29:28] JOB BAND_e_9 RUNNING\n", "[23.03|12:29:28] JOB BAND_p_10 RUNNING\n", "[23.03|12:29:28] JOB BAND_octane RUNNING\n", "[23.03|12:29:28] JOB BAND_ethyne RUNNING\n", "[23.03|12:29:28] JOB BAND_e_10 RUNNING\n", "[23.03|12:29:28] JOB BAND_hexane RUNNING\n", "[23.03|12:29:28] JOB BAND_p_9 RUNNING\n", "[23.03|12:29:40] JOB ANI-1ccx_bicyclo222octane FINISHED\n", "[23.03|12:29:40] JOB ANI-1ccx_31 FINISHED\n", "[23.03|12:29:40] JOB ANI-1ccx_methane FINISHED\n", "[23.03|12:29:40] JOB ANI-1ccx_bicyclo222octane SUCCESSFUL\n", "[23.03|12:29:40] JOB ANI-1ccx_methane SUCCESSFUL\n", "[23.03|12:29:40] JOB ANI-1ccx_31 SUCCESSFUL\n", "[23.03|12:29:40] JOB ANI-1ccx_ethane FINISHED\n", "[23.03|12:29:40] JOB ANI-1ccx_ethane SUCCESSFUL\n", "[23.03|12:29:40] JOB ANI-1ccx_2233tetramethylbutane FINISHED\n", "[23.03|12:29:40] JOB ANI-1ccx_2233tetramethylbutane SUCCESSFUL\n", "[23.03|12:29:40] JOB ANI-1ccx_ethylene FINISHED\n", "[23.03|12:29:40] JOB ANI-1ccx_ethylene SUCCESSFUL\n", "[23.03|12:29:40] Waiting for job ANI-1ccx_hexane to finish\n", "[23.03|12:29:40] JOB ANI-1ccx_22 FINISHED\n", "[23.03|12:29:40] JOB ANI-1ccx_22 SUCCESSFUL\n", "[23.03|12:29:40] JOB ANI-1ccx_ethyne FINISHED\n", "[23.03|12:29:40] JOB ANI-1ccx_hexane FINISHED\n", "[23.03|12:29:40] JOB ANI-1ccx_ethyne SUCCESSFUL\n", "[23.03|12:29:40] JOB ANI-1ccx_hexane SUCCESSFUL\n", "[23.03|12:29:40] Waiting for job ANI-1ccx_adamantane to finish\n", "[23.03|12:29:41] JOB ANI-1ccx_octane FINISHED\n", "[23.03|12:29:41] JOB ANI-1ccx_octane SUCCESSFUL\n", "[23.03|12:29:41] JOB ANI-1ccx_adamantane FINISHED\n", "[23.03|12:29:41] JOB ANI-1ccx_adamantane SUCCESSFUL\n", "[23.03|12:29:41] Waiting for job ANI-1ccx_1 to finish\n", "[23.03|12:29:41] JOB ReaxFF_p_3 FINISHED\n", "[23.03|12:29:41] JOB ANI-1ccx_1 FINISHED\n", "[23.03|12:29:41] JOB ReaxFF_p_3 SUCCESSFUL\n", "[23.03|12:29:41] JOB ANI-1ccx_1 SUCCESSFUL\n", "[23.03|12:29:41] Waiting for job ANI-1ccx_e_14 to finish\n", "[23.03|12:29:41] JOB DFTB_p_14 FINISHED\n", "[23.03|12:29:41] JOB DFTB_p_14 SUCCESSFUL\n", "[23.03|12:29:51] JOB ANI-1ccx_e_10 FINISHED\n", "[23.03|12:29:51] JOB ANI-1ccx_p_9 FINISHED\n", "[23.03|12:29:51] JOB ANI-1ccx_p_9 SUCCESSFUL\n", "[23.03|12:29:51] JOB ANI-1ccx_e_10 SUCCESSFUL\n", "[23.03|12:29:51] JOB ANI-1ccx_p_14 FINISHED\n", "[23.03|12:29:51] JOB ANI-1ccx_p_14 SUCCESSFUL\n", "[23.03|12:29:51] JOB ANI-1ccx_e_14 FINISHED\n", "[23.03|12:29:51] JOB ANI-1ccx_e_14 SUCCESSFUL\n", "[23.03|12:29:51] Waiting for job ANI-1ccx_e_3 to finish\n", "[23.03|12:29:54] JOB ANI-2x_ethyne FINISHED\n", "[23.03|12:29:54] JOB ANI-2x_ethyne SUCCESSFUL\n", "[23.03|12:29:54] JOB DFTB_bicyclo222octane FINISHED\n", "[23.03|12:29:54] JOB DFTB_bicyclo222octane SUCCESSFUL\n", "[23.03|12:29:57] JOB MP2_ethyne FINISHED\n", "[23.03|12:29:57] JOB ADF_methane FINISHED\n", "[23.03|12:29:57] JOB ADF_methane SUCCESSFUL\n", "[23.03|12:29:57] JOB MP2_ethyne SUCCESSFUL\n", "[23.03|12:29:58] JOB DFTB_22 FINISHED\n", "[23.03|12:29:58] JOB DFTB_22 SUCCESSFUL\n", "[23.03|12:30:02] JOB ADF_ethylene FINISHED\n", "[23.03|12:30:02] JOB ADF_ethylene SUCCESSFUL\n", "[23.03|12:30:07] JOB ANI-2x_octane FINISHED\n", "[23.03|12:30:07] JOB ANI-2x_octane SUCCESSFUL\n", "[23.03|12:30:08] JOB ReaxFF_p_14 FINISHED\n", "[23.03|12:30:08] JOB ReaxFF_p_14 SUCCESSFUL\n", "[23.03|12:30:15] JOB ANI-2x_bicyclo222octane FINISHED\n", "[23.03|12:30:15] JOB ANI-2x_bicyclo222octane SUCCESSFUL\n", "[23.03|12:30:15] JOB DFTB_p_3 FINISHED\n", "[23.03|12:30:15] JOB DFTB_p_3 SUCCESSFUL\n", "[23.03|12:31:42] JOB MP2_hexane FINISHED\n", "[23.03|12:31:42] JOB MP2_hexane SUCCESSFUL\n", "[23.03|12:31:42] JOB DFTB_e_14 FINISHED\n", "[23.03|12:31:42] JOB DFTB_e_14 SUCCESSFUL\n", "[23.03|12:31:43] JOB DFTB_e_10 FINISHED\n", "[23.03|12:31:43] JOB DFTB_e_10 SUCCESSFUL\n", "[23.03|12:34:38] JOB ADF_1 FINISHED\n", "[23.03|12:34:38] JOB ADF_1 SUCCESSFUL\n", "[23.03|12:34:39] JOB ReaxFF_e_13 FINISHED\n", "[23.03|12:34:39] JOB ReaxFF_e_13 SUCCESSFUL\n", "[23.03|12:34:39] JOB DFTB_hexane FINISHED\n", "[23.03|12:34:40] JOB DFTB_hexane SUCCESSFUL\n", "[23.03|12:35:01] JOB MP2_ethane FINISHED\n", "[23.03|12:35:01] JOB MP2_ethane SUCCESSFUL\n", "[23.03|12:35:15] JOB MP2_31 FINISHED\n", "[23.03|12:35:15] JOB MP2_31 SUCCESSFUL\n", "[23.03|12:35:16] JOB ANI-1ccx_p_3 FINISHED\n", "[23.03|12:35:16] JOB ANI-1ccx_p_3 SUCCESSFUL\n", "[23.03|12:35:33] JOB ANI-2x_31 FINISHED\n", "[23.03|12:35:34] JOB ANI-2x_31 SUCCESSFUL\n", "[23.03|12:35:46] JOB ANI-2x_ethane FINISHED\n", "[23.03|12:35:46] JOB ANI-2x_ethane SUCCESSFUL\n", "[23.03|12:35:58] JOB ANI-2x_adamantane FINISHED\n", "[23.03|12:35:58] JOB ANI-2x_adamantane SUCCESSFUL\n", "[23.03|12:35:59] JOB ReaxFF_octane FINISHED\n", "[23.03|12:35:59] JOB ReaxFF_octane SUCCESSFUL\n", "[23.03|12:36:10] JOB ANI-1ccx_e_3 FINISHED\n", "[23.03|12:36:10] JOB ANI-1ccx_e_3 SUCCESSFUL\n", "[23.03|12:36:10] Waiting for job ANI-1ccx_e_13 to finish\n", "[23.03|12:36:17] JOB MP2_p_3 FINISHED\n", "[23.03|12:36:17] JOB MP2_p_3 SUCCESSFUL\n", "[23.03|12:36:17] JOB DFTB_e_13 FINISHED\n", "[23.03|12:36:17] JOB DFTB_e_13 SUCCESSFUL\n", "[23.03|12:36:18] JOB DFTB_adamantane FINISHED\n", "[23.03|12:36:18] JOB DFTB_adamantane SUCCESSFUL\n", "[23.03|12:36:18] JOB MP2_e_13 FINISHED\n", "[23.03|12:36:18] JOB MP2_e_13 SUCCESSFUL\n", "[23.03|12:37:01] JOB BAND_ethylene FINISHED\n", "[23.03|12:37:01] JOB BAND_ethylene SUCCESSFUL\n", "[23.03|12:37:30] JOB BAND_ethyne FINISHED\n", "[23.03|12:37:30] JOB BAND_ethyne SUCCESSFUL\n", "[23.03|12:37:42] JOB ANI-2x_e_3 FINISHED\n", "[23.03|12:37:42] JOB ANI-2x_e_3 SUCCESSFUL\n", "[23.03|12:38:32] JOB ADF_p_3 FINISHED\n", "[23.03|12:38:32] JOB ADF_p_3 SUCCESSFUL\n", "[23.03|12:38:33] JOB DFTB_2233tetramethylbutane FINISHED\n", "[23.03|12:38:33] JOB DFTB_2233tetramethylbutane SUCCESSFUL\n", "[23.03|12:38:42] JOB MP2_e_14 FINISHED\n", "[23.03|12:38:42] JOB MP2_e_14 SUCCESSFUL\n", "[23.03|12:39:22] JOB MP2_adamantane FINISHED\n", "[23.03|12:39:22] JOB MP2_adamantane SUCCESSFUL\n", "[23.03|12:39:22] JOB DFTB_p_9 FINISHED\n", "[23.03|12:39:22] JOB DFTB_p_9 SUCCESSFUL\n", "[23.03|12:39:23] JOB DFTB_e_3 FINISHED\n", "[23.03|12:39:23] JOB DFTB_e_3 SUCCESSFUL\n", "[23.03|12:41:12] JOB ADF_e_14 FINISHED\n", "[23.03|12:41:12] JOB ADF_e_14 SUCCESSFUL\n", "[23.03|12:42:27] JOB ADF_p_9 FINISHED\n", "[23.03|12:42:27] JOB ADF_p_9 SUCCESSFUL\n", "[23.03|12:42:28] JOB DFTB_ethyne FINISHED\n", "[23.03|12:42:28] JOB DFTB_ethyne SUCCESSFUL\n", "[23.03|12:42:28] JOB ReaxFF_p_13 FINISHED\n", "[23.03|12:42:28] JOB ReaxFF_p_13 SUCCESSFUL\n", "[23.03|12:44:16] JOB ADF_hexane FINISHED\n", "[23.03|12:44:16] JOB ADF_hexane SUCCESSFUL\n", "[23.03|12:44:46] JOB ADF_22 FINISHED\n", "[23.03|12:44:46] JOB ADF_22 SUCCESSFUL\n", "[23.03|12:44:47] JOB ReaxFF_e_14 FINISHED\n", "[23.03|12:44:47] JOB ReaxFF_e_14 SUCCESSFUL\n", "[23.03|12:44:56] JOB MP2_e_3 FINISHED\n", "[23.03|12:44:56] JOB MP2_e_3 SUCCESSFUL\n", "[23.03|12:44:56] JOB ReaxFF_e_3 FINISHED\n", "[23.03|12:44:56] JOB ReaxFF_e_3 SUCCESSFUL\n", "[23.03|12:44:57] JOB ReaxFF_ethane FINISHED\n", "[23.03|12:44:57] JOB ReaxFF_ethane SUCCESSFUL\n", "[23.03|12:44:57] JOB ReaxFF_e_10 FINISHED\n", "[23.03|12:44:57] JOB ReaxFF_e_10 SUCCESSFUL\n", "[23.03|12:45:47] JOB BAND_adamantane FINISHED\n", "[23.03|12:45:47] JOB BAND_adamantane SUCCESSFUL\n", "[23.03|12:46:00] JOB ANI-2x_hexane FINISHED\n", "[23.03|12:46:00] JOB ANI-2x_hexane SUCCESSFUL\n", "[23.03|12:46:10] JOB ANI-1ccx_p_10 FINISHED\n", "[23.03|12:46:10] JOB ANI-1ccx_p_10 SUCCESSFUL\n", "[23.03|12:46:19] JOB ANI-1ccx_e_9 FINISHED\n", "[23.03|12:46:19] JOB ANI-1ccx_e_9 SUCCESSFUL\n", "[23.03|12:46:52] JOB BAND_e_13 FINISHED\n", "[23.03|12:46:52] JOB BAND_e_13 SUCCESSFUL\n", "[23.03|12:47:06] JOB ANI-2x_e_10 FINISHED\n", "[23.03|12:47:06] JOB ANI-2x_e_10 SUCCESSFUL\n", "[23.03|12:47:10] JOB MP2_p_14 FINISHED\n", "[23.03|12:47:10] JOB MP2_p_14 SUCCESSFUL\n", "[23.03|12:47:20] JOB ANI-2x_ethylene FINISHED\n", "[23.03|12:47:20] JOB ANI-2x_ethylene SUCCESSFUL\n", "[23.03|12:47:46] JOB MP2_22 FINISHED\n", "[23.03|12:47:46] JOB MP2_22 SUCCESSFUL\n", "[23.03|12:49:11] JOB MP2_1 FINISHED\n", "[23.03|12:49:11] JOB MP2_1 SUCCESSFUL\n", "[23.03|12:49:51] JOB MP2_2233tetramethylbutane FINISHED\n", "[23.03|12:49:51] JOB MP2_2233tetramethylbutane SUCCESSFUL\n", "[23.03|12:50:04] JOB ANI-2x_2233tetramethylbutane FINISHED\n", "[23.03|12:50:04] JOB ANI-2x_2233tetramethylbutane SUCCESSFUL\n", "[23.03|12:50:04] JOB DFTB_octane FINISHED\n", "[23.03|12:50:04] JOB DFTB_octane SUCCESSFUL\n", "[23.03|12:50:15] JOB ANI-2x_p_10 FINISHED\n", "[23.03|12:50:15] JOB ANI-2x_p_10 SUCCESSFUL\n", "[23.03|12:50:16] JOB ReaxFF_1 FINISHED\n", "[23.03|12:50:16] JOB ReaxFF_1 SUCCESSFUL\n", "[23.03|12:50:25] JOB MP2_octane FINISHED\n", "[23.03|12:50:25] JOB MP2_octane SUCCESSFUL\n", "[23.03|12:50:32] JOB MP2_bicyclo222octane FINISHED\n", "[23.03|12:50:32] JOB MP2_bicyclo222octane SUCCESSFUL\n", "[23.03|12:51:15] JOB ADF_p_10 FINISHED\n", "[23.03|12:51:15] JOB ADF_p_10 SUCCESSFUL\n", "[23.03|12:51:15] JOB DFTB_ethylene FINISHED\n", "[23.03|12:51:15] JOB DFTB_ethylene SUCCESSFUL\n", "[23.03|12:51:16] JOB ReaxFF_e_9 FINISHED\n", "[23.03|12:51:16] JOB ReaxFF_e_9 SUCCESSFUL\n", "[23.03|12:51:16] JOB ReaxFF_ethylene FINISHED\n", "[23.03|12:51:16] JOB ReaxFF_ethylene SUCCESSFUL\n", "[23.03|12:52:01] JOB ADF_e_3 FINISHED\n", "[23.03|12:52:01] JOB ADF_e_3 SUCCESSFUL\n", "[23.03|12:52:15] JOB ANI-2x_e_13 FINISHED\n", "[23.03|12:52:15] JOB ANI-2x_e_13 SUCCESSFUL\n", "[23.03|12:52:15] JOB ReaxFF_22 FINISHED\n", "[23.03|12:52:15] JOB ReaxFF_22 SUCCESSFUL\n", "[23.03|12:55:54] JOB MP2_p_13 FINISHED\n", "[23.03|12:55:54] JOB MP2_p_13 SUCCESSFUL\n", "[23.03|12:55:59] JOB MP2_methane FINISHED\n", "[23.03|12:55:59] JOB MP2_methane SUCCESSFUL\n", "[23.03|12:56:40] JOB BAND_methane FINISHED\n", "[23.03|12:56:40] JOB BAND_methane SUCCESSFUL\n", "[23.03|12:56:40] JOB DFTB_1 FINISHED\n", "[23.03|12:56:40] JOB DFTB_1 SUCCESSFUL\n", "[23.03|12:56:53] JOB ANI-2x_e_14 FINISHED\n", "[23.03|12:56:53] JOB ANI-2x_e_14 SUCCESSFUL\n", "[23.03|12:57:10] JOB ADF_ethyne FINISHED\n", "[23.03|12:57:10] JOB ADF_ethyne SUCCESSFUL\n", "[23.03|12:57:23] JOB ANI-2x_p_14 FINISHED\n", "[23.03|12:57:23] JOB ANI-2x_p_14 SUCCESSFUL\n", "[23.03|12:57:24] JOB ReaxFF_2233tetramethylbutane FINISHED\n", "[23.03|12:57:24] JOB ReaxFF_2233tetramethylbutane SUCCESSFUL\n", "[23.03|12:57:50] JOB BAND_bicyclo222octane FINISHED\n", "[23.03|12:57:50] JOB BAND_bicyclo222octane SUCCESSFUL\n", "[23.03|12:58:03] JOB ANI-2x_p_13 FINISHED\n", "[23.03|12:58:03] JOB ANI-2x_p_13 SUCCESSFUL\n", "[23.03|12:58:39] JOB BAND_p_14 FINISHED\n", "[23.03|12:58:39] JOB BAND_p_14 SUCCESSFUL\n", "[23.03|12:58:45] JOB ADF_ethane FINISHED\n", "[23.03|12:58:45] JOB ADF_ethane SUCCESSFUL\n", "[23.03|12:58:46] JOB DFTB_p_10 FINISHED\n", "[23.03|12:58:46] JOB DFTB_p_10 SUCCESSFUL\n", "[23.03|12:59:43] JOB MP2_p_10 FINISHED\n", "[23.03|12:59:43] JOB MP2_p_10 SUCCESSFUL\n", "[23.03|12:59:43] JOB ReaxFF_p_9 FINISHED\n", "[23.03|12:59:43] JOB ReaxFF_p_9 SUCCESSFUL\n", "[23.03|12:59:44] JOB BAND_ethane FINISHED\n", "[23.03|12:59:44] JOB BAND_ethane SUCCESSFUL\n", "[23.03|12:59:45] JOB ReaxFF_adamantane FINISHED\n", "[23.03|12:59:45] JOB ReaxFF_adamantane SUCCESSFUL\n", "[23.03|12:59:56] JOB ANI-2x_22 FINISHED\n", "[23.03|12:59:56] JOB ANI-2x_22 SUCCESSFUL\n", "[23.03|13:00:06] JOB BAND_e_14 FINISHED\n", "[23.03|13:00:06] JOB BAND_e_14 SUCCESSFUL\n", "[23.03|13:00:08] JOB ANI-2x_p_9 FINISHED\n", "[23.03|13:00:08] JOB ANI-2x_p_9 SUCCESSFUL\n", "[23.03|13:00:19] JOB ANI-2x_p_3 FINISHED\n", "[23.03|13:00:19] JOB ANI-2x_p_3 SUCCESSFUL\n", "[23.03|13:02:01] JOB ADF_e_9 FINISHED\n", "[23.03|13:02:01] JOB ADF_e_9 SUCCESSFUL\n", "[23.03|13:02:14] JOB ANI-2x_methane FINISHED\n", "[23.03|13:02:14] JOB ANI-2x_methane SUCCESSFUL\n", "[23.03|13:02:15] JOB BAND_p_10 FINISHED\n", "[23.03|13:02:15] JOB BAND_p_10 SUCCESSFUL\n", "[23.03|13:02:16] JOB DFTB_e_9 FINISHED\n", "[23.03|13:02:16] JOB DFTB_e_9 SUCCESSFUL\n", "[23.03|13:02:23] JOB ANI-1ccx_e_13 FINISHED\n", "[23.03|13:02:23] JOB ANI-1ccx_e_13 SUCCESSFUL\n", "[23.03|13:02:23] Waiting for job ANI-1ccx_p_13 to finish\n", "[23.03|13:02:35] JOB ANI-2x_1 FINISHED\n", "[23.03|13:02:35] JOB ANI-2x_1 SUCCESSFUL\n", "[23.03|13:02:35] JOB DFTB_31 FINISHED\n", "[23.03|13:02:35] JOB DFTB_31 SUCCESSFUL\n", "[23.03|13:02:53] JOB ADF_octane FINISHED\n", "[23.03|13:02:53] JOB ADF_octane SUCCESSFUL\n", "[23.03|13:03:03] JOB BAND_e_3 FINISHED\n", "[23.03|13:03:03] JOB BAND_e_3 SUCCESSFUL\n", "[23.03|13:03:03] JOB ReaxFF_ethyne FINISHED\n", "[23.03|13:03:03] JOB ReaxFF_ethyne SUCCESSFUL\n", "[23.03|13:03:45] JOB BAND_e_10 FINISHED\n", "[23.03|13:03:45] JOB BAND_e_10 SUCCESSFUL\n", "[23.03|13:04:46] JOB MP2_e_9 FINISHED\n", "[23.03|13:04:46] JOB MP2_e_9 SUCCESSFUL\n", "[23.03|13:04:54] JOB BAND_p_13 FINISHED\n", "[23.03|13:04:55] JOB BAND_p_13 SUCCESSFUL\n", "[23.03|13:04:55] JOB DFTB_methane FINISHED\n", "[23.03|13:04:55] JOB DFTB_methane SUCCESSFUL\n", "[23.03|13:04:55] JOB ReaxFF_31 FINISHED\n", "[23.03|13:04:55] JOB ReaxFF_31 SUCCESSFUL\n", "[23.03|13:05:02] JOB MP2_ethylene FINISHED\n", "[23.03|13:05:02] JOB MP2_ethylene SUCCESSFUL\n", "[23.03|13:05:03] JOB DFTB_ethane FINISHED\n", "[23.03|13:05:03] JOB DFTB_ethane SUCCESSFUL\n", "[23.03|13:05:41] JOB BAND_31 FINISHED\n", "[23.03|13:05:41] JOB BAND_31 SUCCESSFUL\n", "[23.03|13:06:20] JOB BAND_p_3 FINISHED\n", "[23.03|13:06:20] JOB BAND_p_3 SUCCESSFUL\n", "[23.03|13:06:21] JOB ADF_e_10 FINISHED\n", "[23.03|13:06:21] JOB ADF_e_10 SUCCESSFUL\n", "[23.03|13:07:03] JOB ADF_2233tetramethylbutane FINISHED\n", "[23.03|13:07:03] JOB ADF_2233tetramethylbutane SUCCESSFUL\n", "[23.03|13:07:03] JOB ReaxFF_methane FINISHED\n", "[23.03|13:07:03] JOB ReaxFF_methane SUCCESSFUL\n", "[23.03|13:07:47] JOB BAND_hexane FINISHED\n", "[23.03|13:07:48] JOB BAND_hexane SUCCESSFUL\n", "[23.03|13:07:48] JOB DFTB_p_13 FINISHED\n", "[23.03|13:07:48] JOB DFTB_p_13 SUCCESSFUL\n", "[23.03|13:08:13] JOB ADF_p_13 FINISHED\n", "[23.03|13:08:13] JOB ADF_p_13 SUCCESSFUL\n", "[23.03|13:08:14] JOB ReaxFF_p_10 FINISHED\n", "[23.03|13:08:14] JOB ReaxFF_p_10 SUCCESSFUL\n", "[23.03|13:08:14] JOB ReaxFF_bicyclo222octane FINISHED\n", "[23.03|13:08:14] JOB ReaxFF_bicyclo222octane SUCCESSFUL\n", "[23.03|13:08:45] JOB ADF_e_13 FINISHED\n", "[23.03|13:08:45] JOB ADF_e_13 SUCCESSFUL\n", "[23.03|13:08:45] JOB ReaxFF_hexane FINISHED\n", "[23.03|13:08:45] JOB ReaxFF_hexane SUCCESSFUL\n", "[23.03|13:08:51] JOB ADF_adamantane FINISHED\n", "[23.03|13:08:51] JOB ADF_adamantane SUCCESSFUL\n", "[23.03|13:09:04] JOB ANI-2x_e_9 FINISHED\n", "[23.03|13:09:04] JOB ANI-2x_e_9 SUCCESSFUL\n", "[23.03|13:09:14] JOB ANI-1ccx_p_13 FINISHED\n", "[23.03|13:09:14] JOB ANI-1ccx_p_13 SUCCESSFUL\n", "ANI-1ccx 15.8 30.7 -0.2 7.7 11.7 196.5 127.9 9.2 21.5 3.8 35.4 6.9\n", "\n", "ANI-2x 42.4 48.1 -1.9 5.4 8.0 238.4 156.9 7.9 20.8 -1.5 26.7 0.5\n", "\n", "DFTB 7.1 19.0 0.2 3.6 5.4 223.5 150.8 11.7 22.6 7.9 35.2 8.6\n", "\n", "ReaxFF 34.3 23.0 13.4 2.6 5.5 289.2 168.3 -9.2 24.2 70.7 30.9 89.3\n", "\n", "[23.03|13:09:14] Waiting for job ADF_bicyclo222octane to finish\n", "[23.03|13:09:27] JOB ADF_31 FINISHED\n", "[23.03|13:09:27] JOB ADF_31 SUCCESSFUL\n", "[23.03|13:11:19] JOB ADF_bicyclo222octane FINISHED\n", "[23.03|13:11:19] JOB ADF_bicyclo222octane SUCCESSFUL\n", "[23.03|13:11:19] Waiting for job ADF_p_14 to finish\n", "[23.03|13:11:51] JOB ADF_p_14 FINISHED\n", "[23.03|13:11:51] JOB ADF_p_14 SUCCESSFUL\n", "ADF 20.3 30.9 -2.0 5.5 8.2 211.6 139.7 9.5 20.5 4.7 31.2 4.8\n", "\n", "[23.03|13:11:51] Waiting for job MP2_p_9 to finish\n", "[23.03|13:14:22] JOB BAND_1 FINISHED\n", "[23.03|13:14:22] JOB BAND_1 SUCCESSFUL\n", "[23.03|13:15:10] JOB MP2_p_9 FINISHED\n", "[23.03|13:15:10] JOB MP2_p_9 SUCCESSFUL\n", "[23.03|13:15:10] Waiting for job MP2_e_10 to finish\n", "[23.03|13:15:59] JOB BAND_octane FINISHED\n", "[23.03|13:15:59] JOB BAND_octane SUCCESSFUL\n", "[23.03|13:16:51] JOB BAND_e_9 FINISHED\n", "[23.03|13:16:51] JOB BAND_e_9 SUCCESSFUL\n", "[23.03|13:17:06] JOB BAND_22 FINISHED\n", "[23.03|13:17:06] JOB BAND_22 SUCCESSFUL\n", "[23.03|13:17:08] JOB BAND_2233tetramethylbutane FINISHED\n", "[23.03|13:17:08] JOB BAND_2233tetramethylbutane SUCCESSFUL\n", "[23.03|13:17:18] JOB MP2_e_10 FINISHED\n", "[23.03|13:17:18] JOB MP2_e_10 SUCCESSFUL\n", "MP2 20.5 27.1 5.4 9.9 15.0 214.8 141.3 11.0 24.6 8.4 36.8 6.2\n", "\n", "[23.03|13:17:18] Waiting for job BAND_p_9 to finish\n", "[23.03|13:21:17] JOB BAND_p_9 FINISHED\n", "[23.03|13:21:17] JOB BAND_p_9 SUCCESSFUL\n", "BAND 19.3 30.4 -2.6 7.2 10.9 218.8 141.5 9.9 18.5 5.3 31.7 4.7\n", "\n" ] } ], "source": [ "with open(summary_fname, \"a\", buffering=1) as summary_file:\n", " for engine_name, s_engine in s_engine_dict.items():\n", " s = s_ams.copy() + s_engine.copy()\n", " jobs[engine_name] = dict()\n", "\n", " # call .run() for *all* jobs *before* accessing job.results.get_energy() for *any* job\n", " for mol_name, mol in mol_dict.items():\n", " jobs[engine_name][mol_name] = AMSJob(\n", " settings=s, molecule=mol, name=engine_name + \"_\" + mol_name\n", " )\n", " jobs[engine_name][mol_name].run()\n", "\n", " for engine_name in s_engine_dict:\n", " # for each engine, calculate reaction energies\n", " E = dict()\n", " for mol_name, job in jobs[engine_name].items():\n", " E[mol_name] = job.results.get_energy(unit=\"kcal/mol\")\n", " deltaE_list = [\n", " ##### HC7/11 ######\n", " E[\"22\"] - E[\"1\"],\n", " E[\"31\"] - E[\"1\"],\n", " E[\"octane\"] - E[\"2233tetramethylbutane\"],\n", " 5 * E[\"ethane\"] - E[\"hexane\"] - 4 * E[\"methane\"],\n", " 7 * E[\"ethane\"] - E[\"octane\"] - 6 * E[\"methane\"],\n", " 3 * E[\"ethylene\"] + 2 * E[\"ethyne\"] - E[\"adamantane\"],\n", " 3 * E[\"ethylene\"] + 1 * E[\"ethyne\"] - E[\"bicyclo222octane\"],\n", " ###### start ISOL6 ######\n", " E[\"p_3\"] - E[\"e_3\"],\n", " E[\"p_9\"] - E[\"e_9\"],\n", " E[\"p_10\"] - E[\"e_10\"],\n", " E[\"p_13\"] - E[\"e_13\"],\n", " E[\"p_14\"] - E[\"e_14\"],\n", " ]\n", "\n", " out_str = engine_name\n", " for deltaE in deltaE_list:\n", " out_str += \" {:.1f}\".format(deltaE)\n", " out_str += \"\\n\"\n", "\n", " print(out_str)\n", " summary_file.write(out_str)" ] }, { "cell_type": "markdown", "id": "611d3baf", "metadata": {}, "source": [ "## Results" ] }, { "cell_type": "markdown", "id": "6f1438c7", "metadata": {}, "source": [ "Results can be loaded from the summary file and displayed using pandas. The pandas package is installable with `amspackages`." ] }, { "cell_type": "code", "execution_count": 10, "id": "7963d92c", "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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#MethodHC7_1HC7_2HC7_3HC7_4HC7_5HC7_6HC7_7ISOL6_1ISOL6_2ISOL6_3ISOL6_4ISOL6_5
0Truhlar_ref14.3425.021.909.8114.84193.99127.229.7721.766.8233.525.3
1Smith_wB97X_ref28.7741.091.756.269.30238.83157.659.3220.801.0326.430.4
2ANI-1ccx15.8030.70-0.207.7011.70196.50127.909.2021.503.8035.406.9
3ANI-2x42.4048.10-1.905.408.00238.40156.907.9020.80-1.5026.700.5
4DFTB7.1019.000.203.605.40223.50150.8011.7022.607.9035.208.6
5ReaxFF34.3023.0013.402.605.50289.20168.30-9.2024.2070.7030.9089.3
6ADF20.3030.90-2.005.508.20211.60139.709.5020.504.7031.204.8
7MP220.5027.105.409.9015.00214.80141.3011.0024.608.4036.806.2
8BAND19.3030.40-2.607.2010.90218.80141.509.9018.505.3031.704.7
\n", "
" ], "text/plain": [ " #Method HC7_1 HC7_2 HC7_3 HC7_4 HC7_5 HC7_6 HC7_7 \\\n", "0 Truhlar_ref 14.34 25.02 1.90 9.81 14.84 193.99 127.22 \n", "1 Smith_wB97X_ref 28.77 41.09 1.75 6.26 9.30 238.83 157.65 \n", "2 ANI-1ccx 15.80 30.70 -0.20 7.70 11.70 196.50 127.90 \n", "3 ANI-2x 42.40 48.10 -1.90 5.40 8.00 238.40 156.90 \n", "4 DFTB 7.10 19.00 0.20 3.60 5.40 223.50 150.80 \n", "5 ReaxFF 34.30 23.00 13.40 2.60 5.50 289.20 168.30 \n", "6 ADF 20.30 30.90 -2.00 5.50 8.20 211.60 139.70 \n", "7 MP2 20.50 27.10 5.40 9.90 15.00 214.80 141.30 \n", "8 BAND 19.30 30.40 -2.60 7.20 10.90 218.80 141.50 \n", "\n", " ISOL6_1 ISOL6_2 ISOL6_3 ISOL6_4 ISOL6_5 \n", "0 9.77 21.76 6.82 33.52 5.3 \n", "1 9.32 20.80 1.03 26.43 0.4 \n", "2 9.20 21.50 3.80 35.40 6.9 \n", "3 7.90 20.80 -1.50 26.70 0.5 \n", "4 11.70 22.60 7.90 35.20 8.6 \n", "5 -9.20 24.20 70.70 30.90 89.3 \n", "6 9.50 20.50 4.70 31.20 4.8 \n", "7 11.00 24.60 8.40 36.80 6.2 \n", "8 9.90 18.50 5.30 31.70 4.7 " ] }, "execution_count": 10, "metadata": {}, "output_type": "execute_result" } ], "source": [ "with open(summary_fname) as summary_file:\n", " import pandas as pd\n", "\n", " df = pd.read_csv(summary_file, delim_whitespace=True).iloc[:, :-1]\n", "\n", "df" ] }, { "cell_type": "code", "execution_count": null, "id": "8d285455", "metadata": {}, "outputs": [], "source": [] } ], "metadata": { "kernelspec": { "display_name": "Python 3 (ipykernel)", "language": "python", "name": "python3" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.8.16" } }, "nbformat": 4, "nbformat_minor": 5 }