{ "cells": [ { "cell_type": "markdown", "id": "9f758387-bdb8-4c32-ba8a-c716fd20ba3c", "metadata": {}, "source": [ "## Initial Imports" ] }, { "cell_type": "code", "execution_count": 1, "id": "481dfa30-c992-4d63-b020-fbfe499e5ecb", "metadata": {}, "outputs": [], "source": [ "from scm.plams import read_molecules, Settings, AMSJob, init, config, JobRunner" ] }, { "cell_type": "code", "execution_count": 2, "id": "8293b199-f5f6-44fe-a53a-93a5a77a9112", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "PLAMS working folder: /path/plams/examples/plams_workdir.011\n" ] } ], "source": [ "# this line is not required in AMS2025+\n", "init()" ] }, { "cell_type": "markdown", "id": "0a221083-bae2-4599-a1e9-ef99a1b16230", "metadata": {}, "source": [ "## Summary Text File" ] }, { "cell_type": "markdown", "id": "121e72b9-2187-4c88-812b-20d3ce7b7ea0", "metadata": {}, "source": [ "Set up a results file, `summary.txt`, which will hold a table with reaction energies." ] }, { "cell_type": "code", "execution_count": 3, "id": "f340cae7-f9ef-419e-99eb-0d6c963472b0", "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(\"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", " summary_file.write(\"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\")" ] }, { "cell_type": "markdown", "id": "e6fdf0e0-5643-48dd-8e6d-10aaa0b0e1ac", "metadata": { "tags": [] }, "source": [ "## Benchmark Calculation Setup" ] }, { "cell_type": "markdown", "id": "c5e318f0-1939-41b0-8c23-ab9a81ccd31b", "metadata": {}, "source": [ "The molecules used in the benchmark calculations are loaded, and the settings for each engine created. " ] }, { "cell_type": "code", "execution_count": 4, "id": "45b6ff4a-6c22-4956-b8ff-df7452822504", "metadata": {}, "outputs": [], "source": [ "mol_dict = read_molecules(\"HC7-11\")\n", "mol_dict.update(read_molecules(\"ISOL6\"))" ] }, { "cell_type": "code", "execution_count": 5, "id": "ae8ffc4a-3dde-4413-8db6-60677edb6c9e", "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": "8edc2043-7ce6-4cdc-9298-47b4116eb59d", "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": 14, "id": "46f335be-d36b-40f4-b338-893147a5afcb", "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": 7, "id": "c2ecdac7-c5df-407e-8f19-d6faea834a62", "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": "224b8ef8-4160-4ec7-818d-2e8a4dcddaea", "metadata": {}, "source": [ "## Running Benchmark Calculations" ] }, { "cell_type": "markdown", "id": "d397e027-ba6e-4545-8c42-c02f86a4472b", "metadata": {}, "source": [ "Benchmark calculations are configured to run in parallel with one core per job." ] }, { "cell_type": "code", "execution_count": 19, "id": "99f89d3f-940a-4a11-9841-7e8dab851301", "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": "d1e2e7ea-8dcd-4f05-99a5-bcb5a42d3606", "metadata": {}, "source": [ "Note: calculations will take some time to run, around 1-2 hours on a modern laptop." ] }, { "cell_type": "code", "execution_count": 9, "id": "bb8bdaf3-d77d-4c41-acfd-176401a2112f", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "[05.03|09:22:09] JOB ANI-1ccx_ethylene STARTED\n", "[05.03|09:22:09] JOB ANI-1ccx_hexane STARTED\n", "[05.03|09:22:09] JOB ANI-1ccx_methane STARTED\n", "[05.03|09:22:09] JOB ANI-1ccx_2233tetramethylbutane STARTED\n", "[05.03|09:22:09] JOB ANI-1ccx_bicyclo222octane STARTED\n", "[05.03|09:22:09] JOB ANI-1ccx_ethylene RUNNING\n", "[05.03|09:22:09] JOB ANI-1ccx_31 STARTED\n", "[05.03|09:22:09] JOB ANI-1ccx_adamantane STARTED\n", "[05.03|09:22:09] JOB ANI-1ccx_hexane RUNNING\n", "[05.03|09:22:09] JOB ANI-1ccx_ethyne STARTED\n", "[05.03|09:22:09] JOB ANI-1ccx_22 STARTED\n", "[05.03|09:22:09] JOB ANI-1ccx_1 STARTED\n", "[05.03|09:22:09] JOB ANI-1ccx_ethane STARTED\n", "[05.03|09:22:09] JOB ANI-1ccx_2233tetramethylbutane RUNNING\n", "[05.03|09:22:09] JOB ANI-1ccx_octane STARTED\n", "[05.03|09:22:09] JOB ANI-1ccx_e_14 STARTED\n", "[05.03|09:22:09] JOB ANI-1ccx_p_9 STARTED\n", "[05.03|09:22:09] JOB ANI-1ccx_methane RUNNING\n", "[05.03|09:22:09] JOB ANI-1ccx_e_3 STARTED\n", "[05.03|09:22:09] JOB ANI-1ccx_e_13 STARTED\n", "[05.03|09:22:09] JOB ANI-1ccx_e_10 STARTED\n", "[05.03|09:22:09] JOB ANI-1ccx_bicyclo222octane RUNNING\n", "[05.03|09:22:09] JOB ANI-1ccx_p_14 STARTED\n", "[05.03|09:22:09] JOB ANI-1ccx_p_10 STARTED\n", "[05.03|09:22:09] JOB ANI-1ccx_p_13 STARTED\n", "[05.03|09:22:09] JOB ANI-1ccx_31 RUNNING\n", "[05.03|09:22:09] JOB ANI-1ccx_p_3 STARTED\n", "[05.03|09:22:09] JOB ANI-1ccx_e_9 STARTED\n", "[05.03|09:22:09] JOB ANI-2x_ethylene STARTED\n", "[05.03|09:22:09] JOB ANI-2x_hexane STARTED\n", "[05.03|09:22:09] JOB ANI-2x_methane STARTED\n", "[05.03|09:22:09] JOB ANI-2x_2233tetramethylbutane STARTED\n", "[05.03|09:22:09] JOB ANI-1ccx_adamantane RUNNING\n", "[05.03|09:22:09] JOB ANI-2x_bicyclo222octane STARTED\n", "[05.03|09:22:09] JOB ANI-2x_31 STARTED\n", "[05.03|09:22:09] JOB ANI-2x_adamantane STARTED\n", "[05.03|09:22:09] JOB ANI-2x_ethyne STARTED\n", "[05.03|09:22:09] JOB ANI-2x_22 STARTED\n", "[05.03|09:22:09] JOB ANI-1ccx_1 RUNNING\n", "[05.03|09:22:09] JOB ANI-2x_1 STARTED\n", "[05.03|09:22:09] JOB ANI-1ccx_ethyne RUNNING\n", "[05.03|09:22:09] JOB ANI-2x_ethane STARTED\n", "[05.03|09:22:09] JOB ANI-2x_octane STARTED\n", "[05.03|09:22:09] JOB ANI-1ccx_22 RUNNING\n", "[05.03|09:22:09] JOB ANI-2x_e_14 STARTED\n", "[05.03|09:22:09] JOB ANI-2x_p_9 STARTED\n", "[05.03|09:22:09] JOB ANI-1ccx_ethane RUNNING\n", "[05.03|09:22:09] JOB ANI-2x_e_3 STARTED\n", "[05.03|09:22:09] JOB ANI-2x_e_13 STARTED\n", "[05.03|09:22:09] JOB ANI-2x_e_10 STARTED\n", "[05.03|09:22:09] JOB ANI-2x_p_14 STARTED\n", "[05.03|09:22:09] JOB ANI-2x_p_10 STARTED\n", "[05.03|09:22:09] JOB ANI-1ccx_p_9 RUNNING\n", "[05.03|09:22:09] JOB ANI-1ccx_octane RUNNING\n", "[05.03|09:22:09] JOB ANI-2x_p_13 STARTED\n", "[05.03|09:22:09] JOB ANI-2x_p_3 STARTED\n", "[05.03|09:22:09] JOB ANI-2x_e_9 STARTED\n", "[05.03|09:22:09] JOB DFTB_ethylene STARTED\n", "[05.03|09:22:09] JOB DFTB_hexane STARTED\n", "[05.03|09:22:09] JOB DFTB_methane STARTED\n", "[05.03|09:22:09] JOB DFTB_2233tetramethylbutane STARTED\n", "[05.03|09:22:09] JOB DFTB_bicyclo222octane STARTED\n", "[05.03|09:22:09] JOB DFTB_31 STARTED\n", "[05.03|09:22:09] JOB DFTB_adamantane STARTED\n", "[05.03|09:22:09] JOB ANI-1ccx_e_14 RUNNING\n", "[05.03|09:22:09] JOB DFTB_ethyne STARTED\n", "[05.03|09:22:09] JOB ANI-1ccx_e_13 RUNNING\n", "[05.03|09:22:09] JOB ANI-1ccx_e_3 RUNNING\n", "[05.03|09:22:09] JOB DFTB_22 STARTED\n", "[05.03|09:22:09] JOB ANI-1ccx_e_10 RUNNING\n", "[05.03|09:22:09] JOB DFTB_1 STARTED\n", "[05.03|09:22:09] JOB ANI-1ccx_p_14 RUNNING\n", "[05.03|09:22:09] JOB ANI-1ccx_p_3 RUNNING\n", "[05.03|09:22:09] JOB DFTB_ethane STARTED\n", "[05.03|09:22:09] JOB ANI-1ccx_p_13 RUNNING\n", "[05.03|09:22:09] JOB DFTB_octane STARTED\n", "[05.03|09:22:09] JOB DFTB_e_14 STARTED\n", "[05.03|09:22:09] JOB DFTB_p_9 STARTED\n", "[05.03|09:22:09] JOB DFTB_e_3 STARTED\n", "[05.03|09:22:09] JOB DFTB_e_13 STARTED\n", "[05.03|09:22:09] JOB DFTB_e_10 STARTED\n", "[05.03|09:22:09] JOB DFTB_p_14 STARTED\n", "[05.03|09:22:09] JOB DFTB_p_10 STARTED\n", "[05.03|09:22:09] JOB DFTB_p_13 STARTED\n", "[05.03|09:22:09] JOB DFTB_p_3 STARTED\n", "[05.03|09:22:09] JOB DFTB_e_9 STARTED\n", "[05.03|09:22:09] JOB ReaxFF_ethylene STARTED\n", "[05.03|09:22:09] JOB ReaxFF_hexane STARTED\n", "[05.03|09:22:09] JOB ANI-1ccx_e_9 RUNNING\n", "[05.03|09:22:09] JOB ReaxFF_methane STARTED\n", "[05.03|09:22:09] JOB ANI-1ccx_p_10 RUNNING\n", "[05.03|09:22:09] JOB ReaxFF_2233tetramethylbutane STARTED\n", "[05.03|09:22:09] JOB ReaxFF_bicyclo222octane STARTED\n", "[05.03|09:22:09] JOB ReaxFF_31 STARTED\n", "[05.03|09:22:09] JOB ANI-2x_ethylene RUNNING\n", "[05.03|09:22:09] JOB ANI-2x_hexane RUNNING\n", "[05.03|09:22:09] JOB ReaxFF_adamantane STARTED\n", "[05.03|09:22:09] JOB ReaxFF_ethyne STARTED\n", "[05.03|09:22:09] JOB ReaxFF_22 STARTED\n", "[05.03|09:22:09] JOB ReaxFF_1 STARTED\n", "[05.03|09:22:09] JOB ReaxFF_ethane STARTED\n", "[05.03|09:22:09] JOB ANI-2x_methane RUNNING\n", "[05.03|09:22:09] JOB ReaxFF_octane STARTED\n", "[05.03|09:22:09] JOB ReaxFF_e_14 STARTED\n", "[05.03|09:22:09] JOB ReaxFF_p_9 STARTED\n", "[05.03|09:22:09] JOB ReaxFF_e_3 STARTED\n", "[05.03|09:22:09] JOB ReaxFF_e_13 STARTED\n", "[05.03|09:22:09] JOB ReaxFF_e_10 STARTED\n", "[05.03|09:22:09] JOB ReaxFF_p_14 STARTED\n", "[05.03|09:22:09] JOB ANI-2x_bicyclo222octane RUNNING\n", "[05.03|09:22:09] JOB ReaxFF_p_10 STARTED\n", "[05.03|09:22:09] JOB ReaxFF_p_13 STARTED\n", "[05.03|09:22:09] JOB ReaxFF_p_3 STARTED\n", "[05.03|09:22:09] JOB ReaxFF_e_9 STARTED\n", "[05.03|09:22:09] JOB ANI-2x_2233tetramethylbutane RUNNING\n", "[05.03|09:22:09] JOB ADF_ethylene STARTED\n", "[05.03|09:22:09] JOB ADF_hexane STARTED\n", "[05.03|09:22:09] JOB ADF_methane STARTED\n", "[05.03|09:22:09] JOB ANI-2x_31 RUNNING\n", "[05.03|09:22:09] JOB ANI-2x_adamantane RUNNING\n", "[05.03|09:22:09] JOB ADF_2233tetramethylbutane STARTED\n", "[05.03|09:22:09] JOB ADF_bicyclo222octane STARTED\n", "[05.03|09:22:09] JOB ANI-2x_ethyne RUNNING\n", "[05.03|09:22:09] JOB ANI-2x_22 RUNNING\n", "[05.03|09:22:09] JOB ADF_31 STARTED\n", "[05.03|09:22:09] JOB ADF_adamantane STARTED\n", "[05.03|09:22:09] JOB ADF_ethyne STARTED\n", "[05.03|09:22:09] JOB ANI-2x_1 RUNNING\n", "[05.03|09:22:09] JOB ADF_22 STARTED\n", "[05.03|09:22:09] JOB ANI-2x_octane RUNNING\n", "[05.03|09:22:09] JOB ADF_1 STARTED\n", "[05.03|09:22:09] JOB ADF_ethane STARTED\n", "[05.03|09:22:09] JOB ADF_octane STARTED\n", "[05.03|09:22:09] JOB ADF_e_14 STARTED\n", "[05.03|09:22:09] JOB ADF_p_9 STARTED\n", "[05.03|09:22:09] JOB ADF_e_3 STARTED\n", "[05.03|09:22:09] JOB ANI-2x_p_9 RUNNING\n", "[05.03|09:22:09] JOB ADF_e_13 STARTED\n", "[05.03|09:22:09] JOB ADF_e_10 STARTED\n", "[05.03|09:22:09] JOB ANI-2x_ethane RUNNING\n", "[05.03|09:22:09] JOB ANI-2x_e_14 RUNNING\n", "[05.03|09:22:09] JOB ADF_p_14 STARTED\n", "[05.03|09:22:09] JOB ADF_p_10 STARTED\n", "[05.03|09:22:09] JOB ANI-2x_e_3 RUNNING\n", "[05.03|09:22:09] JOB ADF_p_13 STARTED\n", "[05.03|09:22:09] JOB ADF_p_3 STARTED\n", "[05.03|09:22:09] JOB ADF_e_9 STARTED\n", "[05.03|09:22:09] JOB MP2_ethylene STARTED\n", "[05.03|09:22:09] JOB MP2_hexane STARTED\n", "[05.03|09:22:09] JOB MP2_methane STARTED\n", "[05.03|09:22:09] JOB MP2_2233tetramethylbutane STARTED\n", "[05.03|09:22:09] JOB MP2_bicyclo222octane STARTED\n", "[05.03|09:22:09] JOB ANI-2x_e_13 RUNNING\n", "[05.03|09:22:09] JOB MP2_31 STARTED\n", "[05.03|09:22:09] JOB MP2_adamantane STARTED\n", "[05.03|09:22:09] JOB MP2_ethyne STARTED\n", "[05.03|09:22:09] JOB ANI-2x_p_14 RUNNING\n", "[05.03|09:22:09] JOB ANI-2x_e_10 RUNNING\n", "[05.03|09:22:09] JOB MP2_22 STARTED\n", "[05.03|09:22:09] JOB MP2_1 STARTED\n", "[05.03|09:22:09] JOB MP2_ethane STARTED\n", "[05.03|09:22:09] JOB MP2_octane STARTED\n", "[05.03|09:22:09] JOB ANI-2x_p_3 RUNNING\n", "[05.03|09:22:09] JOB MP2_e_14 STARTED\n", "[05.03|09:22:09] JOB MP2_p_9 STARTED\n", "[05.03|09:22:09] JOB MP2_e_3 STARTED\n", "[05.03|09:22:09] JOB MP2_e_13 STARTED\n", "[05.03|09:22:09] JOB MP2_e_10 STARTED\n", "[05.03|09:22:09] JOB ANI-2x_p_10 RUNNING\n", "[05.03|09:22:09] JOB MP2_p_14 STARTED\n", "[05.03|09:22:09] JOB MP2_p_10 STARTED\n", "[05.03|09:22:09] JOB MP2_p_13 STARTED\n", "[05.03|09:22:09] JOB ANI-2x_e_9 RUNNING\n", "[05.03|09:22:09] JOB ANI-2x_p_13 RUNNING\n", "[05.03|09:22:09] JOB MP2_p_3 STARTED\n", "[05.03|09:22:09] JOB MP2_e_9 STARTED\n", "[05.03|09:22:09] JOB BAND_ethylene STARTED\n", "[05.03|09:22:09] JOB BAND_hexane STARTED\n", "[05.03|09:22:09] JOB BAND_methane STARTED\n", "[05.03|09:22:09] JOB BAND_2233tetramethylbutane STARTED\n", "[05.03|09:22:09] JOB BAND_bicyclo222octane STARTED\n", "[05.03|09:22:09] JOB BAND_31 STARTED\n", "[05.03|09:22:09] JOB BAND_adamantane STARTED\n", "[05.03|09:22:09] JOB BAND_ethyne STARTED\n", "[05.03|09:22:09] JOB BAND_22 STARTED\n", "[05.03|09:22:09] JOB BAND_1 STARTED\n", "[05.03|09:22:09] JOB DFTB_ethylene RUNNING\n", "[05.03|09:22:09] JOB DFTB_hexane RUNNING\n", "[05.03|09:22:09] JOB BAND_ethane STARTED\n", "[05.03|09:22:09] JOB BAND_octane STARTED\n", "[05.03|09:22:09] JOB BAND_e_14 STARTED\n", "[05.03|09:22:09] JOB BAND_p_9 STARTED\n", "[05.03|09:22:09] JOB BAND_e_3 STARTED\n", "[05.03|09:22:09] JOB BAND_e_13 STARTED\n", "[05.03|09:22:09] JOB BAND_e_10 STARTED\n", "[05.03|09:22:09] JOB DFTB_methane RUNNING\n", "[05.03|09:22:09] JOB BAND_p_14 STARTED\n", "[05.03|09:22:09] JOB BAND_p_10 STARTED\n", "[05.03|09:22:09] JOB BAND_p_13 STARTED\n", "[05.03|09:22:09] JOB BAND_p_3 STARTED\n", "[05.03|09:22:09] JOB BAND_e_9 STARTED\n", "[05.03|09:22:09] JOB DFTB_2233tetramethylbutane RUNNING\n", "[05.03|09:22:09] Waiting for job ANI-1ccx_ethylene to finish\n", "[05.03|09:22:09] JOB DFTB_31 RUNNING\n", "[05.03|09:22:09] JOB DFTB_bicyclo222octane RUNNING\n", "[05.03|09:22:09] JOB DFTB_ethyne RUNNING\n", "[05.03|09:22:09] JOB DFTB_adamantane RUNNING\n", "[05.03|09:22:09] JOB DFTB_22 RUNNING\n", "[05.03|09:22:09] JOB DFTB_ethane RUNNING\n", "[05.03|09:22:09] JOB DFTB_octane RUNNING\n", "[05.03|09:22:09] JOB DFTB_1 RUNNING\n", "[05.03|09:22:09] JOB DFTB_e_14 RUNNING\n", "[05.03|09:22:09] JOB DFTB_p_9 RUNNING\n", "[05.03|09:22:09] JOB DFTB_e_3 RUNNING\n", "[05.03|09:22:09] JOB DFTB_e_13 RUNNING\n", "[05.03|09:22:09] JOB DFTB_e_10 RUNNING\n", "[05.03|09:22:09] JOB DFTB_p_10 RUNNING\n", "[05.03|09:22:09] JOB DFTB_p_14 RUNNING\n", "[05.03|09:22:09] JOB DFTB_p_13 RUNNING\n", "[05.03|09:22:09] JOB DFTB_p_3 RUNNING\n", "[05.03|09:22:09] JOB DFTB_e_9 RUNNING\n", "[05.03|09:22:09] JOB ReaxFF_ethylene RUNNING\n", "[05.03|09:22:09] JOB ReaxFF_hexane RUNNING\n", "[05.03|09:22:09] JOB ReaxFF_2233tetramethylbutane RUNNING\n", "[05.03|09:22:09] JOB ReaxFF_bicyclo222octane RUNNING\n", "[05.03|09:22:09] JOB ReaxFF_methane RUNNING\n", "[05.03|09:22:09] JOB ReaxFF_31 RUNNING\n", "[05.03|09:22:09] JOB ReaxFF_ethyne RUNNING\n", "[05.03|09:22:09] JOB ReaxFF_adamantane RUNNING\n", "[05.03|09:22:09] JOB ReaxFF_1 RUNNING\n", "[05.03|09:22:09] JOB ReaxFF_octane RUNNING\n", "[05.03|09:22:09] JOB ReaxFF_22 RUNNING\n", "[05.03|09:22:09] JOB ReaxFF_ethane RUNNING\n", "[05.03|09:22:09] JOB ReaxFF_e_14 RUNNING\n", "[05.03|09:22:10] JOB ReaxFF_p_9 RUNNING\n", "[05.03|09:22:10] JOB ReaxFF_e_3 RUNNING\n", "[05.03|09:22:10] JOB ReaxFF_e_13 RUNNING\n", "[05.03|09:22:10] JOB ReaxFF_e_10 RUNNING\n", "[05.03|09:22:10] JOB ReaxFF_p_14 RUNNING\n", "[05.03|09:22:10] JOB ReaxFF_p_10 RUNNING\n", "[05.03|09:22:10] JOB ReaxFF_p_3 RUNNING\n", "[05.03|09:22:10] JOB ReaxFF_e_9 RUNNING\n", "[05.03|09:22:10] JOB ADF_ethylene RUNNING\n", "[05.03|09:22:10] JOB ADF_bicyclo222octane RUNNING\n", "[05.03|09:22:10] JOB ADF_31 RUNNING\n", "[05.03|09:22:10] JOB ReaxFF_p_13 RUNNING\n", "[05.03|09:22:10] JOB ADF_hexane RUNNING\n", "[05.03|09:22:10] JOB ADF_adamantane RUNNING\n", "[05.03|09:22:10] JOB ADF_p_3 RUNNING\n", "[05.03|09:22:10] JOB ADF_octane RUNNING\n", "[05.03|09:22:10] JOB ADF_ethyne RUNNING\n", "[05.03|09:22:10] JOB ADF_p_9 RUNNING\n", "[05.03|09:22:10] JOB ADF_e_3 RUNNING\n", "[05.03|09:22:10] JOB ADF_2233tetramethylbutane RUNNING\n", "[05.03|09:22:10] JOB ADF_methane RUNNING\n", "[05.03|09:22:10] JOB MP2_methane RUNNING\n", "[05.03|09:22:10] JOB ADF_ethane RUNNING\n", "[05.03|09:22:10] JOB ADF_1 RUNNING\n", "[05.03|09:22:10] JOB ADF_p_10 RUNNING\n", "[05.03|09:22:10] JOB MP2_ethane RUNNING\n", "[05.03|09:22:10] JOB ADF_p_14 RUNNING\n", "[05.03|09:22:10] JOB ADF_e_13 RUNNING\n", "[05.03|09:22:10] JOB ADF_e_10 RUNNING\n", "[05.03|09:22:10] JOB ADF_22 RUNNING\n", "[05.03|09:22:10] JOB ADF_e_14 RUNNING\n", "[05.03|09:22:10] JOB MP2_p_10 RUNNING\n", "[05.03|09:22:10] JOB MP2_bicyclo222octane RUNNING\n", "[05.03|09:22:10] JOB BAND_hexane RUNNING\n", "[05.03|09:22:10] JOB MP2_22 RUNNING\n", "[05.03|09:22:10] JOB BAND_methane RUNNING\n", "[05.03|09:22:10] JOB MP2_e_10 RUNNING\n", "[05.03|09:22:10] JOB BAND_2233tetramethylbutane RUNNING\n", "[05.03|09:22:10] JOB BAND_22 RUNNING\n", "[05.03|09:22:10] JOB BAND_p_3 RUNNING\n", "[05.03|09:22:10] JOB BAND_e_14 RUNNING\n", "[05.03|09:22:10] JOB BAND_31 RUNNING\n", "[05.03|09:22:10] JOB BAND_e_10 RUNNING\n", "[05.03|09:22:10] JOB MP2_p_13 RUNNING\n", "[05.03|09:22:10] JOB MP2_p_14 RUNNING\n", "[05.03|09:22:10] JOB BAND_p_9 RUNNING\n", "[05.03|09:22:10] JOB ADF_e_9 RUNNING\n", "[05.03|09:22:10] JOB MP2_e_9 RUNNING\n", "[05.03|09:22:10] JOB MP2_ethylene RUNNING\n", "[05.03|09:22:10] JOB MP2_p_9 RUNNING\n", "[05.03|09:22:10] JOB MP2_e_14 RUNNING\n", "[05.03|09:22:10] JOB MP2_1 RUNNING\n", "[05.03|09:22:10] JOB BAND_p_13 RUNNING\n", "[05.03|09:22:10] JOB BAND_octane RUNNING\n", "[05.03|09:22:10] JOB MP2_adamantane RUNNING\n", "[05.03|09:22:10] JOB MP2_2233tetramethylbutane RUNNING\n", "[05.03|09:22:10] JOB MP2_octane RUNNING\n", "[05.03|09:22:10] JOB MP2_31 RUNNING\n", "[05.03|09:22:10] JOB BAND_bicyclo222octane RUNNING\n", "[05.03|09:22:10] JOB BAND_e_3 RUNNING\n", "[05.03|09:22:10] JOB ADF_p_13 RUNNING\n", "[05.03|09:22:10] JOB BAND_ethylene RUNNING\n", "[05.03|09:22:10] JOB MP2_e_13 RUNNING\n", "[05.03|09:22:10] JOB MP2_e_3 RUNNING\n", "[05.03|09:22:10] JOB BAND_ethane RUNNING\n", "[05.03|09:22:10] JOB MP2_ethyne RUNNING\n", "[05.03|09:22:10] JOB BAND_adamantane RUNNING\n", "[05.03|09:22:10] JOB BAND_e_13 RUNNING\n", "[05.03|09:22:10] JOB BAND_1 RUNNING\n", "[05.03|09:22:10] JOB BAND_p_10 RUNNING\n", "[05.03|09:22:10] JOB BAND_p_14 RUNNING\n", "[05.03|09:22:10] JOB MP2_p_3 RUNNING\n", "[05.03|09:22:10] JOB BAND_e_9 RUNNING\n", "[05.03|09:22:10] JOB MP2_hexane RUNNING\n", "[05.03|09:22:10] JOB BAND_ethyne RUNNING\n", "[05.03|09:22:18] JOB ANI-1ccx_31 FINISHED\n", "[05.03|09:22:18] JOB ANI-1ccx_hexane FINISHED\n", "[05.03|09:22:18] JOB ANI-1ccx_ethylene FINISHED\n", "[05.03|09:22:18] JOB ANI-1ccx_2233tetramethylbutane FINISHED\n", "[05.03|09:22:18] JOB ANI-1ccx_1 FINISHED\n", "[05.03|09:22:18] JOB ANI-1ccx_methane FINISHED\n", "[05.03|09:22:18] JOB ANI-1ccx_adamantane FINISHED\n", "[05.03|09:22:18] JOB ANI-1ccx_bicyclo222octane FINISHED\n", "[05.03|09:22:18] JOB ANI-1ccx_hexane SUCCESSFUL\n", "[05.03|09:22:18] JOB ANI-1ccx_31 SUCCESSFUL\n", "[05.03|09:22:18] JOB ANI-1ccx_ethylene SUCCESSFUL\n", "[05.03|09:22:18] JOB ANI-1ccx_adamantane SUCCESSFUL\n", "[05.03|09:22:18] JOB ANI-1ccx_1 SUCCESSFUL\n", "[05.03|09:22:18] JOB ANI-1ccx_bicyclo222octane SUCCESSFUL\n", "[05.03|09:22:18] JOB ANI-1ccx_2233tetramethylbutane SUCCESSFUL\n", "[05.03|09:22:18] JOB ANI-1ccx_methane SUCCESSFUL\n", "[05.03|09:22:18] Waiting for job ANI-1ccx_ethyne to finish\n", "[05.03|09:22:19] JOB ReaxFF_2233tetramethylbutane FINISHED\n", "[05.03|09:22:19] JOB ReaxFF_2233tetramethylbutane SUCCESSFUL\n", "[05.03|09:22:19] JOB DFTB_p_10 FINISHED\n", "[05.03|09:22:19] JOB DFTB_p_10 SUCCESSFUL\n", "[05.03|09:22:26] JOB ANI-1ccx_ethyne FINISHED\n", "[05.03|09:22:26] JOB ANI-1ccx_p_9 FINISHED\n", "[05.03|09:22:26] JOB ANI-1ccx_ethyne SUCCESSFUL\n", "[05.03|09:22:26] JOB ANI-1ccx_p_9 SUCCESSFUL\n", "[05.03|09:22:26] Waiting for job ANI-1ccx_22 to finish\n", "[05.03|09:22:26] JOB ANI-1ccx_ethane FINISHED\n", "[05.03|09:22:26] JOB ANI-1ccx_ethane SUCCESSFUL\n", "[05.03|09:22:26] JOB ANI-1ccx_22 FINISHED\n", "[05.03|09:22:26] JOB ANI-1ccx_22 SUCCESSFUL\n", "[05.03|09:22:26] Waiting for job ANI-1ccx_octane to finish\n", "[05.03|09:22:28] JOB ANI-2x_methane FINISHED\n", "[05.03|09:22:28] JOB ANI-2x_methane SUCCESSFUL\n", "[05.03|09:22:28] JOB ANI-2x_ethyne FINISHED\n", "[05.03|09:22:28] JOB ANI-2x_ethyne SUCCESSFUL\n", "[05.03|09:22:29] JOB DFTB_1 FINISHED\n", "[05.03|09:22:29] JOB DFTB_1 SUCCESSFUL\n", "[05.03|09:22:32] JOB MP2_ethyne FINISHED\n", "[05.03|09:22:32] JOB MP2_ethyne SUCCESSFUL\n", "[05.03|09:22:37] JOB ANI-1ccx_p_10 FINISHED\n", "[05.03|09:22:37] JOB ANI-1ccx_p_10 SUCCESSFUL\n", "[05.03|09:22:38] JOB ANI-1ccx_e_10 FINISHED\n", "[05.03|09:22:38] JOB ANI-1ccx_e_10 SUCCESSFUL\n", "[05.03|09:22:39] JOB ANI-2x_e_9 FINISHED\n", "[05.03|09:22:39] JOB ANI-2x_e_9 SUCCESSFUL\n", "[05.03|09:22:44] JOB ANI-2x_p_3 FINISHED\n", "[05.03|09:22:44] JOB ANI-2x_p_3 SUCCESSFUL\n", "[05.03|09:22:47] JOB ANI-1ccx_e_13 FINISHED\n", "[05.03|09:22:47] JOB ANI-1ccx_e_13 SUCCESSFUL\n", "[05.03|09:22:56] JOB ANI-1ccx_p_3 FINISHED\n", "[05.03|09:22:56] JOB ANI-1ccx_p_3 SUCCESSFUL\n", "[05.03|09:23:01] JOB ADF_methane FINISHED\n", "[05.03|09:23:01] JOB ADF_methane SUCCESSFUL\n", "[05.03|09:23:24] JOB BAND_methane FINISHED\n", "[05.03|09:23:24] JOB BAND_methane SUCCESSFUL\n", "[05.03|09:23:34] JOB ADF_ethylene FINISHED\n", "[05.03|09:23:34] JOB ADF_ethylene SUCCESSFUL\n", "[05.03|09:23:44] JOB ANI-1ccx_octane FINISHED\n", "[05.03|09:23:44] JOB ANI-1ccx_octane SUCCESSFUL\n", "[05.03|09:23:44] Waiting for job ANI-1ccx_e_14 to finish\n", "[05.03|09:23:44] JOB ReaxFF_methane FINISHED\n", "[05.03|09:23:44] JOB ReaxFF_methane SUCCESSFUL\n", "[05.03|09:23:45] JOB ReaxFF_e_13 FINISHED\n", "[05.03|09:23:45] JOB ReaxFF_e_13 SUCCESSFUL\n", "[05.03|09:23:55] JOB ANI-2x_ethylene FINISHED\n", "[05.03|09:23:55] JOB ANI-2x_ethylene SUCCESSFUL\n", "[05.03|09:25:31] JOB ADF_octane FINISHED\n", "[05.03|09:25:31] JOB ADF_octane SUCCESSFUL\n", "[05.03|09:25:41] JOB MP2_octane FINISHED\n", "[05.03|09:25:41] JOB MP2_octane SUCCESSFUL\n", "[05.03|09:25:53] JOB ANI-2x_bicyclo222octane FINISHED\n", "[05.03|09:25:53] JOB ANI-2x_bicyclo222octane SUCCESSFUL\n", "[05.03|09:26:41] JOB BAND_ethylene FINISHED\n", "[05.03|09:26:41] JOB BAND_ethylene SUCCESSFUL\n", "[05.03|09:27:39] JOB MP2_22 FINISHED\n", "[05.03|09:27:39] JOB MP2_22 SUCCESSFUL\n", "[05.03|09:32:28] JOB ANI-2x_31 FINISHED\n", "[05.03|09:32:28] JOB ANI-2x_31 SUCCESSFUL\n", "[05.03|09:33:22] JOB ADF_2233tetramethylbutane FINISHED\n", "[05.03|09:33:22] JOB ADF_2233tetramethylbutane SUCCESSFUL\n", "[05.03|09:33:22] JOB ReaxFF_e_9 FINISHED\n", "[05.03|09:33:22] JOB ReaxFF_e_9 SUCCESSFUL\n", "[05.03|09:33:35] JOB MP2_e_14 FINISHED\n", "[05.03|09:33:35] JOB MP2_e_14 SUCCESSFUL\n", "[05.03|09:33:46] JOB ANI-2x_e_3 FINISHED\n", "[05.03|09:33:46] JOB ANI-2x_e_3 SUCCESSFUL\n", "[05.03|09:33:47] JOB DFTB_31 FINISHED\n", "[05.03|09:33:47] JOB DFTB_31 SUCCESSFUL\n", "[05.03|09:33:47] JOB DFTB_22 FINISHED\n", "[05.03|09:33:47] JOB DFTB_22 SUCCESSFUL\n", "[05.03|09:34:04] JOB MP2_ethane FINISHED\n", "[05.03|09:34:04] JOB MP2_ethane SUCCESSFUL\n", "[05.03|09:36:07] JOB BAND_octane FINISHED\n", "[05.03|09:36:07] JOB BAND_octane SUCCESSFUL\n", "[05.03|09:36:48] JOB MP2_1 FINISHED\n", "[05.03|09:36:48] JOB MP2_1 SUCCESSFUL\n", "[05.03|09:36:49] JOB ReaxFF_p_13 FINISHED\n", "[05.03|09:36:49] JOB ReaxFF_p_13 SUCCESSFUL\n", "[05.03|09:39:56] JOB ADF_p_3 FINISHED\n", "[05.03|09:39:56] JOB ADF_p_3 SUCCESSFUL\n", "[05.03|09:40:17] JOB MP2_p_14 FINISHED\n", "[05.03|09:40:17] JOB MP2_p_14 SUCCESSFUL\n", "[05.03|09:40:28] JOB ANI-2x_ethane FINISHED\n", "[05.03|09:40:28] JOB ANI-2x_ethane SUCCESSFUL\n", "[05.03|09:41:13] JOB BAND_hexane FINISHED\n", "[05.03|09:41:13] JOB BAND_hexane SUCCESSFUL\n", "[05.03|09:41:24] JOB ANI-2x_1 FINISHED\n", "[05.03|09:41:24] JOB ANI-2x_1 SUCCESSFUL\n", "[05.03|09:41:34] JOB ANI-2x_p_10 FINISHED\n", "[05.03|09:41:34] JOB ANI-2x_p_10 SUCCESSFUL\n", "[05.03|09:41:34] JOB DFTB_p_13 FINISHED\n", "[05.03|09:41:35] JOB DFTB_p_13 SUCCESSFUL\n", "[05.03|09:41:35] JOB ReaxFF_bicyclo222octane FINISHED\n", "[05.03|09:41:35] JOB ReaxFF_bicyclo222octane SUCCESSFUL\n", "[05.03|09:41:36] JOB BAND_1 FINISHED\n", "[05.03|09:41:36] JOB BAND_1 SUCCESSFUL\n", "[05.03|09:41:36] JOB DFTB_e_10 FINISHED\n", "[05.03|09:41:36] JOB DFTB_e_10 SUCCESSFUL\n", "[05.03|09:41:46] JOB ANI-1ccx_e_3 FINISHED\n", "[05.03|09:41:46] JOB ANI-1ccx_e_3 SUCCESSFUL\n", "[05.03|09:41:46] JOB DFTB_ethane FINISHED\n", "[05.03|09:41:46] JOB DFTB_ethane SUCCESSFUL\n", "[05.03|09:41:56] JOB ANI-2x_e_10 FINISHED\n", "[05.03|09:41:56] JOB ANI-2x_e_10 SUCCESSFUL\n", "[05.03|09:42:03] JOB MP2_ethylene FINISHED\n", "[05.03|09:42:03] JOB MP2_ethylene SUCCESSFUL\n", "[05.03|09:42:34] JOB ADF_adamantane FINISHED\n", "[05.03|09:42:34] JOB ADF_adamantane SUCCESSFUL\n", "[05.03|09:42:35] JOB BAND_p_3 FINISHED\n", "[05.03|09:42:35] JOB BAND_p_3 SUCCESSFUL\n", "[05.03|09:42:36] JOB DFTB_e_14 FINISHED\n", "[05.03|09:42:36] JOB DFTB_e_14 SUCCESSFUL\n", "[05.03|09:42:44] JOB ANI-1ccx_p_14 FINISHED\n", "[05.03|09:42:44] JOB ANI-1ccx_p_14 SUCCESSFUL\n", "[05.03|09:42:45] JOB ReaxFF_p_3 FINISHED\n", "[05.03|09:42:45] JOB ReaxFF_p_3 SUCCESSFUL\n", "[05.03|09:42:46] JOB ANI-2x_e_14 FINISHED\n", "[05.03|09:42:46] JOB ANI-2x_e_14 SUCCESSFUL\n", "[05.03|09:42:47] JOB ReaxFF_ethyne FINISHED\n", "[05.03|09:42:47] JOB ReaxFF_ethyne SUCCESSFUL\n", "[05.03|09:42:47] JOB ReaxFF_ethane FINISHED\n", "[05.03|09:42:47] JOB ReaxFF_ethane SUCCESSFUL\n", "[05.03|09:42:55] JOB ANI-2x_e_13 FINISHED\n", "[05.03|09:42:55] JOB ANI-2x_e_13 SUCCESSFUL\n", "[05.03|09:42:57] JOB ANI-2x_adamantane FINISHED\n", "[05.03|09:42:57] JOB ANI-2x_adamantane SUCCESSFUL\n", "[05.03|09:42:58] JOB ReaxFF_p_9 FINISHED\n", "[05.03|09:42:58] JOB ReaxFF_p_9 SUCCESSFUL\n", "[05.03|09:43:00] JOB MP2_hexane FINISHED\n", "[05.03|09:43:00] JOB MP2_hexane SUCCESSFUL\n", "[05.03|09:43:55] JOB ADF_ethane FINISHED\n", "[05.03|09:43:55] JOB ADF_ethane SUCCESSFUL\n", "[05.03|09:44:11] JOB BAND_e_14 FINISHED\n", "[05.03|09:44:11] JOB BAND_e_14 SUCCESSFUL\n", "[05.03|09:44:46] JOB MP2_e_13 FINISHED\n", "[05.03|09:44:46] JOB MP2_e_13 SUCCESSFUL\n", "[05.03|09:48:27] JOB ADF_31 FINISHED\n", "[05.03|09:48:27] JOB ADF_31 SUCCESSFUL\n", "[05.03|09:48:28] JOB DFTB_p_14 FINISHED\n", "[05.03|09:48:28] JOB DFTB_p_14 SUCCESSFUL\n", "[05.03|09:48:28] JOB MP2_p_3 FINISHED\n", "[05.03|09:48:28] JOB MP2_p_3 SUCCESSFUL\n", "[05.03|09:50:01] JOB ADF_e_13 FINISHED\n", "[05.03|09:50:01] JOB ADF_e_13 SUCCESSFUL\n", "[05.03|09:52:31] JOB BAND_e_9 FINISHED\n", "[05.03|09:52:31] JOB BAND_e_9 SUCCESSFUL\n", "[05.03|09:52:32] JOB ReaxFF_31 FINISHED\n", "[05.03|09:52:32] JOB ReaxFF_31 SUCCESSFUL\n", "[05.03|09:52:44] JOB ANI-2x_2233tetramethylbutane FINISHED\n", "[05.03|09:52:44] JOB ANI-2x_2233tetramethylbutane SUCCESSFUL\n", "[05.03|09:53:56] JOB BAND_p_10 FINISHED\n", "[05.03|09:53:56] JOB BAND_p_10 SUCCESSFUL\n", "[05.03|09:53:56] JOB ReaxFF_p_14 FINISHED\n", "[05.03|09:53:56] JOB ReaxFF_p_14 SUCCESSFUL\n", "[05.03|09:54:06] JOB ANI-2x_p_14 FINISHED\n", "[05.03|09:54:06] JOB ANI-2x_p_14 SUCCESSFUL\n", "[05.03|09:54:07] JOB DFTB_ethyne FINISHED\n", "[05.03|09:54:07] JOB DFTB_ethyne SUCCESSFUL\n", "[05.03|09:54:51] JOB MP2_p_13 FINISHED\n", "[05.03|09:54:51] JOB MP2_p_13 SUCCESSFUL\n", "[05.03|09:54:52] JOB DFTB_bicyclo222octane FINISHED\n", "[05.03|09:54:52] JOB DFTB_bicyclo222octane SUCCESSFUL\n", "[05.03|09:55:04] JOB BAND_e_3 FINISHED\n", "[05.03|09:55:04] JOB BAND_e_3 SUCCESSFUL\n", "[05.03|09:55:50] JOB MP2_p_10 FINISHED\n", "[05.03|09:55:50] JOB MP2_p_10 SUCCESSFUL\n", "[05.03|09:56:56] JOB MP2_adamantane FINISHED\n", "[05.03|09:56:56] JOB MP2_adamantane SUCCESSFUL\n", "[05.03|09:56:56] JOB ReaxFF_e_10 FINISHED\n", "[05.03|09:56:56] JOB ReaxFF_e_10 SUCCESSFUL\n", "[05.03|09:56:56] JOB ReaxFF_octane FINISHED\n", "[05.03|09:56:56] JOB ReaxFF_octane SUCCESSFUL\n", "[05.03|09:56:57] JOB DFTB_p_9 FINISHED\n", "[05.03|09:56:57] JOB DFTB_p_9 SUCCESSFUL\n", "[05.03|09:59:16] JOB BAND_31 FINISHED\n", "[05.03|09:59:16] JOB BAND_31 SUCCESSFUL\n", "[05.03|09:59:26] JOB ANI-2x_p_9 FINISHED\n", "[05.03|09:59:26] JOB ANI-2x_p_9 SUCCESSFUL\n", "[05.03|09:59:26] JOB DFTB_e_3 FINISHED\n", "[05.03|09:59:26] JOB DFTB_e_3 SUCCESSFUL\n", "[05.03|09:59:52] JOB ADF_bicyclo222octane FINISHED\n", "[05.03|09:59:52] JOB ADF_bicyclo222octane SUCCESSFUL\n", "[05.03|10:00:08] JOB ADF_22 FINISHED\n", "[05.03|10:00:08] JOB ADF_22 SUCCESSFUL\n", "[05.03|10:00:09] JOB ReaxFF_e_14 FINISHED\n", "[05.03|10:00:09] JOB ReaxFF_e_14 SUCCESSFUL\n", "[05.03|10:00:09] JOB ReaxFF_e_3 FINISHED\n", "[05.03|10:00:09] JOB ReaxFF_e_3 SUCCESSFUL\n", "[05.03|10:00:09] JOB ReaxFF_22 FINISHED\n", "[05.03|10:00:09] JOB ReaxFF_22 SUCCESSFUL\n", "[05.03|10:00:20] JOB ANI-2x_hexane FINISHED\n", "[05.03|10:00:20] JOB ANI-2x_hexane SUCCESSFUL\n", "[05.03|10:00:24] JOB ADF_ethyne FINISHED\n", "[05.03|10:00:24] JOB ADF_ethyne SUCCESSFUL\n", "[05.03|10:00:57] JOB ADF_p_10 FINISHED\n", "[05.03|10:00:57] JOB ADF_p_10 SUCCESSFUL\n", "[05.03|10:00:57] JOB DFTB_2233tetramethylbutane FINISHED\n", "[05.03|10:00:57] JOB DFTB_2233tetramethylbutane SUCCESSFUL\n", "[05.03|10:00:58] JOB ReaxFF_p_10 FINISHED\n", "[05.03|10:00:58] JOB ReaxFF_p_10 SUCCESSFUL\n", "[05.03|10:02:21] JOB MP2_e_9 FINISHED\n", "[05.03|10:02:21] JOB MP2_e_9 SUCCESSFUL\n", "[05.03|10:02:25] JOB MP2_p_9 FINISHED\n", "[05.03|10:02:25] JOB MP2_p_9 SUCCESSFUL\n", "[05.03|10:02:30] JOB ANI-1ccx_e_9 FINISHED\n", "[05.03|10:02:30] JOB ANI-1ccx_e_9 SUCCESSFUL\n", "[05.03|10:02:31] JOB DFTB_e_9 FINISHED\n", "[05.03|10:02:31] JOB DFTB_e_9 SUCCESSFUL\n", "[05.03|10:02:39] JOB ANI-1ccx_p_13 FINISHED\n", "[05.03|10:02:39] JOB ANI-1ccx_p_13 SUCCESSFUL\n", "[05.03|10:04:50] JOB ADF_1 FINISHED\n", "[05.03|10:04:50] JOB ADF_1 SUCCESSFUL\n", "[05.03|10:05:42] JOB ADF_e_14 FINISHED\n", "[05.03|10:05:42] JOB ADF_e_14 SUCCESSFUL\n", "[05.03|10:06:16] JOB MP2_2233tetramethylbutane FINISHED\n", "[05.03|10:06:16] JOB MP2_2233tetramethylbutane SUCCESSFUL\n", "[05.03|10:07:41] JOB MP2_bicyclo222octane FINISHED\n", "[05.03|10:07:41] JOB MP2_bicyclo222octane SUCCESSFUL\n", "[05.03|10:09:27] JOB ADF_hexane FINISHED\n", "[05.03|10:09:27] JOB ADF_hexane SUCCESSFUL\n", "[05.03|10:10:18] JOB BAND_e_13 FINISHED\n", "[05.03|10:10:18] JOB BAND_e_13 SUCCESSFUL\n", "[05.03|10:10:41] JOB MP2_e_3 FINISHED\n", "[05.03|10:10:41] JOB MP2_e_3 SUCCESSFUL\n", "[05.03|10:11:06] JOB ADF_p_9 FINISHED\n", "[05.03|10:11:06] JOB ADF_p_9 SUCCESSFUL\n", "[05.03|10:11:40] JOB BAND_ethane FINISHED\n", "[05.03|10:11:40] JOB BAND_ethane SUCCESSFUL\n", "[05.03|10:11:41] JOB DFTB_hexane FINISHED\n", "[05.03|10:11:41] JOB DFTB_hexane SUCCESSFUL\n", "[05.03|10:12:57] JOB BAND_22 FINISHED\n", "[05.03|10:12:57] JOB BAND_22 SUCCESSFUL\n", "[05.03|10:12:58] JOB DFTB_adamantane FINISHED\n", "[05.03|10:12:58] JOB DFTB_adamantane SUCCESSFUL\n", "[05.03|10:12:58] JOB ReaxFF_adamantane FINISHED\n", "[05.03|10:12:58] JOB ReaxFF_adamantane SUCCESSFUL\n", "[05.03|10:12:59] JOB DFTB_e_13 FINISHED\n", "[05.03|10:12:59] JOB DFTB_e_13 SUCCESSFUL\n", "[05.03|10:13:06] JOB BAND_p_13 FINISHED\n", "[05.03|10:13:06] JOB BAND_p_13 SUCCESSFUL\n", "[05.03|10:13:56] JOB BAND_e_10 FINISHED\n", "[05.03|10:13:56] JOB BAND_e_10 SUCCESSFUL\n", "[05.03|10:17:43] JOB ADF_e_3 FINISHED\n", "[05.03|10:17:43] JOB ADF_e_3 SUCCESSFUL\n", "[05.03|10:17:43] JOB ReaxFF_hexane FINISHED\n", "[05.03|10:17:43] JOB ReaxFF_hexane SUCCESSFUL\n", "[05.03|10:17:44] JOB DFTB_p_3 FINISHED\n", "[05.03|10:17:44] JOB DFTB_p_3 SUCCESSFUL\n", "[05.03|10:18:16] JOB BAND_ethyne FINISHED\n", "[05.03|10:18:16] JOB BAND_ethyne SUCCESSFUL\n", "[05.03|10:20:04] JOB BAND_adamantane FINISHED\n", "[05.03|10:20:04] JOB BAND_adamantane SUCCESSFUL\n", "[05.03|10:20:13] JOB ANI-1ccx_e_14 FINISHED\n", "[05.03|10:20:13] JOB ANI-1ccx_e_14 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", "[05.03|10:20:13] Waiting for job ANI-2x_22 to finish\n", "[05.03|10:20:50] JOB ADF_p_14 FINISHED\n", "[05.03|10:20:50] JOB ADF_p_14 SUCCESSFUL\n", "[05.03|10:22:48] JOB BAND_2233tetramethylbutane FINISHED\n", "[05.03|10:22:48] JOB BAND_2233tetramethylbutane SUCCESSFUL\n", "[05.03|10:22:59] JOB ANI-2x_p_13 FINISHED\n", "[05.03|10:22:59] JOB ANI-2x_p_13 SUCCESSFUL\n", "[05.03|10:23:00] JOB DFTB_octane FINISHED\n", "[05.03|10:23:00] JOB DFTB_octane SUCCESSFUL\n", "[05.03|10:23:04] JOB MP2_methane FINISHED\n", "[05.03|10:23:04] JOB MP2_methane SUCCESSFUL\n", "[05.03|10:23:04] JOB ReaxFF_ethylene FINISHED\n", "[05.03|10:23:04] JOB ReaxFF_ethylene SUCCESSFUL\n", "[05.03|10:23:04] JOB DFTB_methane FINISHED\n", "[05.03|10:23:04] JOB DFTB_methane SUCCESSFUL\n", "[05.03|10:23:14] JOB ANI-2x_octane FINISHED\n", "[05.03|10:23:14] JOB ANI-2x_octane SUCCESSFUL\n", "[05.03|10:23:14] JOB ReaxFF_1 FINISHED\n", "[05.03|10:23:14] JOB ReaxFF_1 SUCCESSFUL\n", "[05.03|10:23:23] JOB ANI-2x_22 FINISHED\n", "[05.03|10:23:23] JOB ANI-2x_22 SUCCESSFUL\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", "[05.03|10:23:23] Waiting for job DFTB_ethylene to finish\n", "[05.03|10:23:24] JOB DFTB_ethylene FINISHED\n", "[05.03|10:23:24] JOB DFTB_ethylene SUCCESSFUL\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", "[05.03|10:23:24] Waiting for job ADF_e_10 to finish\n", "[05.03|10:23:40] JOB BAND_p_9 FINISHED\n", "[05.03|10:23:40] JOB BAND_p_9 SUCCESSFUL\n", "[05.03|10:23:43] JOB ADF_p_13 FINISHED\n", "[05.03|10:23:43] JOB ADF_p_13 SUCCESSFUL\n", "[05.03|10:24:27] JOB MP2_e_10 FINISHED\n", "[05.03|10:24:27] JOB MP2_e_10 SUCCESSFUL\n", "[05.03|10:24:48] JOB ADF_e_9 FINISHED\n", "[05.03|10:24:48] JOB ADF_e_9 SUCCESSFUL\n", "[05.03|10:24:49] JOB MP2_31 FINISHED\n", "[05.03|10:24:49] JOB MP2_31 SUCCESSFUL\n", "[05.03|10:26:23] JOB BAND_p_14 FINISHED\n", "[05.03|10:26:23] JOB BAND_p_14 SUCCESSFUL\n", "[05.03|10:27:29] JOB ADF_e_10 FINISHED\n", "[05.03|10:27:29] JOB ADF_e_10 SUCCESSFUL\n", "ADF 20.8 31.4 -1.9 6.7 9.9 214.5 139.7 9.5 20.5 4.7 31.0 4.8\n", "\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", "[05.03|10:27:29] Waiting for job BAND_bicyclo222octane to finish\n", "[05.03|10:28:14] JOB BAND_bicyclo222octane FINISHED\n", "[05.03|10:28:14] JOB BAND_bicyclo222octane SUCCESSFUL\n", "BAND 19.2 30.2 -2.7 7.3 11.0 218.5 141.3 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(settings=s, molecule=mol, name=engine_name + \"_\" + mol_name)\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": "e807301f-9f82-43c2-86ea-22471b4ff33e", "metadata": {}, "source": [ "## Results" ] }, { "cell_type": "markdown", "id": "a3c21bbb-97c8-4b18-875e-832ab5883ef2", "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": 71, "id": "5f0cd5ee-c298-44e1-8319-d8c746a615ca", "metadata": {}, "outputs": [ { "data": { "text/markdown": [ "| | #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 |\n", "|---:|:----------------|--------:|--------:|--------:|--------:|--------:|--------:|--------:|----------:|----------:|----------:|----------:|----------:|\n", "| 0 | Truhlar_ref | 14.34 | 25.02 | 1.9 | 9.81 | 14.84 | 193.99 | 127.22 | 9.77 | 21.76 | 6.82 | 33.52 | 5.3 |\n", "| 1 | Smith_wB97X_ref | 28.77 | 41.09 | 1.75 | 6.26 | 9.3 | 238.83 | 157.65 | 9.32 | 20.8 | 1.03 | 26.43 | 0.4 |\n", "| 2 | 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", "| 3 | ANI-2x | 42.4 | 48.1 | -1.9 | 5.4 | 8 | 238.4 | 156.9 | 7.9 | 20.8 | -1.5 | 26.7 | 0.5 |\n", "| 4 | DFTB | 7.1 | 19 | 0.2 | 3.6 | 5.4 | 223.5 | 150.8 | 11.7 | 22.6 | 7.9 | 35.2 | 8.6 |\n", "| 5 | ReaxFF | 34.3 | 23 | 13.4 | 2.6 | 5.5 | 289.2 | 168.3 | -9.2 | 24.2 | 70.7 | 30.9 | 89.3 |\n", "| 6 | ADF | 20.8 | 31.4 | -1.9 | 6.7 | 9.9 | 214.5 | 139.7 | 9.5 | 20.5 | 4.7 | 31 | 4.8 |\n", "| 7 | MP2 | 20.5 | 27.1 | 5.4 | 9.9 | 15 | 214.8 | 141.3 | 11 | 24.6 | 8.4 | 36.8 | 6.2 |\n", "| 8 | BAND | 19.2 | 30.2 | -2.7 | 7.3 | 11 | 218.5 | 141.3 | 9.9 | 18.5 | 5.3 | 31.7 | 4.7 |" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "with open(summary_fname) as summary_file:\n", " try:\n", " import pandas as pd\n", " from IPython.display import display, Markdown\n", " import sys\n", "\n", " data = pd.read_csv(summary_file, delim_whitespace=True).iloc[:, :-1]\n", "\n", " # Pretty-print if in notebook\n", " if \"ipykernel\" in sys.modules:\n", " display(Markdown(data.to_markdown()))\n", " else:\n", " print(data.to_markdown())\n", "\n", " except ImportError:\n", " data = summary_file.read()\n", " print(data)" ] }, { "cell_type": "code", "execution_count": null, "id": "3be777b3-0f76-4641-91a6-0c171fe3c15f", "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 }