{ "cells": [ { "cell_type": "markdown", "metadata": { "tags": [] }, "source": [ "# ESgamess: molecule and Gamess job handling class (symmetry and transformations demo)\n", "01/12/23, 23/01/24 (debugged)\n", "\n", "Demo for using ESgamess class for more advances Gamess jobs, including symmetry and frame transformations.\n", "\n", "For an intro demo, see [the basic demo page](ESgamess_class_demo_221123-tidy.html)." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Imports" ] }, { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [], "source": [ "# Import class\n", "from epsman.elecStructure.gamess import ESgamess" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Create molecule\n", "\n", "See [the basic demo page](ESgamess_class_demo_221123-tidy.html) for alternative methods, here just set from SMILES." ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Set name = None\n", "Set smiles = O=C=O\n", "Set molFile = None\n", "Set xyz = None\n", "Set molOverride = None\n", "Set job = None\n", "Set sym = C1\n", "Set atomList = None\n", "Set precision = 4\n", "Set atomsDict = {}\n", "Set refDict = {}\n", "Set atomsHist = {}\n", "*** Updating coords (Pandas version).\n" ] }, { "data": { "image/png": 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IndSpeciesAtomic Num.xyz
00O8-1.23750.00.0
11C60.00000.00.0
22O81.23750.00.0
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" ], "text/plain": [ " Ind Species Atomic Num. x y z\n", "0 0 O 8 -1.2375 0.0 0.0\n", "1 1 C 6 0.0000 0.0 0.0\n", "2 2 O 8 1.2375 0.0 0.0" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "# Molecule from PubChem\n", "# testDL = ESgamess(searchName = 'CO2')\n", "\n", "# Molecule from Smiles\n", "testDL = ESgamess(smiles='O=C=O', precision = 4)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## pyGamess wrapper" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Setup Gamess job" ] }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "*** Init pyGamess job.\n", "Default Gamess input card set (use self.params to modify options dictionary, self.setGamess() to test):\n", "\n", " $contrl scftyp=rhf runtyp=energy $end\n", " $basis gbasis=sto ngauss=3 $end\n", " $system mwords=30 $end\n", " $DATA\n", "None\n", "C1\n", "O 8.0 -1.2375000000 0.0000000000 0.0000000000 \n", "C 6.0 0.0000000000 0.0000000000 0.0000000000 \n", "O 8.0 1.2375000000 0.0000000000 0.0000000000 \n", " $END\n", "\n", "*** Found Gamess executable: /opt/gamess/gamess.00.x\n" ] } ], "source": [ "# Init the pyGamess job.\n", "# This minimally needs a gamess_path set, which defaults to '/opt/gamess'\n", "testDL.initGamess() # Using defaults" ] }, { "cell_type": "code", "execution_count": 4, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "INFO:pygamess.gamess:Executeing py_rungms with command /opt/gamess/ddikick.x /opt/gamess/gamess.00.x fdpotu -ddi 1 1 jake -scr /tmp/tmpn3cbn17h > /tmp/tmpn3cbn17h/fdpotu.out\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "*** ddikick exit status OK: ddikick.x: exited gracefully.\n", "*** Gamess run completed OK.\n", "E = -185.05856527930001\n" ] } ], "source": [ "# Run quick energy job to test all working OK\n", "testDL.runGamess()" ] }, { "cell_type": "code", "execution_count": 5, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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IndSpeciesAtomic Num.xyz
00O8-1.23750.00.0
11C60.00000.00.0
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" ], "text/plain": [ " Ind Species Atomic Num. x y z\n", "0 0 O 8 -1.2375 0.0 0.0\n", "1 1 C 6 0.0000 0.0 0.0\n", "2 2 O 8 1.2375 0.0 0.0" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "testDL.printTable()" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Symmetry & frame transformations\n", "\n", "\n", "### Reference frame orientation\n", "\n", "To use symmetry in the Gamess calculations, the system must be oriented such that the Z-axis is the highest symmetry axis. In tests both PubChem and RDkit seem to use the X-axis as the symmetry axis, so the frame needs to be rotated in general.\n", "\n", "From the [Gamess manual](https://www.msg.chem.iastate.edu/gamess/GAMESS_Manual/docs-input.txt):\n", "\n", "```\n", " The 'master frame' is just a standard orientation for\n", "the molecule. By default, the 'master frame' assumes that\n", " 1. z is the principal rotation axis (if any),\n", " 2. x is a perpendicular two-fold axis (if any),\n", " 3. xz is the sigma-v plane (if any), and\n", " 4. xy is the sigma-h plane (if any).\n", "Use the lowest number rule that applies to your molecule.\n", "\n", " Some examples of these rules:\n", "Ammonia (C3v): the unique H lies in the XZ plane (R1,R3).\n", "Ethane (D3d): the unique H lies in the YZ plane (R1,R2).\n", "Methane (Td): the H lies in the XYZ direction (R2). Since\n", " there is more than one 3-fold, R1 does not apply.\n", "HP=O (Cs): the mirror plane is the XY plane (R4).\n", "\n", "In general, it is a poor idea to try to reorient the\n", "molecule. Certain sections of the program, such as the\n", "orbital symmetry assignment, do not know how to deal with\n", "cases where the 'master frame' has been changed.\n", "\n", "Linear molecules (C4v or D4h) must lie along the z axis,\n", "so do not try to reorient linear molecules.\n", "```\n", "\n", "This is set with `self.rotateFrame()`, which can set arbitrary rotations, but defaults to X > Z axis transformation. This uses the RDkit canoicalise and transformation functions, with rotation matrices, as per [Github user iwatobipen's example notebook](https://nbviewer.jupyter.org/github/iwatobipen/playground/blob/master/rotation_mol.ipynb). (Thanks to [iwatobipen](https://github.com/iwatobipen) and the [RDkit list](https://sourceforge.net/p/rdkit/mailman/message/36598250/).)" ] }, { "cell_type": "code", "execution_count": 6, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "*** Updating coords (Pandas version).\n", "*** Set frame rotations, new coord table:\n" ] }, { "data": { "text/html": [ "
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IndSpeciesAtomic Num.xyz
00O80.00.01.2375
11C60.00.00.0000
22O80.00.0-1.2375
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" ], "text/plain": [ " Ind Species Atomic Num. x y z\n", "0 0 O 8 0.0 0.0 1.2375\n", "1 1 C 6 0.0 0.0 0.0000\n", "2 2 O 8 0.0 0.0 -1.2375" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "# Rotate the frame - default should align to Z-axis\n", "testDL.rotateFrame()" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Set symmetry (point group)\n", "\n", "Symmetry groups supported (from the [Gamess manual](https://www.msg.chem.iastate.edu/gamess/GAMESS_Manual/docs-input.txt)):\n", "\n", "```\n", "GROUP is the Schoenflies symbol of the symmetry group,\n", "you may choose from\n", " C1, Cs, Ci, Cn, S2n, Cnh, Cnv, Dn, Dnh, Dnd,\n", " T, Th, Td, O, Oh.\n", "\n", "NAXIS is the order of the highest rotation axis, and\n", "must be given when the name of the group contains an N.\n", "For example, \"Cnv 2\" is C2v. \"S2n 3\" means S6. Use of\n", "NAXIS up to 8 is supported in each axial groups.\n", "\n", "For linear molecules, choose either Cnv or Dnh, and enter\n", "NAXIS as 4. Enter atoms as Dnh with NAXIS=2. If the\n", "electronic state of either is degenerate, check the note\n", "about the effect of symmetry in the electronic state\n", "in the SCF section of REFS.DOC.\n", "```" ] }, { "cell_type": "code", "execution_count": 7, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Set sym = DNH 8\n", "\n", "*** Gamess input card:\n", " $contrl scftyp=rhf runtyp=energy $end\n", " $basis gbasis=sto ngauss=3 $end\n", " $system mwords=30 $end\n", " $DATA\n", "CO2 sym testing\n", "DNH 8\n", "\n", "O 8.0 0.0000000000 0.0000000000 1.2375000000 \n", "C 6.0 0.0000000000 0.0000000000 0.0000000000 \n", "O 8.0 0.0000000000 0.0000000000 -1.2375000000 \n", " $END\n", "\n" ] } ], "source": [ "# Set Gamess input with symmetry\n", "testDL.setGamess(note='CO2 sym testing', sym='DNH 8')" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Finally, **symmetrized jobs require only the symmetry unique atoms to be given on the input card.** This is currently accomplished here rather crudely, via a list of atom indices (rows) to the input builder. Note that an incorrect setting here will potentially result in a Gamess run with a wildly incorrect molecular geometry, potentially including additional atoms, depending on the symmetry group applied.\n", "\n", "For example..." ] }, { "cell_type": "code", "execution_count": 8, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Set sym = DNH 8\n", "Set atomList = [0, 1]\n", "\n", "*** Gamess input card:\n", " $contrl scftyp=rhf runtyp=energy $end\n", " $basis gbasis=sto ngauss=3 $end\n", " $system mwords=30 $end\n", " $DATA\n", "CO2 sym testing\n", "DNH 8\n", "\n", "O 8.0 0.0000000000 0.0000000000 1.2375000000 \n", "C 6.0 0.0000000000 0.0000000000 0.0000000000 \n", " $END\n", "\n" ] } ], "source": [ "testDL.setGamess(note='CO2 sym testing', sym='DNH 8', atomList = [0,1])" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Where `self.params['extra']['atomList']` gives the sub-selection on which atoms are listed on the input card for symmetrized jobs (TODO: make this better/automated!)." ] }, { "cell_type": "code", "execution_count": 9, "metadata": {}, "outputs": [ { "data": { "text/plain": [ "{'job': 'CO2 sym testing', 'sym': 'DNH 8', 'atomList': [0, 1]}" ] }, "execution_count": 9, "metadata": {}, "output_type": "execute_result" } ], "source": [ "testDL.params['extra']" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Run single-point symmetrized calculation\n", "\n", "Once the point group and atom list are set, `self.runGamess` will result in a symmetrized calculation run..." ] }, { "cell_type": "code", "execution_count": 10, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "INFO:pygamess.gamess:Executeing py_rungms with command /opt/gamess/ddikick.x /opt/gamess/gamess.00.x eijdcf -ddi 1 1 jake -scr /tmp/tmpn3cbn17h > /tmp/tmpn3cbn17h/eijdcf.out\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "*** ddikick exit status OK: ddikick.x: exited gracefully.\n", "*** Gamess run completed OK.\n", "E = -185.05856527700001\n", "*** Gamess output file moved to /tmp/testCO2.out\n" ] } ], "source": [ "# Run symmetrized calc\n", "testDL.runGamess(fileOut = '/tmp/testCO2.out')" ] }, { "cell_type": "code", "execution_count": 11, "metadata": { "tags": [] }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "*** Contents from file /tmp/testCO2.out.\n", "\n", " Distributed Data Interface kickoff program.\n", " Initiating 1 compute processes on 1 nodes to run the following command:\n", " /opt/gamess/gamess.00.x eijdcf \n", "\n", " ******************************************************\n", " * GAMESS VERSION = 30 SEP 2018 (R3) *\n", " * FROM IOWA STATE UNIVERSITY *\n", " * M.W.SCHMIDT, K.K.BALDRIDGE, J.A.BOATZ, S.T.ELBERT, *\n", " * M.S.GORDON, J.H.JENSEN, S.KOSEKI, N.MATSUNAGA, *\n", " * K.A.NGUYEN, S.J.SU, T.L.WINDUS, *\n", " * TOGETHER WITH M.DUPUIS, J.A.MONTGOMERY *\n", " * J.COMPUT.CHEM. 14, 1347-1363(1993) *\n", " **************** 64 BIT LINUX VERSION ****************\n", "\n", " SINCE 1993, STUDENTS AND POSTDOCS WORKING AT IOWA STATE UNIVERSITY\n", " AND ALSO IN THEIR VARIOUS JOBS AFTER LEAVING ISU HAVE MADE IMPORTANT\n", " CONTRIBUTIONS TO THE CODE:\n", " IVANA ADAMOVIC, CHRISTINE AIKENS, YURI ALEXEEV, POOJA ARORA,\n", " ANDREY ASADCHEV, ROB BELL, PRADIPTA BANDYOPADHYAY, JONATHAN BENTZ,\n", " BRETT BODE, KURT BRORSEN, CALEB CARLIN, GALINA CHABAN, WEI CHEN,\n", " CHEOL HO CHOI, PAUL DAY, ALBERT DEFUSCO, NUWAN DESILVA, TIM DUDLEY,\n", " DMITRI FEDOROV, ALEX FINDLATER, GRAHAM FLETCHER, MARK FREITAG,\n", " KURT GLAESEMANN, ANASTASIA GUNINA,\n", " DAN KEMP, GRANT MERRILL, NORIYUKI MINEZAWA, JONATHAN MULLIN,\n", " TAKESHI NAGATA, SEAN NEDD, HEATHER NETZLOFF, BOSILJKA NJEGIC, RYAN OLSON,\n", " MIKE PAK, BUU PHAM,\n", " SPENCER PRUITT, LUKE ROSKOP, JIM SHOEMAKER, LYUDMILA SLIPCHENKO,\n", " TONY SMITH, SAROM SOK LEANG, JIE SONG, TETSUYA TAKETSUGU, SIMON WEBB,\n", " PENG XU, SOOHAENG YOO, FEDERICO ZAHARIEV\n", "\n", " ADDITIONAL CODE HAS BEEN PROVIDED BY COLLABORATORS IN OTHER GROUPS:\n", " IOWA STATE UNIVERSITY:\n", " JOE IVANIC, AARON WEST, LAIMUTIS BYTAUTAS, KLAUS RUEDENBERG\n", " UNIVERSITY OF TOKYO: KIMIHIKO HIRAO, TAKAHITO NAKAJIMA,\n", " TAKAO TSUNEDA, MUNEAKI KAMIYA, SUSUMU YANAGISAWA,\n", " KIYOSHI YAGI, MAHITO CHIBA, SEIKEN TOKURA, NAOAKI KAWAKAMI\n", " UNIVERSITY OF AARHUS: FRANK JENSEN\n", " UNIVERSITY OF IOWA: VISVALDAS KAIRYS, HUI LI\n", " NATIONAL INST. OF STANDARDS AND TECHNOLOGY: WALT STEVENS, DAVID GARMER\n", " UNIVERSITY OF PISA: BENEDETTA MENNUCCI, JACOPO TOMASI\n", " UNIVERSITY OF MEMPHIS: HENRY KURTZ, PRAKASHAN KORAMBATH\n", " UNIVERSITY OF ALBERTA: TOBY ZENG, MARIUSZ KLOBUKOWSKI\n", " UNIVERSITY OF NEW ENGLAND: MARK SPACKMAN\n", " MIE UNIVERSITY: HIROAKI UMEDA\n", " NAT. INST. OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY: KAZUO KITAURA\n", " MICHIGAN STATE UNIVERSITY:\n", " KAROL KOWALSKI, MARTA WLOCH, JEFFREY GOUR, JESSE LUTZ,\n", " WEI LI, JUN SHEN, J. EMILIANO DEUSTUA, PIOTR PIECUCH\n", " UNIVERSITY OF MINNESOTA:\n", " YINAN SHU\n", " UNIVERSITY OF SILESIA: MONIKA MUSIAL, STANISLAW KUCHARSKI\n", " FACULTES UNIVERSITAIRES NOTRE-DAME DE LA PAIX:\n", " OLIVIER QUINET, BENOIT CHAMPAGNE\n", " UNIVERSITY OF CALIFORNIA - SANTA BARBARA: BERNARD KIRTMAN\n", " INSTITUTE FOR MOLECULAR SCIENCE:\n", " KAZUYA ISHIMURA, MICHIO KATOUDA, AND SHIGERU NAGASE\n", " UNIVERSITY OF NOTRE DAME: ANNA POMOGAEVA, DAN CHIPMAN\n", " KYUSHU UNIVERSITY:\n", " HARUYUKI NAKANO,\n", " FENG LONG GU, JACEK KORCHOWIEC, MARCIN MAKOWSKI, AND YURIKO AOKI,\n", " HIROTOSHI MORI AND EISAKU MIYOSHI\n", " PENNSYLVANIA STATE UNIVERSITY:\n", " TZVETELIN IORDANOV, CHET SWALINA, JONATHAN SKONE,\n", " SHARON HAMMES-SCHIFFER\n", " WASEDA UNIVERSITY:\n", " MASATO KOBAYASHI, TOMOKO AKAMA, TSUGUKI TOUMA,\n", " TAKESHI YOSHIKAWA, YASUHIRO IKABATA, JUNJI SEINO,\n", " YUYA NAKAJIMA, HIROMI NAKAI\n", " NANJING UNIVERSITY: SHUHUA LI\n", " UNIVERSITY OF NEBRASKA:\n", " PEIFENG SU, DEJUN SI, NANDUN THELLAMUREGE, YALI WANG, HUI LI\n", " UNIVERSITY OF ZURICH: ROBERTO PEVERATI, KIM BALDRIDGE\n", " N. COPERNICUS UNIVERSITY AND JACKSON STATE UNIVERSITY:\n", " MARIA BARYSZ\n", " UNIVERSITY OF COPENHAGEN: Jimmy Kromann, CASPER STEINMANN\n", " TOKYO INSTITUTE OF TECHNOLOGY: HIROYA NAKATA\n", " NAGOYA UNIVERSITY: YOSHIO NISHIMOTO, STEPHAN IRLE\n", " MOSCOW STATE UNIVERSITY: VLADIMIR MIRONOV\n", "\n", " EXECUTION OF GAMESS BEGUN Tue Jan 23 18:11:32 2024\n", "\n", " ECHO OF THE FIRST FEW INPUT CARDS -\n", " INPUT CARD> $contrl scftyp=rhf runtyp=energy $end \n", " INPUT CARD> $basis gbasis=sto ngauss=3 $end \n", " INPUT CARD> $system mwords=30 $end \n", " INPUT CARD> $DATA \n", " INPUT CARD>CO2 sym testing \n", " INPUT CARD>DNH 8 \n", " INPUT CARD> \n", " INPUT CARD>O 8.0 0.0000000000 0.0000000000 1.2375000000 \n", " INPUT CARD>C 6.0 0.0000000000 0.0000000000 0.0000000000 \n", " INPUT CARD> $END \n", " 30000000 WORDS OF MEMORY AVAILABLE\n", "\n", " BASIS OPTIONS\n", " -------------\n", " GBASIS=STO IGAUSS= 3 POLAR=NONE \n", " NDFUNC= 0 NFFUNC= 0 DIFFSP= F\n", " NPFUNC= 0 DIFFS= F BASNAM= \n", "\n", "\n", " RUN TITLE\n", " ---------\n", " CO2 sym testing \n", "\n", " THE POINT GROUP OF THE MOLECULE IS DNH \n", " THE ORDER OF THE PRINCIPAL AXIS IS 8\n", "\n", " ATOM ATOMIC COORDINATES (BOHR)\n", " CHARGE X Y Z\n", " O 8.0 0.0000000000 0.0000000000 -2.3385359098\n", " O 8.0 0.0000000000 0.0000000000 2.3385359098\n", " C 6.0 0.0000000000 0.0000000000 0.0000000000\n", "\n", " INTERNUCLEAR DISTANCES (ANGS.)\n", " ------------------------------\n", "\n", " 1 O 2 O 3 C \n", "\n", " 1 O 0.0000000 2.4750000 * 1.2375000 *\n", " 2 O 2.4750000 * 0.0000000 1.2375000 *\n", " 3 C 1.2375000 * 1.2375000 * 0.0000000 \n", "\n", " * ... LESS THAN 3.000\n", "\n", "\n", " ATOMIC BASIS SET\n", " ----------------\n", " THE CONTRACTED PRIMITIVE FUNCTIONS HAVE BEEN UNNORMALIZED\n", " THE CONTRACTED BASIS FUNCTIONS ARE NOW NORMALIZED TO UNITY\n", "\n", " SHELL TYPE PRIMITIVE EXPONENT CONTRACTION COEFFICIENT(S)\n", "\n", " O \n", "\n", " 3 S 1 130.7093214 0.154328967295\n", " 3 S 2 23.8088661 0.535328142282\n", " 3 S 3 6.4436083 0.444634542185\n", "\n", " 4 L 4 5.0331513 -0.099967229187 0.155916274999\n", " 4 L 5 1.1695961 0.399512826089 0.607683718598\n", " 4 L 6 0.3803890 0.700115468880 0.391957393099\n", "\n", " C \n", "\n", " 5 S 7 71.6168373 0.154328967295\n", " 5 S 8 13.0450963 0.535328142282\n", " 5 S 9 3.5305122 0.444634542185\n", "\n", " 6 L 10 2.9412494 -0.099967229187 0.155916274999\n", " 6 L 11 0.6834831 0.399512826089 0.607683718598\n", " 6 L 12 0.2222899 0.700115468880 0.391957393099\n", "\n", " TOTAL NUMBER OF BASIS SET SHELLS = 6\n", " NUMBER OF CARTESIAN GAUSSIAN BASIS FUNCTIONS = 15\n", " NUMBER OF ELECTRONS = 22\n", " CHARGE OF MOLECULE = 0\n", " SPIN MULTIPLICITY = 1\n", " NUMBER OF OCCUPIED ORBITALS (ALPHA) = 11\n", " NUMBER OF OCCUPIED ORBITALS (BETA ) = 11\n", " TOTAL NUMBER OF ATOMS = 3\n", " THE NUCLEAR REPULSION ENERGY IS 54.7351013355\n", "\n", " THIS MOLECULE IS RECOGNIZED AS BEING LINEAR,\n", " ORBITAL LZ DEGENERACY TOLERANCE ETOLLZ= 1.00E-06\n", "\n", " $CONTRL OPTIONS\n", " ---------------\n", " SCFTYP=RHF RUNTYP=ENERGY EXETYP=RUN \n", " MPLEVL= 0 CITYP =NONE CCTYP =NONE VBTYP =NONE \n", " DFTTYP=NONE TDDFT =NONE \n", " MULT = 1 ICHARG= 0 NZVAR = 0 COORD =UNIQUE \n", " PP =NONE RELWFN=NONE LOCAL =NONE NUMGRD= F\n", " ISPHER= -1 NOSYM = 0 MAXIT = 30 UNITS =ANGS \n", " PLTORB= F MOLPLT= F AIMPAC= F FRIEND= \n", " NPRINT= 7 IREST = 0 GEOM =INPUT \n", " NORMF = 0 NORMP = 0 ITOL = 20 ICUT = 9\n", " INTTYP=BEST GRDTYP=BEST QMTTOL= 1.0E-06\n", "\n", " $SYSTEM OPTIONS\n", " ---------------\n", " REPLICATED MEMORY= 30000000 WORDS (ON EVERY NODE).\n", " DISTRIBUTED MEMDDI= 0 MILLION WORDS IN AGGREGATE,\n", " MEMDDI DISTRIBUTED OVER 1 PROCESSORS IS 0 WORDS/PROCESSOR.\n", " TOTAL MEMORY REQUESTED ON EACH PROCESSOR= 30000000 WORDS.\n", " TIMLIM= 525600.00 MINUTES, OR 365.0 DAYS.\n", " PARALL= F BALTYP= DLB KDIAG= 0 COREFL= F\n", " MXSEQ2= 300 MXSEQ3= 150 mem10= 0\n", "\n", " ----------------\n", " PROPERTIES INPUT\n", " ----------------\n", "\n", " MOMENTS FIELD POTENTIAL DENSITY\n", " IEMOM = 1 IEFLD = 0 IEPOT = 0 IEDEN = 0\n", " WHERE =COMASS WHERE =NUCLEI WHERE =NUCLEI WHERE =NUCLEI \n", " OUTPUT=BOTH OUTPUT=BOTH OUTPUT=BOTH OUTPUT=BOTH \n", " IEMINT= 0 IEFINT= 0 IEDINT= 0\n", " MORB = 0\n", " EXTRAPOLATION IN EFFECT\n", " DIIS IN EFFECT\n", " ORBITAL PRINTING OPTION: NPREO= 1 15 2 1\n", "\n", " -------------------------------\n", " INTEGRAL TRANSFORMATION OPTIONS\n", " -------------------------------\n", " NWORD = 0\n", " CUTOFF = 1.0E-09 MPTRAN = 0\n", " DIRTRF = F AOINTS =DUP \n", "\n", " ----------------------\n", " INTEGRAL INPUT OPTIONS\n", " ----------------------\n", " NOPK = 1 NORDER= 0 SCHWRZ= F\n", "\n", " ------------------------------------------\n", " THE POINT GROUP IS DNH, NAXIS= 8, ORDER=32\n", " ------------------------------------------\n", "\n", " DIMENSIONS OF THE SYMMETRY SUBSPACES ARE\n", " A1G = 5 A1U = 0 B1G = 0 B1U = 0 A2G = 0\n", " A2U = 4 B2G = 0 B2U = 0 E1G = 1 E1U = 2\n", " E2U = 0 E2G = 0 E3G = 0 E3U = 0\n", "\n", " ..... DONE SETTING UP THE RUN .....\n", " STEP CPU TIME = 0.00 TOTAL CPU TIME = 0.0 ( 0.0 MIN)\n", " TOTAL WALL CLOCK TIME= 0.0 SECONDS, CPU UTILIZATION IS 0.00%\n", "\n", " ********************\n", " 1 ELECTRON INTEGRALS\n", " ********************\n", " ...... END OF ONE-ELECTRON INTEGRALS ......\n", " STEP CPU TIME = 0.00 TOTAL CPU TIME = 0.0 ( 0.0 MIN)\n", " TOTAL WALL CLOCK TIME= 0.0 SECONDS, CPU UTILIZATION IS 0.00%\n", "\n", " -------------\n", " GUESS OPTIONS\n", " -------------\n", " GUESS =HUCKEL NORB = 0 NORDER= 0\n", " MIX = F PRTMO = F PUNMO = F\n", " TOLZ = 1.0E-08 TOLE = 1.0E-05\n", " SYMDEN= F PURIFY= F\n", "\n", " INITIAL GUESS ORBITALS GENERATED BY HUCKEL ROUTINE.\n", " HUCKEL GUESS REQUIRES 4764 WORDS.\n", "\n", " SYMMETRIES FOR INITIAL GUESS ORBITALS FOLLOW. BOTH SET(S).\n", " 11 ORBITALS ARE OCCUPIED ( 3 CORE ORBITALS).\n", " 4=A1G 5=A2U 6=E1U 7=E1U 8=A1G 9=A2U 10=E1G \n", " 11=E1G 12=E1U 13=E1U 14=A1G 15=A2U \n", " ...... END OF INITIAL ORBITAL SELECTION ......\n", " STEP CPU TIME = 0.00 TOTAL CPU TIME = 0.0 ( 0.0 MIN)\n", " TOTAL WALL CLOCK TIME= 0.0 SECONDS, CPU UTILIZATION IS 0.00%\n", "\n", " ----------------------\n", " AO INTEGRAL TECHNOLOGY\n", " ----------------------\n", " S,P,L SHELL ROTATED AXIS INTEGRALS, REPROGRAMMED BY\n", " KAZUYA ISHIMURA (IMS) AND JOSE SIERRA (SYNSTAR).\n", " S,P,D,L SHELL ROTATED AXIS INTEGRALS PROGRAMMED BY\n", " KAZUYA ISHIMURA (INSTITUTE FOR MOLECULAR SCIENCE).\n", " S,P,D,F,G SHELL TO TOTAL QUARTET ANGULAR MOMENTUM SUM 5,\n", " ERIC PROGRAM BY GRAHAM FLETCHER (ELORET AND NASA ADVANCED\n", " SUPERCOMPUTING DIVISION, AMES RESEARCH CENTER).\n", " S,P,D,F,G,L SHELL GENERAL RYS QUADRATURE PROGRAMMED BY\n", " MICHEL DUPUIS (PACIFIC NORTHWEST NATIONAL LABORATORY).\n", "\n", " --------------------\n", " 2 ELECTRON INTEGRALS\n", " --------------------\n", "\n", " THE -PK- OPTION IS OFF, THE INTEGRALS ARE NOT IN SUPERMATRIX FORM.\n", " STORING 15000 INTEGRALS/RECORD ON DISK, USING 12 BYTES/INTEGRAL.\n", " TWO ELECTRON INTEGRAL EVALUATION REQUIRES 89377 WORDS OF MEMORY.\n", " II,JST,KST,LST = 1 1 1 1 NREC = 1 INTLOC = 1\n", " II,JST,KST,LST = 2 1 1 1 NREC = 1 INTLOC = 1\n", " II,JST,KST,LST = 3 1 1 1 NREC = 1 INTLOC = 1\n", " II,JST,KST,LST = 4 1 1 1 NREC = 1 INTLOC = 3\n", " II,JST,KST,LST = 5 1 1 1 NREC = 1 INTLOC = 284\n", " II,JST,KST,LST = 6 1 1 1 NREC = 1 INTLOC = 415\n", " TOTAL NUMBER OF NONZERO TWO-ELECTRON INTEGRALS = 1293\n", " 1 INTEGRAL RECORDS WERE STORED ON DISK FILE 8.\n", " ...... END OF TWO-ELECTRON INTEGRALS .....\n", " STEP CPU TIME = 0.01 TOTAL CPU TIME = 0.0 ( 0.0 MIN)\n", " TOTAL WALL CLOCK TIME= 0.0 SECONDS, CPU UTILIZATION IS 50.00%\n", "\n", " --------------------------\n", " RHF SCF CALCULATION\n", " --------------------------\n", "\n", " NUCLEAR ENERGY = 54.7351013355\n", " MAXIT = 30 NPUNCH= 2\n", " EXTRAP=T DAMP=F SHIFT=F RSTRCT=F DIIS=T DEM=F SOSCF=F\n", " DENSITY MATRIX CONV= 1.00E-05\n", " MEMORY REQUIRED FOR RHF ITERS= 32450 WORDS.\n", "\n", " ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR\n", " 1 0 0 -184.7725028435 -184.7725028435 0.517477062 0.807497030\n", " * * * INITIATING DIIS PROCEDURE * * *\n", " 2 1 0 -185.0312007503 -0.2586979068 0.131494822 0.115106962\n", " 3 2 0 -185.0528054004 -0.0216046501 0.079488582 0.073136962\n", " 4 3 0 -185.0574747346 -0.0046693342 0.030216154 0.022996377\n", " 5 4 0 -185.0585051627 -0.0010304280 0.014574288 0.005917499\n", " 6 5 0 -185.0585648484 -0.0000596857 0.000955415 0.000775604\n", " 7 6 0 -185.0585652757 -0.0000004273 0.000050826 0.000037583\n", " 8 7 0 -185.0585652770 -0.0000000013 0.000002912 0.000003075\n", " 9 8 0 -185.0585652770 -0.0000000000 0.000000249 0.000000267\n", "\n", " -----------------\n", " DENSITY CONVERGED\n", " -----------------\n", " TIME TO FORM FOCK OPERATORS= 0.0 SECONDS ( 0.0 SEC/ITER)\n", " TIME TO SOLVE SCF EQUATIONS= 0.0 SECONDS ( 0.0 SEC/ITER)\n", "\n", " FINAL RHF ENERGY IS -185.0585652770 AFTER 9 ITERATIONS\n", "\n", " LZ VALUE ANALYSIS FOR THE MOS\n", " ----------------------------------------\n", " MO 1 ( 1) HAS LZ(WEIGHT)= 0.00(100.0%) \n", " MO 2 ( 2) HAS LZ(WEIGHT)= 0.00(100.0%) \n", " MO 3 ( 3) HAS LZ(WEIGHT)= 0.00(100.0%) \n", " MO 4 ( 4) HAS LZ(WEIGHT)= 0.00(100.0%) \n", " MO 5 ( 5) HAS LZ(WEIGHT)= 0.00(100.0%) \n", " MO 6 ( 6) HAS LZ(WEIGHT)= 0.00(100.0%) \n", " MO 7 ( 7) HAS LZ(WEIGHT)=-1.00( 50.0%) 1.00( 50.0%) \n", " MO 8 ( 7) HAS LZ(WEIGHT)=-1.00( 50.0%) 1.00( 50.0%) \n", " MO 9 ( 8) HAS LZ(WEIGHT)= 0.00(100.0%) \n", " MO 10 ( 9) HAS LZ(WEIGHT)=-1.00( 50.0%) 1.00( 50.0%) \n", " MO 11 ( 9) HAS LZ(WEIGHT)=-1.00( 50.0%) 1.00( 50.0%) \n", " MO 12 ( 10) HAS LZ(WEIGHT)=-1.00( 50.0%) 1.00( 50.0%) \n", " MO 13 ( 10) HAS LZ(WEIGHT)=-1.00( 50.0%) 1.00( 50.0%) \n", " MO 14 ( 11) HAS LZ(WEIGHT)= 0.00(100.0%) \n", " MO 15 ( 12) HAS LZ(WEIGHT)= 0.00(100.0%) \n", "\n", " ------------\n", " EIGENVECTORS\n", " ------------\n", "\n", " 1 2 3 4 5\n", " -20.3471 -20.3468 -11.2495 -1.3956 -1.3354\n", " A2U A1G A1G A1G A2U \n", " 1 O 1 S 0.703019 0.703154 0.000059 -0.150026 -0.162960\n", " 2 O 1 S 0.019106 0.017301 -0.004448 0.530965 0.564074\n", " 3 O 1 X -0.000000 0.000000 0.000000 -0.000000 -0.000000\n", " 4 O 1 Y -0.000000 0.000000 0.000000 -0.000000 -0.000000\n", " 5 O 1 Z 0.004548 0.003383 -0.001017 0.126588 0.100899\n", " 6 O 2 S -0.703019 0.703154 0.000059 -0.150026 0.162960\n", " 7 O 2 S -0.019106 0.017301 -0.004448 0.530965 -0.564074\n", " 8 O 2 X -0.000000 0.000000 0.000000 -0.000000 -0.000000\n", " 9 O 2 Y -0.000000 0.000000 0.000000 -0.000000 -0.000000\n", " 10 O 2 Z 0.004548 -0.003383 0.001017 -0.126588 0.100899\n", " 11 C 3 S -0.000000 0.000625 0.993406 -0.153424 -0.000000\n", " 12 C 3 S -0.000000 -0.008525 0.027131 0.358284 -0.000000\n", " 13 C 3 X -0.000000 0.000000 0.000000 -0.000000 -0.000000\n", " 14 C 3 Y -0.000000 0.000000 0.000000 -0.000000 -0.000000\n", " 15 C 3 Z 0.010105 0.000000 0.000000 -0.000000 -0.287020\n", "\n", " 6 7 8 9 10\n", " -0.6822 -0.5885 -0.5885 -0.5679 -0.3776\n", " A1G E1U E1U A2U E1G \n", " 1 O 1 S 0.108265 0.000000 0.000000 0.080062 -0.000000\n", " 2 O 1 S -0.516003 0.000000 0.000000 -0.433314 -0.000000\n", " 3 O 1 X 0.000000 0.489129 0.000000 0.000000 -0.000000\n", " 4 O 1 Y 0.000000 0.000000 0.489129 0.000000 0.708177\n", " 5 O 1 Z 0.384953 0.000000 0.000000 0.490261 -0.000000\n", " 6 O 2 S 0.108265 0.000000 0.000000 -0.080062 -0.000000\n", " 7 O 2 S -0.516003 0.000000 0.000000 0.433314 -0.000000\n", " 8 O 2 X 0.000000 0.489129 0.000000 0.000000 -0.000000\n", " 9 O 2 Y 0.000000 0.000000 0.489129 0.000000 -0.708177\n", " 10 O 2 Z -0.384953 0.000000 0.000000 0.490261 -0.000000\n", " 11 C 3 S -0.171446 0.000000 0.000000 0.000000 -0.000000\n", " 12 C 3 S 0.599730 0.000000 0.000000 0.000000 -0.000000\n", " 13 C 3 X 0.000000 0.551624 0.000000 0.000000 -0.000000\n", " 14 C 3 Y 0.000000 0.000000 0.551624 0.000000 -0.000000\n", " 15 C 3 Z 0.000000 0.000000 0.000000 -0.468743 -0.000000\n", "\n", " 11 12 13 14 15\n", " -0.3776 0.2796 0.2796 0.4889 1.1804\n", " E1G E1U E1U A1G A2U \n", " 1 O 1 S 0.000000 0.000000 0.000000 0.071465 -0.091599\n", " 2 O 1 S 0.000000 0.000000 0.000000 -0.453084 0.721160\n", " 3 O 1 X 0.708177 -0.549924 0.000000 -0.000000 0.000000\n", " 4 O 1 Y 0.000000 0.000000 -0.549924 -0.000000 0.000000\n", " 5 O 1 Z 0.000000 0.000000 0.000000 -0.696967 0.722648\n", " 6 O 2 S 0.000000 0.000000 0.000000 0.071465 0.091599\n", " 7 O 2 S 0.000000 0.000000 0.000000 -0.453084 -0.721160\n", " 8 O 2 X -0.708177 -0.549924 0.000000 -0.000000 0.000000\n", " 9 O 2 Y 0.000000 0.000000 -0.549924 -0.000000 0.000000\n", " 10 O 2 Z 0.000000 0.000000 0.000000 0.696967 0.722648\n", " 11 C 3 S 0.000000 0.000000 0.000000 -0.196289 0.000000\n", " 12 C 3 S 0.000000 0.000000 0.000000 1.181804 0.000000\n", " 13 C 3 X 0.000000 0.884483 0.000000 -0.000000 0.000000\n", " 14 C 3 Y 0.000000 0.000000 0.884483 -0.000000 0.000000\n", " 15 C 3 Z 0.000000 0.000000 0.000000 -0.000000 1.456045\n", " ...... END OF RHF CALCULATION ......\n", " STEP CPU TIME = 0.01 TOTAL CPU TIME = 0.0 ( 0.0 MIN)\n", " TOTAL WALL CLOCK TIME= 0.0 SECONDS, CPU UTILIZATION IS 100.00%\n", "\n", " ----------------------------------------------------------------\n", " PROPERTY VALUES FOR THE RHF SELF-CONSISTENT FIELD WAVEFUNCTION\n", " ----------------------------------------------------------------\n", "\n", " -----------------\n", " ENERGY COMPONENTS\n", " -----------------\n", "\n", " WAVEFUNCTION NORMALIZATION = 1.0000000000\n", "\n", " ONE ELECTRON ENERGY = -363.8739809363\n", " TWO ELECTRON ENERGY = 124.0803143238\n", " NUCLEAR REPULSION ENERGY = 54.7351013355\n", " ------------------\n", " TOTAL ENERGY = -185.0585652770\n", "\n", " ELECTRON-ELECTRON POTENTIAL ENERGY = 124.0803143238\n", " NUCLEUS-ELECTRON POTENTIAL ENERGY = -546.9256846942\n", " NUCLEUS-NUCLEUS POTENTIAL ENERGY = 54.7351013355\n", " ------------------\n", " TOTAL POTENTIAL ENERGY = -368.1102690349\n", " TOTAL KINETIC ENERGY = 183.0517037579\n", " VIRIAL RATIO (V/T) = 2.0109633589\n", "\n", " ...... PI ENERGY ANALYSIS ......\n", "\n", " ENERGY ANALYSIS:\n", " FOCK ENERGY= -115.7133527291\n", " BARE H ENERGY= -363.8739809363\n", " ELECTRONIC ENERGY = -239.7936668327\n", " KINETIC ENERGY= 183.0517037579\n", " N-N REPULSION= 54.7351013355\n", " TOTAL ENERGY= -185.0585654971\n", " SIGMA PART(1+2)= -196.1374004056\n", " (K,V1,2)= 165.8811218167 -446.3069876091 84.2884653868\n", " PI PART(1+2)= -43.6562664271\n", " (K,V1,2)= 17.1705819412 -100.6186970852 39.7918487169\n", " SIGMA SKELETON, ERROR= -141.4022990700 0.0000000000\n", " MIXED PART= 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00\n", " ...... END OF PI ENERGY ANALYSIS ......\n", "\n", " ---------------------------------------\n", " MULLIKEN AND LOWDIN POPULATION ANALYSES\n", " ---------------------------------------\n", "\n", " ATOMIC MULLIKEN POPULATION IN EACH MOLECULAR ORBITAL\n", "\n", " 1 2 3 4 5\n", "\n", " 2.000000 2.000000 2.000000 2.000000 2.000000\n", "\n", " 1 1.000921 1.000466 -0.000469 0.725223 0.765578\n", " 2 1.000921 1.000466 -0.000469 0.725223 0.765578\n", " 3 -0.001842 -0.000933 2.000937 0.549555 0.468844\n", "\n", " 6 7 8 9 10\n", "\n", " 2.000000 2.000000 2.000000 2.000000 2.000000\n", "\n", " 1 0.730724 0.587825 0.587825 0.807032 1.000000\n", " 2 0.730724 0.587825 0.587825 0.807032 1.000000\n", " 3 0.538553 0.824349 0.824349 0.385935 0.000000\n", "\n", " 11\n", "\n", " 2.000000\n", "\n", " 1 1.000000\n", " 2 1.000000\n", " 3 0.000000\n", "\n", " ----- POPULATIONS IN EACH AO -----\n", " MULLIKEN LOWDIN\n", " 1 O 1 S 1.99819 1.99734\n", " 2 O 1 S 1.88000 1.77776\n", " 3 O 1 X 1.58783 1.58436\n", " 4 O 1 Y 1.58783 1.58436\n", " 5 O 1 Z 1.15129 1.21553\n", " 6 O 2 S 1.99819 1.99734\n", " 7 O 2 S 1.88000 1.77776\n", " 8 O 2 X 1.58783 1.58436\n", " 9 O 2 Y 1.58783 1.58436\n", " 10 O 2 Z 1.15129 1.21553\n", " 11 C 3 S 1.99544 1.98817\n", " 12 C 3 S 1.09267 1.09428\n", " 13 C 3 X 0.82435 0.83128\n", " 14 C 3 Y 0.82435 0.83128\n", " 15 C 3 Z 0.85294 0.93628\n", "\n", " ----- MULLIKEN ATOMIC OVERLAP POPULATIONS -----\n", " (OFF-DIAGONAL ELEMENTS NEED TO BE MULTIPLIED BY 2)\n", "\n", " 1 2 3\n", "\n", " 1 7.7899842\n", " 2 -0.0053029 7.7899842\n", " 3 0.4204447 0.4204447 4.7488588\n", "\n", " TOTAL MULLIKEN AND LOWDIN ATOMIC POPULATIONS\n", " ATOM MULL.POP. CHARGE LOW.POP. CHARGE\n", " 1 O 8.205126 -0.205126 8.159355 -0.159355\n", " 2 O 8.205126 -0.205126 8.159355 -0.159355\n", " 3 C 5.589748 0.410252 5.681291 0.318709\n", "\n", " -------------------------------\n", " BOND ORDER AND VALENCE ANALYSIS BOND ORDER THRESHOLD=0.050\n", " -------------------------------\n", "\n", " BOND BOND BOND\n", " ATOM PAIR DIST ORDER ATOM PAIR DIST ORDER ATOM PAIR DIST ORDER\n", " 1 2 2.475 0.367 1 3 1.238 1.954 2 3 1.238 1.954\n", "\n", " TOTAL BONDED FREE\n", " ATOM VALENCE VALENCE VALENCE\n", " 1 O 2.322 2.322 0.000\n", " 2 O 2.322 2.322 0.000\n", " 3 C 3.909 3.909 0.000\n", "\n", " ---------------------\n", " ELECTROSTATIC MOMENTS\n", " ---------------------\n", "\n", " POINT 1 X Y Z (BOHR) CHARGE\n", " 0.000000 0.000000 0.000000 -0.00 (A.U.)\n", " DX DY DZ /D/ (DEBYE)\n", " 0.000000 0.000000 0.000000 0.000000\n", " ...... END OF PROPERTY EVALUATION ......\n", " STEP CPU TIME = 0.00 TOTAL CPU TIME = 0.0 ( 0.0 MIN)\n", " TOTAL WALL CLOCK TIME= 0.0 SECONDS, CPU UTILIZATION IS 66.67%\n", " 580000 WORDS OF DYNAMIC MEMORY USED\n", " EXECUTION OF GAMESS TERMINATED NORMALLY Tue Jan 23 18:11:32 2024\n", " DDI: 263640 bytes (0.3 MB / 0 MWords) used by master data server.\n", "\n", " ----------------------------------------\n", " CPU timing information for all processes\n", " ========================================\n", " 0: 0.15 + 0.12 = 0.27\n", " ----------------------------------------\n", " ddikick.x: exited gracefully.\n", "\n" ] } ], "source": [ "# View full output card for details\n", "testDL.printGamess()" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Geometry optimization (symmetrized)\n", "\n", "Running an optimization should now just also work, but there are some potential gotchas in this case.\n", "\n", "1. the output atom ordering may change in the symmetrized case, so further use of the results may require changes to `self.params['extra']['atomList']`.\n", "\n", "2. It is also of note that Gamess requirements are not enforced automatically here, so some massaging of the input settings may be required - for example the ordering of the atoms on the input card." ] }, { "cell_type": "code", "execution_count": 12, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "INFO:pygamess.gamess:Executeing py_rungms with command /opt/gamess/ddikick.x /opt/gamess/gamess.00.x svzrwn -ddi 1 1 jake -scr /tmp/tmpn3cbn17h > /tmp/tmpn3cbn17h/svzrwn.out\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "*** Warning: found errors in Gamess output, type: Warnings\n", "*** Check self.mol.GetProp('Warnings') for details.\n", "*** Warning: found errors in Gamess output, type: ddikick\n", "*** Check self.mol.GetProp('ddikick') for details.\n", "*** Gamess run completed with warnings.\n", "E = -185.05856527700001\n", "\n", "*** Gamess optimization run - reseting self.mol with updated coords.\n", "Note that atom ordering may change depending on Gamess output.\n", "Found 1 geometry iterations in Gamess output.\n", "Updating with new coords, output set to self.mol\n" ] }, { "data": { "text/html": [ "
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IndSpeciesAtomic Num.xyz
00O80.00.0-1.2375
11O80.00.01.2375
22C60.00.00.0000
\n", "
" ], "text/plain": [ " Ind Species Atomic Num. x y z\n", "0 0 O 8 0.0 0.0 -1.2375\n", "1 1 O 8 0.0 0.0 1.2375\n", "2 2 C 6 0.0 0.0 0.0000" ] }, "metadata": {}, "output_type": "display_data" }, { "name": "stdout", "output_type": "stream", "text": [ "*** WARNINGS FOUND IN GAMESS OUTPUT, values for E and molecular coords may reflect input molecule if run did not complete.\n", "Set geom opt coord outputs to self.geomOpt.\n", "*** Gamess output file moved to /tmp/test_CO2_geomOpt.out\n" ] } ], "source": [ "# Test geom opt with symmetrization, no changes from previous input\n", "testDL.runGamess(runType='optimize',fileOut = '/tmp/test_CO2_geomOpt.out')" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "In this case note that warnings are generated, indicating problems with the Gamess run - possibly due to the input geometry, or other optimization settings.\n", "\n", "Note, also, the line \"Found 1 geometry iterations in Gamess output\", indicating that no geometry optimization iterations were completed (i.e. only the input geometry is present), and updated geometry table. The geometry has now been updated from the Gamess output file, which may have a different ordering to the inputs for the symmetrized case, as noted above, even if the run failed." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### Troubleshooting Gamess optimization runs" ] }, { "cell_type": "code", "execution_count": 13, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " WARNING: EIGENVECTOR ROUTINE -EINVIT- DID NOT CONVERGE FOR VECTOR 4\n", " WARNING: EIGENVECTOR ROUTINE -EINVIT- DID NOT CONVERGE FOR VECTOR 7\n", " ddikick.x: application process 0 quit unexpectedly.\n", " ddikick.x: Sending kill signal to DDI processes.\n", " ddikick.x: Execution terminated due to error(s).\n" ] } ], "source": [ "# As noted in the error messages above, the specific Gamess error messages can be investigated\n", "print(testDL.mol.GetProp('Warnings'))\n", "print(testDL.mol.GetProp('ddikick'))" ] }, { "cell_type": "code", "execution_count": 14, "metadata": {}, "outputs": [ { "data": { "text/plain": [ "{'Warnings': {'re': re.compile(r'.*WARNING: .*', re.UNICODE),\n", " 'matches': ' WARNING: EIGENVECTOR ROUTINE -EINVIT- DID NOT CONVERGE FOR VECTOR 4\\n WARNING: EIGENVECTOR ROUTINE -EINVIT- DID NOT CONVERGE FOR VECTOR 7',\n", " 'warnFlag': 1},\n", " 'ddikick': {'re': re.compile(r'.*ddikick.x: .*', re.UNICODE),\n", " 'matches': ' ddikick.x: application process 0 quit unexpectedly.\\n ddikick.x: Sending kill signal to DDI processes.\\n ddikick.x: Execution terminated due to error(s).',\n", " 'warnFlag': 1}}" ] }, "execution_count": 14, "metadata": {}, "output_type": "execute_result" } ], "source": [ "# These are also set as a full dict of outputs\n", "testDL.mol.errorDict" ] }, { "cell_type": "code", "execution_count": 15, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "*** Contents from file /tmp/test_CO2_geomOpt.out.\n", "Showing 20 tail lines.\n", " MAXIMUM GRADIENT = 0.0992719 RMS GRADIENT = 0.0467972\n", "\n", " NSERCH: 0 E= -185.0585652770 GRAD. MAX= 0.0992719 R.M.S.= 0.0467972\n", "\n", " FORCE CONSTANT MATRIX NOT UPDATED --- TAKING FIRST STEP\n", " WARNING: EIGENVECTOR ROUTINE -EINVIT- DID NOT CONVERGE FOR VECTOR 4\n", " NORM = 9.12E-04 PERFORMANCE INDEX = 5.48E+01\n", " A HALT WILL OCCUR IF THE PERF.IND. EXCEEDS 100.0\n", " WARNING: EIGENVECTOR ROUTINE -EINVIT- DID NOT CONVERGE FOR VECTOR 7\n", " NORM = 1.22E-04 PERFORMANCE INDEX = 4.12E+02\n", " A HALT WILL OCCUR IF THE PERF.IND. EXCEEDS 100.0\n", " EINVIT HAS FAILED TO CONVERGE FOR VECTOR 7\n", " GLDIAG FAILURE IN -BKRNR-\n", " EXECUTION OF GAMESS TERMINATED -ABNORMALLY- AT Tue Jan 23 18:11:35 2024\n", " 580000 WORDS OF DYNAMIC MEMORY USED\n", " STEP CPU TIME = 0.00 TOTAL CPU TIME = 0.0 ( 0.0 MIN)\n", " TOTAL WALL CLOCK TIME= 0.0 SECONDS, CPU UTILIZATION IS 66.67%\n", " ddikick.x: application process 0 quit unexpectedly.\n", " ddikick.x: Sending kill signal to DDI processes.\n", " ddikick.x: Execution terminated due to error(s).\n" ] } ], "source": [ "# For a quick look, checking the end of the file is also useful\n", "testDL.tail()" ] }, { "cell_type": "code", "execution_count": 16, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "*** Contents from file /tmp/test_CO2_geomOpt.out.\n", "Showing 20 header lines, starting from line 80.\n", " EXECUTION OF GAMESS BEGUN Tue Jan 23 18:11:35 2024\n", "\n", " ECHO OF THE FIRST FEW INPUT CARDS -\n", " INPUT CARD> $contrl scftyp=rhf runtyp=optimize $end \n", " INPUT CARD> $basis gbasis=sto ngauss=3 $end \n", " INPUT CARD> $system mwords=30 $end \n", " INPUT CARD> $statpt opttol=0.0001 nstep=20 $end \n", " INPUT CARD> $DATA \n", " INPUT CARD>CO2 sym testing \n", " INPUT CARD>DNH 8 \n", " INPUT CARD> \n", " INPUT CARD>O 8.0 0.0000000000 0.0000000000 1.2375000000 \n", " INPUT CARD>C 6.0 0.0000000000 0.0000000000 0.0000000000 \n", " INPUT CARD> $END \n", " 30000000 WORDS OF MEMORY AVAILABLE\n", "\n", " BASIS OPTIONS\n", " -------------\n", " GBASIS=STO IGAUSS= 3 POLAR=NONE \n", " NDFUNC= 0 NFFUNC= 0 DIFFSP= F\n" ] } ], "source": [ "# Check the header lines... this looks OK, but note the atom ordering.\n", "testDL.head(20)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "In this case, the error is (2) - the atom ordering is not as Gamess prefers. This can be modified as required, including the ordering, again via the `atomList` configuration." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### Rerunning geom opt with updated parameters" ] }, { "cell_type": "code", "execution_count": 17, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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IndSpeciesAtomic Num.xyz
00O80.00.0-1.2375
11O80.00.01.2375
22C60.00.00.0000
\n", "
" ], "text/plain": [ " Ind Species Atomic Num. x y z\n", "0 0 O 8 0.0 0.0 -1.2375\n", "1 1 O 8 0.0 0.0 1.2375\n", "2 2 C 6 0.0 0.0 0.0000" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "# Check current geom table - note this HAS changed with the symmetrized run geom return from Gamess.\n", "# This may be updated even if the run fails.\n", "testDL.printTable()" ] }, { "cell_type": "code", "execution_count": 18, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "INFO:pygamess.gamess:Executeing py_rungms with command /opt/gamess/ddikick.x /opt/gamess/gamess.00.x leskvl -ddi 1 1 jake -scr /tmp/tmpn3cbn17h > /tmp/tmpn3cbn17h/leskvl.out\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Set sym = DNH 8\n", "Set atomList = [2, 1]\n", "\n", "*** Gamess input card:\n", " $contrl scftyp=rhf runtyp=optimize $end\n", " $basis gbasis=sto ngauss=3 $end\n", " $system mwords=30 $end\n", " $statpt opttol=0.0001 nstep=20 $end\n", " $DATA\n", "CO2 sym testing v2\n", "DNH 8\n", "\n", "C 6.0 0.0000000000 0.0000000000 0.0000000000 \n", "O 8.0 0.0000000000 0.0000000000 1.2375000000 \n", " $END\n", "\n", "*** ddikick exit status OK: ddikick.x: exited gracefully.\n", "*** Gamess run completed OK.\n", "E = -185.0683906077\n", "\n", "*** Gamess optimization run - reseting self.mol with updated coords.\n", "Note that atom ordering may change depending on Gamess output.\n", "Found 6 geometry iterations in Gamess output.\n", "Updating with new coords, output set to self.mol\n" ] }, { "data": { "text/html": [ "
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IndSpeciesAtomic Num.xyz
00C60.00.00.0000
11O80.00.0-1.1879
22O80.00.01.1879
\n", "
" ], "text/plain": [ " Ind Species Atomic Num. x y z\n", "0 0 C 6 0.0 0.0 0.0000\n", "1 1 O 8 0.0 0.0 -1.1879\n", "2 2 O 8 0.0 0.0 1.1879" ] }, "metadata": {}, "output_type": "display_data" }, { "name": "stdout", "output_type": "stream", "text": [ "Set geom opt coord outputs to self.geomOpt.\n", "*** Gamess output file moved to /tmp/test_CO2_geomOpt_v2.out\n" ] } ], "source": [ "# Try updating the atom ordering, so that the Z=0 atom is set first, and create a new job with this.\n", "testDL.setGamess(note='CO2 sym testing v2', sym='DNH 8', atomList = [2,1])\n", "\n", "# Run geom opt with new parameters\n", "testDL.runGamess(runType='optimize',fileOut = '/tmp/test_CO2_geomOpt_v2.out')" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Success! In this case the atom ordering needed some massaging for the Gamess input. Note:\n", "\n", "- Output E has changed.\n", "- `Found 6 geometry iterations in Gamess output.` in the printed info.\n", "- Updated coords table has different Z values." ] }, { "cell_type": "code", "execution_count": 19, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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IndSpeciesAtomic Num.xyz
Geom iterAtom index
000C60.00.00.0000
11O80.00.0-1.2375
22O80.00.01.2375
103C60.00.00.0000
14O80.00.0-1.1499
25O80.00.01.1499
206C60.00.00.0000
17O80.00.0-1.1942
28O80.00.01.1942
309C60.00.00.0000
110O80.00.0-1.1887
211O80.00.01.1887
4012C60.00.00.0000
113O80.00.0-1.1879
214O80.00.01.1879
5015C60.00.00.0000
116O80.00.0-1.1879
217O80.00.01.1879
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" ], "text/plain": [ " Ind Species Atomic Num. x y z\n", "Geom iter Atom index \n", "0 0 0 C 6 0.0 0.0 0.0000\n", " 1 1 O 8 0.0 0.0 -1.2375\n", " 2 2 O 8 0.0 0.0 1.2375\n", "1 0 3 C 6 0.0 0.0 0.0000\n", " 1 4 O 8 0.0 0.0 -1.1499\n", " 2 5 O 8 0.0 0.0 1.1499\n", "2 0 6 C 6 0.0 0.0 0.0000\n", " 1 7 O 8 0.0 0.0 -1.1942\n", " 2 8 O 8 0.0 0.0 1.1942\n", "3 0 9 C 6 0.0 0.0 0.0000\n", " 1 10 O 8 0.0 0.0 -1.1887\n", " 2 11 O 8 0.0 0.0 1.1887\n", "4 0 12 C 6 0.0 0.0 0.0000\n", " 1 13 O 8 0.0 0.0 -1.1879\n", " 2 14 O 8 0.0 0.0 1.1879\n", "5 0 15 C 6 0.0 0.0 0.0000\n", " 1 16 O 8 0.0 0.0 -1.1879\n", " 2 17 O 8 0.0 0.0 1.1879" ] }, "execution_count": 19, "metadata": {}, "output_type": "execute_result" } ], "source": [ "# The full set of geometries sampled can be investigated, and are set in self.geomOpt in the default case\n", "testDL.geomOpt" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Versions" ] }, { "cell_type": "code", "execution_count": 20, "metadata": {}, "outputs": [ { "data": { "text/html": [ "\n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
Tue Jan 23 18:11:41 2024 EST
OSLinuxCPU(s)64Machinex86_64
Architecture64bitEnvironmentJupyter
Python 3.7.10 (default, Feb 26 2021, 18:47:35) \n", "[GCC 7.3.0]
epsman0.0.1cclib1.7rdkit2023.03.2
numpy1.19.2scipy1.6.1IPython7.21.0
matplotlib3.3.4scooby0.5.6
Intel(R) Math Kernel Library Version 2020.0.2 Product Build 20200624 for Intel(R) 64 architecture applications
" ], "text/plain": [ "\n", "--------------------------------------------------------------------------------\n", " Date: Tue Jan 23 18:11:41 2024 EST\n", "\n", " OS : Linux\n", " CPU(s) : 64\n", " Machine : x86_64\n", " Architecture : 64bit\n", " Environment : Jupyter\n", "\n", " Python 3.7.10 (default, Feb 26 2021, 18:47:35) [GCC 7.3.0]\n", "\n", " epsman : 0.0.1\n", " cclib : 1.7\n", " rdkit : 2023.03.2\n", " numpy : 1.19.2\n", " scipy : 1.6.1\n", " IPython : 7.21.0\n", " matplotlib : 3.3.4\n", " scooby : 0.5.6\n", "\n", " Intel(R) Math Kernel Library Version 2020.0.2 Product Build 20200624 for\n", " Intel(R) 64 architecture applications\n", "--------------------------------------------------------------------------------" ] }, "execution_count": 20, "metadata": {}, "output_type": "execute_result" } ], "source": [ "import scooby\n", "scooby.Report(additional=['epsman', 'cclib', 'rdkit'])" ] }, { "cell_type": "code", "execution_count": 21, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " master\u001b[m\n", "* \u001b[32mrestructure160221\u001b[m\n", "29b4057dd2ede80974fd6e17e28c91aaebeae6a5\n" ] } ], "source": [ "# Check current Git commit for local ePSproc version\n", "from pathlib import Path\n", "import epsman as em\n", "\n", "!git -C {Path(em.__file__).parent} branch\n", "!git -C {Path(em.__file__).parent} log --format=\"%H\" -n 1" ] }, { "cell_type": "code", "execution_count": 22, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "21b4357a169baf9fa7887c68bd1cf8f92c59642c\trefs/heads/master\n", "29b4057dd2ede80974fd6e17e28c91aaebeae6a5\trefs/heads/restructure160221\n" ] } ], "source": [ "# Check current remote commits\n", "!git ls-remote --heads https://github.com/phockett/epsman" ] } ], "metadata": { "jupytext": { "formats": "ipynb,md:myst" }, "kernelspec": { "display_name": "Python [conda env:epsman-dev-shared-310122]", "language": "python", "name": "conda-env-epsman-dev-shared-310122-py" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.7.10" } }, "nbformat": 4, "nbformat_minor": 4 }