diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml index 7b5a39c162..5183002095 100644 --- a/.github/workflows/CI.yml +++ b/.github/workflows/CI.yml @@ -25,6 +25,7 @@ # 2023-07-17 - made it pass by default # 2023-07-21 - upload the regression results summary as artifact (for use as a comment on PRs) # 2023-07-31 - removed option to run from RMG-database with GitHub resuable workflows +# 2024-10-01 - deprecated Mambaforge with Miniforge3 for environment creation name: Continuous Integration @@ -61,14 +62,25 @@ jobs: - name: Checkout RMG-Py uses: actions/checkout@v4 + # Step to create a custom condarc.yml before setting up conda + - name: Create custom conda config file + run: | + RUNNER_CWD=$(pwd) + echo "channels:" > $RUNNER_CWD/condarc.yml + echo " - conda-forge" >> $RUNNER_CWD/condarc.yml + echo " - rmg" >> $RUNNER_CWD/condarc.yml + echo " - cantera" >> $RUNNER_CWD/condarc.yml + echo "show_channel_urls: true" >> $RUNNER_CWD/condarc.yml + # configures the mamba environment manager and builds the environment - - name: Setup Mambaforge Python 3.7 + - name: Setup Miniforge Python 3.7 uses: conda-incubator/setup-miniconda@v3 with: environment-file: environment.yml - miniforge-variant: Mambaforge + miniforge-variant: Miniforge3 miniforge-version: latest python-version: 3.7 + condarc-file: condarc.yml activate-environment: rmg_env use-mamba: true @@ -111,14 +123,25 @@ jobs: - name: Checkout RMG-Py uses: actions/checkout@v4 + # Step to create a custom condarc.yml before setting up conda + - name: Create custom condarc.yml + run: | + RUNNER_CWD=$(pwd) + echo "channels:" > $RUNNER_CWD/condarc.yml + echo " - conda-forge" >> $RUNNER_CWD/condarc.yml + echo " - rmg" >> $RUNNER_CWD/condarc.yml + echo " - cantera" >> $RUNNER_CWD/condarc.yml + echo "show_channel_urls: true" >> $RUNNER_CWD/condarc.yml + # configures the mamba environment manager and builds the environment - - name: Setup Mambaforge Python 3.7 + - name: Setup Miniforge Python 3.7 uses: conda-incubator/setup-miniconda@v3 with: environment-file: environment.yml - miniforge-variant: Mambaforge + miniforge-variant: Miniforge3 miniforge-version: latest python-version: 3.7 + condarc-file: condarc.yml activate-environment: rmg_env use-mamba: true @@ -167,7 +190,7 @@ jobs: id: regression-execution timeout-minutes: 60 run: | - for regr_test in aromatics liquid_oxidation nitrogen oxidation sulfur superminimal RMS_constantVIdealGasReactor_superminimal RMS_CSTR_liquid_oxidation RMS_liquidSurface_ch4o2cat fragment RMS_constantVIdealGasReactor_fragment; + for regr_test in aromatics liquid_oxidation nitrogen oxidation sulfur superminimal RMS_constantVIdealGasReactor_superminimal RMS_CSTR_liquid_oxidation RMS_liquidSurface_ch4o2cat fragment RMS_constantVIdealGasReactor_fragment minimal_surface; do if python-jl rmg.py test/regression/"$regr_test"/input.py; then echo "$regr_test" "Executed Successfully" @@ -218,16 +241,16 @@ jobs: - name : Find ID of Reference Results env: GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} + # this will search for the last successful execution of CI on main run: | - run_id=$(gh run list -R ReactionMechanismGenerator/RMG-Py --workflow="Continuous Integration" --branch main --limit 1 --json databaseId --jq '.[0].databaseId') + run_id=$(gh run list -R ReactionMechanismGenerator/RMG-Py --workflow="Continuous Integration" --branch main --limit 15 --json databaseId,conclusion --jq 'map(select(.conclusion == "success")) | .[0].databaseId') echo "CI_RUN_ID=$run_id" >> $GITHUB_ENV - name: Retrieve Stable Regression Results if: ${{ env.REFERENCE_JOB == 'false' }} uses: actions/download-artifact@v4 with: - # this will search for the last successful execution of CI on main and download - # the stable regression results + # download stable regression results run-id: ${{ env.CI_RUN_ID }} repository: ReactionMechanismGenerator/RMG-Py github-token: ${{ secrets.GITHUB_TOKEN }} @@ -243,7 +266,7 @@ jobs: run: | exec 2> >(tee -a regression.stderr >&2) 1> >(tee -a regression.stdout) mkdir -p "test/regression-diff" - for regr_test in aromatics liquid_oxidation nitrogen oxidation sulfur superminimal RMS_constantVIdealGasReactor_superminimal RMS_CSTR_liquid_oxidation fragment RMS_constantVIdealGasReactor_fragment; + for regr_test in aromatics liquid_oxidation nitrogen oxidation sulfur superminimal RMS_constantVIdealGasReactor_superminimal RMS_CSTR_liquid_oxidation fragment RMS_constantVIdealGasReactor_fragment minimal_surface; do echo "" echo "### Regression test $regr_test:" @@ -378,7 +401,7 @@ jobs: password: ${{ secrets.DOCKERHUB_TOKEN }} - name: Build and Push - uses: docker/build-push-action@v4 + uses: docker/build-push-action@v6 with: push: true tags: reactionmechanismgenerator/rmg:latest diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index 8ef810f67f..43ab6b0ab1 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -27,10 +27,10 @@ jobs: fetch-depth: 0 - name: Setup Mambaforge Python 3.7 - uses: conda-incubator/setup-miniconda@v2 + uses: conda-incubator/setup-miniconda@v3 with: environment-file: environment.yml - miniforge-variant: Mambaforge + miniforge-variant: Miniforge3 miniforge-version: latest python-version: 3.7 activate-environment: rmg_env diff --git a/Dockerfile b/Dockerfile index a263199c89..cafc18c2a9 100644 --- a/Dockerfile +++ b/Dockerfile @@ -23,10 +23,10 @@ RUN apt-get update && \ apt-get clean -y # Install conda -RUN wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh && \ - bash Miniconda3-latest-Linux-x86_64.sh -b -p /miniconda && \ - rm Miniconda3-latest-Linux-x86_64.sh -ENV PATH="$PATH:/miniconda/bin" +RUN wget "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh" && \ + bash Miniforge3-Linux-x86_64.sh -b -p /miniforge && \ + rm Miniforge3-Linux-x86_64.sh +ENV PATH="$PATH:/miniforge/bin" # Set solver backend to mamba for speed RUN conda install -n base conda-libmamba-solver && \ @@ -35,12 +35,18 @@ RUN conda install -n base conda-libmamba-solver && \ # Set Bash as the default shell for following commands SHELL ["/bin/bash", "-c"] +# Add build arguments for RMG-Py, RMG-database, and RMS branches. +ARG RMG_Py_Branch=main +ARG RMG_Database_Branch=main +ARG RMS_Branch=main +ENV rmsbranch=${RMS_Branch} + # cd WORKDIR /rmg # Clone the RMG base and database repositories -RUN git clone --single-branch --branch main --depth 1 https://github.com/ReactionMechanismGenerator/RMG-Py.git && \ - git clone --single-branch --branch main --depth 1 https://github.com/ReactionMechanismGenerator/RMG-database.git +RUN git clone --single-branch --branch ${RMG_Py_Branch} --depth 1 https://github.com/ReactionMechanismGenerator/RMG-Py.git && \ + git clone --single-branch --branch ${RMG_Database_Branch} --depth 1 https://github.com/ReactionMechanismGenerator/RMG-database.git WORKDIR /rmg/RMG-Py # build the conda environment @@ -64,7 +70,7 @@ ENV PATH="$RUNNER_CWD/RMG-Py:$PATH" # setting this env variable fixes an issue with Julia precompilation on Windows ENV JULIA_CPU_TARGET="x86-64,haswell,skylake,broadwell,znver1,znver2,znver3,cascadelake,icelake-client,cooperlake,generic" RUN make && \ - julia -e 'using Pkg; Pkg.add(PackageSpec(name="PyCall",rev="master")); Pkg.add(PackageSpec(name="ReactionMechanismSimulator",rev="main")); using ReactionMechanismSimulator' && \ + julia -e 'using Pkg; Pkg.add(PackageSpec(name="PyCall",rev="master")); Pkg.add(PackageSpec(name="ReactionMechanismSimulator",rev=ENV["rmsbranch"])); using ReactionMechanismSimulator' && \ python -c "import julia; julia.install(); import diffeqpy; diffeqpy.install()" # RMG-Py should now be installed and ready - trigger precompilation and test run diff --git a/arkane/data/molpro/HO2_RS2C.out b/arkane/data/molpro/HO2_RS2C.out new file mode 100644 index 0000000000..9142f71520 --- /dev/null +++ b/arkane/data/molpro/HO2_RS2C.out @@ -0,0 +1,531 @@ + + Working directory : /gtmp/molpro.T66wyGqmSD/ + Global scratch directory : /gtmp/molpro.T66wyGqmSD/ + Wavefunction directory : /home/alon/wfu/ + Main file repository : /gtmp/molpro.T66wyGqmSD/ + + id : dana + + Nodes nprocs + n136 16 + GA implementation: MPI file + GA implementation (serial work in mppx): MPI file + + Using customized tuning parameters: mindgm=1; mindgv=20; mindgc=4; mindgr=1; noblas=0; minvec=7 + default implementation of scratch files=sf + + + Variables initialized (1025), CPU time= 0.01 sec + ***,HO2 + memory,Total=15625,m; + + geometry={angstrom; + O -0.16513900 0.44815400 0.00000000 + O 1.00112100 -0.18975400 -0.00000000 + H -0.83598100 -0.25840000 0.00000000} + + gprint,orbitals; + + basis=aug-cc-pvtz + + + + int; + + {hf; + maxit,999; + wf,spin=1,charge=0; + } + + + {mp2; + wf,spin=1,charge=0; + } + + {casscf; + maxit,999; + wf,spin=1,charge=0; + occ,8,2; + closed,5,1; + state,1; + } + + {rs2c; + maxit,999; + wf,spin=1,charge=0; + } + + + + + Commands initialized (840), CPU time= 0.00 sec, 684 directives. + Default parameters read. Elapsed time= 0.32 sec + + Checking input... + Passed +1 + + + *** PROGRAM SYSTEM MOLPRO *** + Copyright, TTI GmbH Stuttgart, 2015 + Version 2022.3 linked Wed Nov 30 13:40:34 2022 + + + ********************************************************************************************************************************** + LABEL * HO2 + 64 bit mpp version DATE: 08-Sep-24 TIME: 09:43:40 + ********************************************************************************************************************************** + + SHA1: e31ec9a5ea85254ab76f59d122cbdd51c71cf98b + ********************************************************************************************************************************** + + Memory per process: 732 MW + Total memory per node: 15625 MW + Total GA space: 3906 MW + + GA preallocation enabled + GA check enabled + + Variable memory set to 732.4 MW + + + Geometry recognized as XYZ + + + SETTING BASIS = AUG-CC-PVTZ + + + Using spherical harmonics + + Library entry O S aug-cc-pVTZ selected for orbital group 1 + Library entry O P aug-cc-pVTZ selected for orbital group 1 + Library entry O D aug-cc-pVTZ selected for orbital group 1 + Library entry O F aug-cc-pVTZ selected for orbital group 1 + Library entry H S aug-cc-pVTZ selected for orbital group 2 + Library entry H P aug-cc-pVTZ selected for orbital group 2 + Library entry H D aug-cc-pVTZ selected for orbital group 2 + + + PROGRAM * SEWARD (Integral evaluation for generally contracted gaussian basis sets) Author: Roland Lindh, 1990 + + Geometry written to block 1 of record 700 + + + Point group Cs + + + + ATOMIC COORDINATES + + NR ATOM CHARGE X Y Z + + 1 O 8.00 -0.312067482 0.846888322 0.000000000 + 2 O 8.00 1.891844508 -0.358583091 0.000000000 + 3 H 1.00 -1.579775135 -0.488305231 0.000000000 + + Bond lengths in Bohr (Angstrom) + + 1-2 2.512048842 1-3 1.841147608 + ( 1.329319000) ( 0.974293356) + + Bond angles + + 2-1-3 104.83752478 + + NUCLEAR CHARGE: 17 + NUMBER OF PRIMITIVE AOS: 161 + NUMBER OF SYMMETRY AOS: 141 + NUMBER OF CONTRACTIONS: 115 ( 76A' + 39A" ) + NUMBER OF INNER CORE ORBITALS: 0 ( 0A' + 0A" ) + NUMBER OF OUTER CORE ORBITALS: 2 ( 2A' + 0A" ) + NUMBER OF VALENCE ORBITALS: 9 ( 7A' + 2A" ) + + + NUCLEAR REPULSION ENERGY 32.12512051 + + + Allocated 245 MW GA space on the current processor, total: 3907 MW. Time: 0.00 sec + + Eigenvalues of metric + + 1 0.240E-03 0.415E-03 0.122E-02 0.267E-02 0.374E-02 0.493E-02 0.520E-02 0.693E-02 + 2 0.587E-02 0.114E-01 0.380E-01 0.419E-01 0.523E-01 0.813E-01 0.118E+00 0.128E+00 + + + Contracted 2-electron integrals neglected if value below 1.0D-11 + AO integral compression algorithm 1 Integral accuracy 1.0D-11 + + 65.798 MB (compressed) written to integral file ( 55.4%) + + Node minimum: 3.408 MB, node maximum: 5.243 MB + + + NUMBER OF SORTED TWO-ELECTRON INTEGRALS: 706608. BUFFER LENGTH: 32768 + NUMBER OF SEGMENTS: 1 SEGMENT LENGTH: 706608 RECORD LENGTH: 524288 + + Memory used in sort: 1.26 MW + + SORT1 READ 14525730. AND WROTE 675498. INTEGRALS IN 2 RECORDS. CPU TIME: 0.14 SEC, REAL TIME: 0.15 SEC + SORT2 READ 10930363. AND WROTE 11433631. INTEGRALS IN 272 RECORDS. CPU TIME: 0.01 SEC, REAL TIME: 0.01 SEC + + Node minimum: 706378. Node maximum: 718170. integrals + + OPERATOR DM FOR CENTER 0 COORDINATES: 0.000000 0.000000 0.000000 + + + ********************************************************************************************************************************** + DATASETS * FILE NREC LENGTH (MB) RECORD NAMES + 1 18 28.86 500 610 700 900 950 970 1000 129 960 1100 + VAR BASINP GEOM SYMINP ZMAT AOBASIS BASIS P2S ABASIS S + 1400 1410 1200 1210 1080 1600 1650 1700 + T V H0 H01 AOSYM SMH MOLCAS OPER + + PROGRAMS * TOTAL INT + CPU TIMES * 0.60 0.47 + REAL TIME * 1.03 SEC + DISK USED * 29.18 MB (local), 644.53 MB (total) + GA USED * 0.00 MB (max) 0.00 MB (current) + ********************************************************************************************************************************** + + + Program * Restricted Hartree-Fock + + Orbital guess generated from atomic densities. Full valence occupancy: 9 2 + + Initial alpha occupancy: 7 2 + Initial beta occupancy: 7 1 + + NELEC= 17 SYM=2 MS2= 1 THRE=1.0D-08 THRD=3.2D-06 THRG=3.2D-06 HFMA2=F DIIS_START=2 DIIS_MAX=10 DIIS_INCORE=F + + Level shifts: 0.00 (CLOSED) 0.00 (OPEN) 0.30 (GAP_MIN) + + ITER ETOT DE GRAD DDIFF DIIS NEXP TIME(IT) TIME(TOT) DIAG + 1 -150.17011817 -150.17011817 0.00D+00 0.88D-01 0 0 0.00 0.00 start + 2 -150.20465019 -0.03453202 0.90D-02 0.92D-02 1 0 0.01 0.01 diag2 + 3 -150.22033330 -0.01568311 0.64D-02 0.47D-02 2 0 0.00 0.01 diag2 + 4 -150.22490807 -0.00457477 0.13D-02 0.14D-02 3 0 0.01 0.02 diag2 + 5 -150.22856663 -0.00365856 0.12D-02 0.11D-02 4 0 0.01 0.03 diag2 + 6 -150.23199458 -0.00342794 0.80D-03 0.16D-02 5 0 0.00 0.03 diag2 + 7 -150.23257275 -0.00057817 0.35D-03 0.88D-03 6 0 0.00 0.03 diag2 + 8 -150.23258496 -0.00001221 0.98D-04 0.16D-03 7 0 0.01 0.04 fixocc + 9 -150.23259040 -0.00000544 0.69D-04 0.13D-03 8 0 0.00 0.04 diag2 + 10 -150.23259103 -0.00000063 0.28D-04 0.43D-04 9 0 0.01 0.05 diag2/orth + 11 -150.23259126 -0.00000022 0.13D-04 0.19D-04 9 0 0.00 0.05 diag2 + 12 -150.23259126 -0.00000000 0.95D-06 0.19D-05 9 0 0.01 0.06 diag2 + 13 -150.23259126 -0.00000000 0.51D-06 0.64D-06 0 0 0.00 0.06 diag + + Final alpha occupancy: 7 2 + Final beta occupancy: 7 1 + + !RHF STATE 1.2 Energy -150.232591258293 + RHF One-electron energy -270.928629502666 + RHF Two-electron energy 88.570917737861 + RHF Kinetic energy 150.046375775003 + RHF Nuclear energy 32.125120506513 + RHF Virial quotient -1.001241052857 + + !RHF STATE 1.2 Dipole moment -0.62605931 -0.43865566 0.00000000 + Dipole moment /Debye -1.59128405 -1.11495147 0.00000000 + + ELECTRON ORBITALS + ================= + + Orbital Occupation Energy Cen Mu Typ Coefficients + 1.1 2.00000 -20.67277 2 1 s 0.99737 + 2.1 2.00000 -20.66835 1 1 s 0.99740 + 3.1 2.00000 -1.54217 1 2 s 0.68214 2 2 s 0.56715 + 4.1 2.00000 -1.15777 1 2 s -0.57468 1 1 px 0.25089 2 2 s 0.74537 3 1 s -0.36249 + 5.1 2.00000 -0.76227 1 1 px 0.46397 1 1 py 0.46612 2 1 py 0.47384 3 1 s -0.53346 + 6.1 2.00000 -0.66270 1 1 px -0.39599 1 1 py 0.48511 2 1 px 0.64562 + 7.1 2.00000 -0.50672 1 1 py -0.47553 2 1 px 0.32427 2 1 py 0.79533 3 1 s 0.36930 + 1.2 2.00000 -0.62448 1 1 pz 0.88505 + 2.2 1.00000 -0.59233 1 1 pz -0.36862 2 1 pz 0.99301 + + + HOMO 7.1 -0.506721 = -13.7886eV + LUMO 8.1 0.030590 = 0.8324eV + LUMO-HOMO 0.537311 = 14.6210eV + + Orbitals saved in record 2100.2 + + + ********************************************************************************************************************************** + DATASETS * FILE NREC LENGTH (MB) RECORD NAMES + 1 18 28.87 500 610 700 900 950 970 1000 129 960 1100 + VAR BASINP GEOM SYMINP ZMAT AOBASIS BASIS P2S ABASIS S + 1400 1410 1200 1210 1080 1600 1650 1700 + T V H0 H01 AOSYM SMH MOLCAS OPER + + 2 4 0.62 700 1000 520 2100 + GEOM BASIS MCVARS RHF + + PROGRAMS * TOTAL HF-SCF INT + CPU TIMES * 0.74 0.14 0.47 + REAL TIME * 5.11 SEC + DISK USED * 30.56 MB (local), 666.61 MB (total) + GA USED * 0.00 MB (max) 0.00 MB (current) + ********************************************************************************************************************************** + + + PROGRAM * RMP2 (Restricted open-shell) Authors: H.-J. Werner, 2001 + + + Convergence thresholds: THRVAR = 1.00D-08 THRDEN = 1.00D-06 + + Number of core orbitals: 2 ( 2 0 ) + Number of closed-shell orbitals: 6 ( 5 1 ) + Number of active orbitals: 1 ( 0 1 ) + Number of external orbitals: 106 ( 69 37 ) + + Reading RHF information from record 2100.2 + + TOTAL A-A B-B A-B + Pair energies: -0.45576889 -0.06238867 -0.05285220 -0.34052802 + Singles energies: -0.00441624 -0.00220300 -0.00221324 + + !Reference STATE 1.2 energy -150.232591258293 + !RMP2 STATE 1.2 correl. energy -0.460185122779 + !RMP2 STATE 1.2 total energy -150.692776381072 + + !SCS-RMP2 STATE 1.2 correl. energy -0.447047243835 + !SCS-RMP2 STATE 1.2 total energy -150.679638502128 + + + ********************************************************************************************************************************** + DATASETS * FILE NREC LENGTH (MB) RECORD NAMES + 1 18 28.87 500 610 700 900 950 970 1000 129 960 1100 + VAR BASINP GEOM SYMINP ZMAT AOBASIS BASIS P2S ABASIS S + 1400 1410 1200 1210 1080 1600 1650 1700 + T V H0 H01 AOSYM SMH MOLCAS OPER + + 2 4 0.62 700 1000 520 2100 + GEOM BASIS MCVARS RHF + + PROGRAMS * TOTAL MP2 HF-SCF INT + CPU TIMES * 0.81 0.06 0.14 0.47 + REAL TIME * 5.19 SEC + DISK USED * 30.56 MB (local), 666.61 MB (total) + SF USED * 8.12 MB + GA USED * 0.00 MB (max) 0.00 MB (current) + ********************************************************************************************************************************** + + PROGRAM * MULTI (Direct Multiconfiguration SCF) Authors: P.J. Knowles, H.-J. Werner (1984) + D.A. Kreplin, P.J. Knowles, H.-J. Werner (2019) + + Number of closed-shell orbitals: 6 ( 5 1) + Number of active orbitals: 4 ( 3 1) + Number of external orbitals: 105 ( 68 37) + + State symmetry 1 + + Number of active electrons: 5 Spin symmetry=Doublet Space symmetry=2 + Number of states: 1 + Number of CSFs: 9 (12 determinants, 24 intermediate states) + + Molecular orbitals read from record 2100.2 Type=RHF/CANONICAL + + Wavefunction dump at record 2140.2 + + Convergence thresholds 0.10E-04 (gradient) 0.10E-05 (energy) + + Number of orbital rotations: 634 ( 16 closed/active, 377 closed/virtual, 0 active/active, 241 active/virtual ) + Total number of variables: 646 + + Second-order MCSCF: L-BFGS accelerated + + ITER MIC NCI NEG ENERGY(VAR) ENERGY(PROJ) ENERGY CHANGE GRAD(0) GRAD(ORB) GRAD(CI) STEP TIME + 1 55 20 28 -150.23260182 -150.25752980 -0.02492798 0.00026496 0.00000027 0.00000000 0.94E+00 2.24 + 2 26 13 0 -150.26507911 -150.26990559 -0.00482648 0.06074391 0.00034661 0.00000000 0.23E+00 2.53 + 3 31 12 0 -150.27012384 -150.27015191 -0.00002807 0.00393155 0.00000450 0.00000000 0.19E-01 2.83 + 4 23 9 0 -150.27015263 -150.27015272 -0.00000009 0.00025798 0.00000025 0.00000000 0.98E-03 3.07 + + CONVERGENCE REACHED! Final gradient: 0.00000052 ( 0.52E-06) + Final energy: -150.27015272 + + First order charge density matrix for state 1.2 saved on record 2140.2 (density set 1) + + Results for state 1.2 + ===================== + !MCSCF STATE 1.2 Energy -150.270152720089 + Nuclear energy 32.12512051 + Kinetic energy 150.20743631 + One electron energy -270.97568640 + Two electron energy 88.58041317 + Virial ratio 2.00041753 + + !MCSCF STATE 1.2 Dipole moment -0.62063164 -0.43831921 0.00000000 + Dipole moment /Debye -1.57748829 -1.11409631 0.00000000 + + No non-zero expectation values + + NATURAL ORBITALS + ================ + + Orbital Occupation Energy Cen Mu Typ Coefficients + 1.1 2.00000 -20.65876 1 1 s 0.91254 2 1 s 0.40637 + 2.1 2.00000 -20.64159 1 1 s -0.40589 2 1 s 0.91190 + 3.1 2.00000 -1.40648 1 2 s 0.81184 2 2 s 0.37367 3 1 s 0.37720 + 4.1 2.00000 -0.75836 1 1 px 0.31043 1 1 py 0.64168 2 1 py 0.35375 3 1 s -0.54763 + 5.1 2.00000 -0.52211 1 1 py 0.34480 2 1 px -0.43218 2 1 py -0.78756 3 1 s -0.38960 + 6.1 1.99791 -1.14889 1 2 s -0.42578 2 2 s 0.89357 + 7.1 1.95773 -0.78780 1 1 px -0.54740 1 1 py 0.37155 2 1 px 0.55821 2 1 py -0.33506 + 8.1 0.04436 0.48087 1 2 s -0.40162 1 4 s -0.35196 1 1 px -0.82535 1 1 py 0.49487 + 2 2 s 0.35945 2 4 s 0.38540 2 5 s 0.26437 2 1 px -0.86572 + 2 1 py 0.48426 + 1.2 2.00000 -0.62077 1 1 pz 0.88536 + 2.2 1.00000 -0.21314 1 1 pz -0.36073 2 1 pz 0.99357 + + Natural orbital dump at molpro section 2140.2 (Orbital set 2) + + + ********************************************************************************************************************************** + DATASETS * FILE NREC LENGTH (MB) RECORD NAMES + 1 19 33.34 500 610 700 900 950 970 1000 129 960 1100 + VAR BASINP GEOM SYMINP ZMAT AOBASIS BASIS P2S ABASIS S + 1400 1410 1200 1210 1080 1600 1650 1700 1380 + T V H0 H01 AOSYM SMH MOLCAS OPER JKOP + + 2 5 0.97 700 1000 520 2100 2140 + GEOM BASIS MCVARS RHF MCSCF + + PROGRAMS * TOTAL CASSCF MP2 HF-SCF INT + CPU TIMES * 2.08 1.27 0.06 0.14 0.47 + REAL TIME * 9.10 SEC + DISK USED * 34.37 MB (local), 727.57 MB (total) + SF USED * 12.99 MB + GA USED * 0.00 MB (max) 0.00 MB (current) + ********************************************************************************************************************************** + + + PROGRAM * RS2C (Multireference RS Perturbation Theory) Authors: H.-J. Werner (1993), P. Celani (1998) + + + Convergence thresholds: THRVAR = 1.00D-06 THRDEN = 1.00D-06 + + Number of optimized states: 1 Roots: 1 + Number of reference states: 1 Roots: 1 + + Using rs2c + + Reference symmetry: 2 Doublet + Number of electrons: 17 + Maximum number of shells: 4 + Maximum number of spin couplings: 14 + + Reference space: 6 conf 9 CSFs + N elec internal: 16 conf 20 CSFs + N-1 el internal: 19 conf 35 CSFs + N-2 el internal: 13 conf 38 CSFs + + Number of electrons in valence space: 13 + Maximum number of open shell orbitals in reference space: 3 + Maximum number of open shell orbitals in internal spaces: 7 + + + Number of core orbitals: 2 ( 2 0 ) + Number of closed-shell orbitals: 4 ( 3 1 ) + Number of active orbitals: 4 ( 3 1 ) + Number of external orbitals: 105 ( 68 37 ) + + Molecular orbitals read from record 2140.2 Type=MCSCF/NATURAL (state 1.2) + + Integral transformation finished. Total CPU: 0.02 sec, npass= 1 Memory used: 0.36 MW + + Number of p-space configurations: 1 + + Reference wavefunction optimized for reference space (refopt=1) + + State Reference Energy + 1 -150.27015272 + + Number of blocks in overlap matrix: 4 Smallest eigenvalue: 0.28D-03 + Number of N-2 electron functions: 63 + Number of N-1 electron functions: 35 + + Number of internal configurations: 9 + Number of singly external configurations: 1822 + Number of doubly external configurations: 177615 + Total number of contracted configurations: 179446 + Total number of uncontracted configurations: 107372 + + Weight factors for SA-density in H0: 1.000000 + + FIMAX= 0.28D+00 FXMAX= 0.11D-08 DIAG= F F NOREF=1 NOINT=0 IHPPD=2 + + Nuclear energy: 32.12512051 + Core energy: -130.99803678 + Zeroth-order valence energy: -10.64492796 + Zeroth-order total energy: -109.51784424 + First-order energy: -40.75230848 + + + Using contracted singles + + Number of contracted N-1 electron functions: 180 + Number of contracted internal configurations: 8 + + + Diagonal Coupling coefficients finished. Storage: 175576 words, CPU-Time: 0.00 seconds. + Energy denominators for pairs finished in 0 passes. Storage: 189560 words, CPU-time: 0.00 seconds. + + ITER. STATE ROOT SQ.NORM CORR.ENERGY TOTAL ENERGY ENERGY CHANGE DEN1 VAR(S) VAR(P) TIME + 1 1 1 1.03247754 0.00000000 -150.27015272 0.00000000 -0.41711899 0.32D-01 0.63D-01 0.04 + 2 1 1 1.10304126 -0.42756068 -150.69771340 -0.42756068 -0.00025015 0.45D-03 0.16D-03 0.05 + 3 1 1 1.10435585 -0.42946425 -150.69961697 -0.00190357 -0.00181114 0.19D-03 0.17D-05 0.06 + 4 1 1 1.10498583 -0.42995826 -150.70011098 -0.00049401 0.00003012 0.64D-05 0.57D-06 0.07 + 5 1 1 1.10513054 -0.42999346 -150.70014618 -0.00003519 -0.00008892 0.17D-05 0.18D-07 0.08 + 6 1 1 1.10517684 -0.42999665 -150.70014937 -0.00000319 0.00000193 0.38D-06 0.52D-08 0.09 + 7 1 1 1.10519789 -0.42999869 -150.70015141 -0.00000204 -0.00000860 0.15D-06 0.10D-08 0.10 + 8 1 1 1.10520600 -0.42999909 -150.70015181 -0.00000040 -0.00000018 0.62D-07 0.38D-09 0.10 + + Energy contributions for state 1.2: + =================================== + + Energy contr. SQ.Norm of FOWF + Space I0 0.00000000 0.00000000 + Space I1 -0.01058738 0.00712445 + Space I2 -0.00124151 0.00064953 + Space S0 -0.02885894 0.00870840 + Space S1 -0.05688864 0.01910554 + Space S2 -0.01800045 0.00649351 + Space P0 -0.04231239 0.00657076 + Space P1 -0.15768459 0.03130729 + Space P2 -0.11442520 0.02524654 + + + RESULTS FOR STATE 1.2 + ===================== + + + Reference energy -150.27015272 + Nuclear energy 32.12512051 + Correlation energy -0.42999909 + !RSPT2 STATE 1.2 Energy -150.700151809954 + !RS2C STATE 1.2 Dipole moment -0.65532698 -0.41398806 0.00000000 + Dipole moment /Debye -1.66567504 -1.05225269 0.00000000 + + + ********************************************************************************************************************************** + DATASETS * FILE NREC LENGTH (MB) RECORD NAMES + 1 19 33.34 500 610 700 900 950 970 1000 129 960 1100 + VAR BASINP GEOM SYMINP ZMAT AOBASIS BASIS P2S ABASIS S + 1400 1410 1200 1210 1080 1600 1650 1700 1380 + T V H0 H01 AOSYM SMH MOLCAS OPER JKOP + + 2 5 0.97 700 1000 520 2100 2140 + GEOM BASIS MCVARS RHF MCSCF + + PROGRAMS * TOTAL RS2C CASSCF MP2 HF-SCF INT + CPU TIMES * 2.22 0.14 1.27 0.06 0.14 0.47 + REAL TIME * 9.81 SEC + DISK USED * 34.37 MB (local), 727.57 MB (total) + SF USED * 18.18 MB + GA USED * 0.00 MB (max) 0.00 MB (current) + ********************************************************************************************************************************** + + RS2C/aug-cc-pVTZ energy= -150.700151809954 + + RS2C CASSCF MP2 HF-SCF + -150.70015181 -150.27015272 -150.69277638 -150.23259126 + ********************************************************************************************************************************** + Molpro calculation terminated diff --git a/arkane/data/orca/N_MRCI.log b/arkane/data/orca/N_MRCI.log new file mode 100644 index 0000000000..8043093678 --- /dev/null +++ b/arkane/data/orca/N_MRCI.log @@ -0,0 +1,1662 @@ + + ***************** + * O R C A * + ***************** + + #, + ### + #### + ##### + ###### + ########, + ,,################,,,,, + ,,#################################,, + ,,##########################################,, + ,#########################################, ''#####, + ,#############################################,, '####, + ,##################################################,,,,####, + ,###########'''' ''''############################### + ,#####'' ,,,,##########,,,, '''####''' '#### + ,##' ,,,,###########################,,, '## + ' ,,###'''' '''############,,, + ,,##'' '''############,,,, ,,,,,,###'' + ,#'' '''#######################''' + ' ''''####'''' + ,#######, #######, ,#######, ## + ,#' '#, ## ## ,#' '#, #''# ###### ,####, + ## ## ## ,#' ## #' '# # #' '# + ## ## ####### ## ,######, #####, # # + '#, ,#' ## ## '#, ,#' ,# #, ## #, ,# + '#######' ## ## '#######' #' '# #####' # '####' + + + + ####################################################### + # -***- # + # Department of theory and spectroscopy # + # Directorship and core code : Frank Neese # + # Max Planck Institute fuer Kohlenforschung # + # Kaiser Wilhelm Platz 1 # + # D-45470 Muelheim/Ruhr # + # Germany # + # # + # All rights reserved # + # -***- # + ####################################################### + + + Program Version 5.0.4 - RELEASE - + + + With contributions from (in alphabetic order): + Daniel Aravena : Magnetic Suceptibility + Michael Atanasov : Ab Initio Ligand Field Theory (pilot matlab implementation) + Alexander A. Auer : GIAO ZORA, VPT2 properties, NMR spectrum + Ute Becker : Parallelization + Giovanni Bistoni : ED, misc. LED, open-shell LED, HFLD + Martin Brehm : Molecular dynamics + Dmytro Bykov : SCF Hessian + Vijay G. Chilkuri : MRCI spin determinant printing, contributions to CSF-ICE + Dipayan Datta : RHF DLPNO-CCSD density + Achintya Kumar Dutta : EOM-CC, STEOM-CC + Dmitry Ganyushin : Spin-Orbit,Spin-Spin,Magnetic field MRCI + Miquel Garcia : C-PCM and meta-GGA Hessian, CC/C-PCM, Gaussian charge scheme + Yang Guo : DLPNO-NEVPT2, F12-NEVPT2, CIM, IAO-localization + Andreas Hansen : Spin unrestricted coupled pair/coupled cluster methods + Benjamin Helmich-Paris : MC-RPA, TRAH-SCF, COSX integrals + Lee Huntington : MR-EOM, pCC + Robert Izsak : Overlap fitted RIJCOSX, COSX-SCS-MP3, EOM + Marcus Kettner : VPT2 + Christian Kollmar : KDIIS, OOCD, Brueckner-CCSD(T), CCSD density, CASPT2, CASPT2-K + Simone Kossmann : Meta GGA functionals, TD-DFT gradient, OOMP2, MP2 Hessian + Martin Krupicka : Initial AUTO-CI + Lucas Lang : DCDCAS + Marvin Lechner : AUTO-CI (C++ implementation), FIC-MRCC + Dagmar Lenk : GEPOL surface, SMD + Dimitrios Liakos : Extrapolation schemes; Compound Job, initial MDCI parallelization + Dimitrios Manganas : Further ROCIS development; embedding schemes + Dimitrios Pantazis : SARC Basis sets + Anastasios Papadopoulos: AUTO-CI, single reference methods and gradients + Taras Petrenko : DFT Hessian,TD-DFT gradient, ASA, ECA, R-Raman, ABS, FL, XAS/XES, NRVS + Peter Pinski : DLPNO-MP2, DLPNO-MP2 Gradient + Christoph Reimann : Effective Core Potentials + Marius Retegan : Local ZFS, SOC + Christoph Riplinger : Optimizer, TS searches, QM/MM, DLPNO-CCSD(T), (RO)-DLPNO pert. Triples + Tobias Risthaus : Range-separated hybrids, TD-DFT gradient, RPA, STAB + Michael Roemelt : Original ROCIS implementation + Masaaki Saitow : Open-shell DLPNO-CCSD energy and density + Barbara Sandhoefer : DKH picture change effects + Avijit Sen : IP-ROCIS + Kantharuban Sivalingam : CASSCF convergence, NEVPT2, FIC-MRCI + Bernardo de Souza : ESD, SOC TD-DFT + Georgi Stoychev : AutoAux, RI-MP2 NMR, DLPNO-MP2 response + Willem Van den Heuvel : Paramagnetic NMR + Boris Wezisla : Elementary symmetry handling + Frank Wennmohs : Technical directorship + + + We gratefully acknowledge several colleagues who have allowed us to + interface, adapt or use parts of their codes: + Stefan Grimme, W. Hujo, H. Kruse, P. Pracht, : VdW corrections, initial TS optimization, + C. Bannwarth, S. Ehlert DFT functionals, gCP, sTDA/sTD-DF + Ed Valeev, F. Pavosevic, A. Kumar : LibInt (2-el integral package), F12 methods + Garnet Chan, S. Sharma, J. Yang, R. Olivares : DMRG + Ulf Ekstrom : XCFun DFT Library + Mihaly Kallay : mrcc (arbitrary order and MRCC methods) + Jiri Pittner, Ondrej Demel : Mk-CCSD + Frank Weinhold : gennbo (NPA and NBO analysis) + Christopher J. Cramer and Donald G. Truhlar : smd solvation model + Lars Goerigk : TD-DFT with DH, B97 family of functionals + V. Asgeirsson, H. Jonsson : NEB implementation + FAccTs GmbH : IRC, NEB, NEB-TS, DLPNO-Multilevel, CI-OPT + MM, QMMM, 2- and 3-layer-ONIOM, Crystal-QMMM, + LR-CPCM, SF, NACMEs, symmetry and pop. for TD-DFT, + nearIR, NL-DFT gradient (VV10), updates on ESD, + ML-optimized integration grids + S Lehtola, MJT Oliveira, MAL Marques : LibXC Library + Liviu Ungur et al : ANISO software + + + Your calculation uses the libint2 library for the computation of 2-el integrals + For citations please refer to: http://libint.valeyev.net + + Your ORCA version has been built with support for libXC version: 5.1.0 + For citations please refer to: https://tddft.org/programs/libxc/ + + This ORCA versions uses: + CBLAS interface : Fast vector & matrix operations + LAPACKE interface : Fast linear algebra routines + SCALAPACK package : Parallel linear algebra routines + Shared memory : Shared parallel matrices + BLAS/LAPACK : OpenBLAS 0.3.15 USE64BITINT DYNAMIC_ARCH NO_AFFINITY Zen SINGLE_THREADED + Core in use : Zen + Copyright (c) 2011-2014, The OpenBLAS Project + + +================================================================================ + +----- Orbital basis set information ----- +Your calculation utilizes the basis: aug-cc-pVTZ + H, B-Ne : Obtained from the ccRepo (grant-hill.group.shef.ac.uk/ccrepo) Feb. 2017 + R. A. Kendall, T. H. Dunning, Jr., R. J. Harrison, J. Chem. Phys. 96, 6796 (1992) + He : Obtained from the ccRepo (grant-hill.group.shef.ac.uk/ccrepo) Feb. 2017 + D. E. Woon, T. H. Dunning, Jr., J. Chem. Phys. 100, 2975 (1994) + Li-Be, Na : Obtained from the ccRepo (grant-hill.group.shef.ac.uk/ccrepo) Feb. 2017 + B. P. Prascher, D. E. Woon, K. A. Peterson, T. H. Dunning, Jr., A. K. Wilson, Theor. Chem. Acc. 128, 69 (2011) + Mg : Obtained from the Peterson Research Group Website (tyr0.chem.wsu.edu/~kipeters) Feb. 2017 + B. P. Prascher, D. E. Woon, K. A. Peterson, T. H. Dunning, Jr., A. K. Wilson, Theor. Chem. Acc. 128, 69 (2011) + Al-Ar : Obtained from the ccRepo (grant-hill.group.shef.ac.uk/ccrepo) Feb. 2017 + D. E. Woon, T. H. Dunning, Jr., J. Chem. Phys. 98, 1358 (1993) + Sc-Zn : Obtained from the ccRepo (grant-hill.group.shef.ac.uk/ccrepo) Feb. 2017 + N. B. Balabanov, K. A. Peterson, J. Chem. Phys. 123, 064107 (2005) + N. B. Balabanov, K. A. Peterson, J. Chem. Phys. 125, 074110 (2006) + Ga-Kr : Obtained from the ccRepo (grant-hill.group.shef.ac.uk/ccrepo) Feb. 2017 + A. K. Wilson, D. E. Woon, K. A. Peterson, T. H. Dunning, Jr., J. Chem. Phys. 110, 7667 (1999) + Ag, Au : Obtained from the Peterson Research Group Website (tyr0.chem.wsu.edu/~kipeters) Feb. 2017 + K. A. Peterson, C. Puzzarini, Theor. Chem. Acc. 114, 283 (2005) + +================================================================================ + WARNINGS + Please study these warnings very carefully! +================================================================================ + + +INFO : the flag for use of the SHARK integral package has been found! + +================================================================================ + INPUT FILE +================================================================================ +NAME = input.in +| 1> !uHF aug-cc-pvtz tightscf +| 2> !sp +| 3> +| 4> %maxcore 3200 +| 5> %pal nprocs 16 end +| 6> +| 7> * xyz 0 4 +| 8> N 0.00000000 0.00000000 0.00000000 +| 9> * +| 10> +| 11> %scf +| 12> MaxIter 999 +| 13> end +| 14> +| 15> +| 16> %mp2 +| 17> RI true +| 18> end +| 19> +| 20> %casscf +| 21> nel 5 +| 22> norb 4 +| 23> nroots 1 +| 24> maxiter 999 +| 25> end +| 26> +| 27> %mrci +| 28> citype MRCI +| 29> davidsonopt true +| 30> maxiter 999 +| 31> end +| 32> +| 33> +| 34> ****END OF INPUT**** +================================================================================ + + **************************** + * Single Point Calculation * + **************************** + +--------------------------------- +CARTESIAN COORDINATES (ANGSTROEM) +--------------------------------- + N 0.000000 0.000000 0.000000 + +---------------------------- +CARTESIAN COORDINATES (A.U.) +---------------------------- + NO LB ZA FRAG MASS X Y Z + 0 N 7.0000 0 14.007 0.000000 0.000000 0.000000 + +-------------------------------- +INTERNAL COORDINATES (ANGSTROEM) +-------------------------------- + N 0 0 0 0.000000000000 0.00000000 0.00000000 + +--------------------------- +INTERNAL COORDINATES (A.U.) +--------------------------- + N 0 0 0 0.000000000000 0.00000000 0.00000000 + +--------------------- +BASIS SET INFORMATION +--------------------- +There are 1 groups of distinct atoms + + Group 1 Type N : 19s6p3d2f contracted to 5s4p3d2f pattern {88111/3111/111/11} + +Atom 0N basis set group => 1 + + + ************************************************************ + * Program running with 16 parallel MPI-processes * + * working on a common directory * + ************************************************************ +------------------------------------------------------------------------------ + ORCA GTO INTEGRAL CALCULATION +------------------------------------------------------------------------------ +------------------------------------------------------------------------------ + ___ + / \ - P O W E R E D B Y - + / \ + | | | _ _ __ _____ __ __ + | | | | | | | / \ | _ \ | | / | + \ \/ | | | | / \ | | | | | | / / + / \ \ | |__| | / /\ \ | |_| | | |/ / + | | | | __ | / /__\ \ | / | \ + | | | | | | | | __ | | \ | |\ \ + \ / | | | | | | | | | |\ \ | | \ \ + \___/ |_| |_| |__| |__| |_| \__\ |__| \__/ + + - O R C A' S B I G F R I E N D - + & + - I N T E G R A L F E E D E R - + + v1 FN, 2020, v2 2021 +------------------------------------------------------------------------------ + + +Reading SHARK input file input.SHARKINP.tmp ... ok +---------------------- +SHARK INTEGRAL PACKAGE +---------------------- + +Number of atoms ... 1 +Number of basis functions ... 52 +Number of shells ... 20 +Maximum angular momentum ... 3 +Integral batch strategy ... SHARK/LIBINT Hybrid +RI-J (if used) integral strategy ... SPLIT-RIJ (Revised 2003 algorithm where possible) +Printlevel ... 1 +Contraction scheme used ... PARTIAL GENERAL contraction +Coulomb Range Separation ... NOT USED +Exchange Range Separation ... NOT USED +Finite Nucleus Model ... NOT USED +Auxiliary Coulomb fitting basis ... NOT available +Auxiliary J/K fitting basis ... NOT available +Auxiliary Correlation fitting basis ... NOT available +Auxiliary 'external' fitting basis ... NOT available +Integral threshold ... 2.500000e-11 +Primitive cut-off ... 2.500000e-12 +Primitive pair pre-selection threshold ... 2.500000e-12 + +Calculating pre-screening integrals ... done ( 0.0 sec) Dimension = 20 +Calculating pre-screening integrals (ORCA) ... done ( 0.1 sec) Dimension = 14 +Organizing shell pair data ... done ( 0.0 sec) +Shell pair information +Total number of shell pairs ... 210 +Shell pairs after pre-screening ... 210 +Total number of primitive shell pairs ... 256 +Primitive shell pairs kept ... 256 + la=0 lb=0: 66 shell pairs + la=1 lb=0: 44 shell pairs + la=1 lb=1: 10 shell pairs + la=2 lb=0: 33 shell pairs + la=2 lb=1: 12 shell pairs + la=2 lb=2: 6 shell pairs + la=3 lb=0: 22 shell pairs + la=3 lb=1: 8 shell pairs + la=3 lb=2: 6 shell pairs + la=3 lb=3: 3 shell pairs + +Calculating one electron integrals ... done ( 0.0 sec) +Calculating Nuclear repulsion ... done ( 0.0 sec) ENN= 0.000000000000 Eh + +SHARK setup successfully completed in 0.2 seconds + +Maximum memory used throughout the entire GTOINT-calculation: 16.0 MB + + + ************************************************************ + * Program running with 16 parallel MPI-processes * + * working on a common directory * + ************************************************************ +------------------------------------------------------------------------------- + ORCA SCF +------------------------------------------------------------------------------- + +------------ +SCF SETTINGS +------------ +Hamiltonian: + Ab initio Hamiltonian Method .... Hartree-Fock(GTOs) + + +General Settings: + Integral files IntName .... input + Hartree-Fock type HFTyp .... CASSCF + Total Charge Charge .... 0 + Multiplicity Mult .... 4 + Number of Electrons NEL .... 7 + Basis Dimension Dim .... 46 + Nuclear Repulsion ENuc .... 0.0000000000 Eh + + +Diagonalization of the overlap matrix: +Smallest eigenvalue ... 2.690e-02 +Time for diagonalization ... 0.000 sec +Threshold for overlap eigenvalues ... 1.000e-08 +Number of eigenvalues below threshold ... 0 +Time for construction of square roots ... 0.001 sec +Total time needed ... 0.001 sec + +Time for model grid setup = 0.007 sec + +------------------------------ +INITIAL GUESS: MODEL POTENTIAL +------------------------------ +Loading Hartree-Fock densities ... done +Calculating cut-offs ... done +Initializing the effective Hamiltonian ... done +Setting up the integral package (SHARK) ... done +Starting the Coulomb interaction ... done ( 0.0 sec) +Reading the grid ... done +Mapping shells ... done +Starting the XC term evaluation ... done ( 0.0 sec) +Transforming the Hamiltonian ... done ( 0.0 sec) +Diagonalizing the Hamiltonian ... done ( 0.0 sec) +Back transforming the eigenvectors ... done ( 0.0 sec) +Now organizing SCF variables ... done + ------------------ + INITIAL GUESS DONE ( 0.0 sec) + ------------------ + + + ... the calculation is a CASSCF calculation -I'm leaving here GOOD LUCK!!! + + + + ************************************************************ + * Program running with 16 parallel MPI-processes * + * working on a common directory * + ************************************************************ +------------------------------------------------------------------------------- + ORCA-CASSCF +------------------------------------------------------------------------------- + +Setting up the integral package ... done +Building the CAS space ... done (4 configurations for Mult=4) + +SYSTEM-SPECIFIC SETTINGS: +Number of active electrons ... 5 +Number of active orbitals ... 4 +Total number of electrons ... 7 +Total number of orbitals ... 46 + +Determined orbital ranges: + Internal 0 - 0 ( 1 orbitals) + Active 1 - 4 ( 4 orbitals) + External 5 - 45 ( 41 orbitals) +Number of rotation parameters ... 209 + +CI-STEP: +CI strategy ... General CI +Number of multiplicity blocks ... 1 +BLOCK 1 WEIGHT= 1.0000 + Multiplicity ... 4 + #(Configurations) ... 4 + #(CSFs) ... 4 + #(Roots) ... 1 + ROOT=0 WEIGHT= 1.000000 + + PrintLevel ... 1 + N(GuessMat) ... 512 + MaxDim(CI) ... 10 + MaxIter(CI) ... 64 + Energy Tolerance CI ... 2.50e-09 + Residual Tolerance CI ... 2.50e-09 + Shift(CI) ... 1.00e-04 + +INTEGRAL-TRANSFORMATION-STEP: + Algorithm ... EXACT + +ORBITAL-IMPROVEMENT-STEP: + Algorithm ... SuperCI(PT) + Default Parametrization ... CAYLEY + Act-Act rotations ... depends on algorithm used + + Note: SuperCI(PT) will ignore FreezeIE, FreezeAct and FreezeGrad. In general Default settings are encouraged. + In conjunction with ShiftUp, ShiftDn or GradScaling the performance of SuperCI(PT) is less optimal. + + MaxRot ... 2.00e-01 + Max. no of vectors (DIIS) ... 15 + DThresh (cut-off) metric ... 1.00e-06 + Switch step at gradient ... 3.00e-02 + Switch step at iteration ... 50 + Switch step to ... SuperCI(PT) + +SCF-SETTINGS: + Incremental ... on + RIJCOSX approximation ... off + RI-JK approximation ... off + AO integral handling ... DIRECT + Integral Neglect Thresh ... 2.50e-11 + Primitive cutoff TCut ... 2.50e-12 + Energy convergence tolerance ... 2.50e-08 + Orbital gradient convergence ... 2.50e-04 + Max. number of iterations ... 999 + + +FINAL ORBITALS: + Active Orbitals ... natural + Internal Orbitals ... canonical + External Orbitals ... canonical + +------------------ +CAS-SCF ITERATIONS +------------------ + + +MACRO-ITERATION 1: + --- Inactive Energy E0 = -44.72092697 Eh +CI-ITERATION 0: + -54.381848153 0.000000000000 ( 0.00) + CI-PROBLEM SOLVED + DENSITIES MADE + + <<<<<<<<<<<<<<<<<>>>>>>>>>>>>>>>>> + +BLOCK 1 MULT= 4 NROOTS= 1 +ROOT 0: E= -54.3818481526 Eh + 1.00000 [ 3]: 2111 + + <<<<<<<<<<<<<<<<<>>>>>>>>>>>>>>>>> + + E(CAS)= -54.381848153 Eh DE= 0.000000e+00 + --- Energy gap subspaces: Ext-Act = 0.358 Act-Int = 14.743 + N(occ)= 2.00000 1.00000 1.00000 1.00000 + ||g|| = 8.377747e-01 Max(G)= -7.011926e-01 Rot=45,0 + --- Orbital Update [SuperCI(PT)] + --- Canonicalize Internal Space + --- Canonicalize External Space + --- SX_PT (Skipped TA=0 IT=1): ||X|| = 0.097273197 Max(X)(6,2) = -0.044359639 + --- SFit(Active Orbitals) + +MACRO-ITERATION 2: + --- Inactive Energy E0 = -44.72879418 Eh +CI-ITERATION 0: + -54.396929340 0.000000000000 ( 0.00) + CI-PROBLEM SOLVED + DENSITIES MADE + E(CAS)= -54.396929340 Eh DE= -1.508119e-02 + --- Energy gap subspaces: Ext-Act = 0.317 Act-Int = 14.676 + N(occ)= 2.00000 1.00000 1.00000 1.00000 + ||g|| = 8.661958e-02 Max(G)= -4.686820e-02 Rot=45,1 + --- Orbital Update [SuperCI(PT)] + --- Canonicalize Internal Space + --- Canonicalize External Space + --- SX_PT (Skipped TA=0 IT=1): ||X|| = 0.018251693 Max(X)(6,2) = -0.008989526 + --- SFit(Active Orbitals) + +MACRO-ITERATION 3: + --- Inactive Energy E0 = -44.72888355 Eh +CI-ITERATION 0: + -54.397580561 0.000000000000 ( 0.00) + CI-PROBLEM SOLVED + DENSITIES MADE + E(CAS)= -54.397580561 Eh DE= -6.512206e-04 + --- Energy gap subspaces: Ext-Act = 0.318 Act-Int = 14.686 + N(occ)= 2.00000 1.00000 1.00000 1.00000 + ||g|| = 1.169199e-02 Max(G)= -3.787582e-03 Rot=17,0 + --- Orbital Update [SuperCI(PT)] + --- Canonicalize Internal Space + --- Canonicalize External Space + --- SX_PT (Skipped TA=0 IT=1): ||X|| = 0.004765813 Max(X)(8,2) = 0.002361881 + --- SFit(Active Orbitals) + +MACRO-ITERATION 4: + --- Inactive Energy E0 = -44.72891366 Eh +CI-ITERATION 0: + -54.397608742 0.000000000000 ( 0.00) + CI-PROBLEM SOLVED + DENSITIES MADE + E(CAS)= -54.397608742 Eh DE= -2.818090e-05 + --- Energy gap subspaces: Ext-Act = 0.316 Act-Int = 14.684 + N(occ)= 2.00000 1.00000 1.00000 1.00000 + ||g|| = 3.401689e-03 Max(G)= 1.928798e-03 Rot=45,0 + --- Orbital Update [SuperCI(PT)] + --- Canonicalize Internal Space + --- Canonicalize External Space + --- SX_PT (Skipped TA=0 IT=1): ||X|| = 0.000448352 Max(X)(5,1) = -0.000198017 + --- SFit(Active Orbitals) + +MACRO-ITERATION 5: + --- Inactive Energy E0 = -44.72890218 Eh +CI-ITERATION 0: + -54.397609514 0.000000000000 ( 0.00) + CI-PROBLEM SOLVED + DENSITIES MADE + E(CAS)= -54.397609514 Eh DE= -7.726311e-07 + --- Energy gap subspaces: Ext-Act = 0.316 Act-Int = 14.684 + N(occ)= 2.00000 1.00000 1.00000 1.00000 + ||g|| = 3.651368e-04 Max(G)= -2.086419e-04 Rot=45,1 + --- Orbital Update [SuperCI(PT)] + --- Canonicalize Internal Space + --- Canonicalize External Space + --- SX_PT (Skipped TA=0 IT=1): ||X|| = 0.000048550 Max(X)(5,1) = -0.000029015 + --- SFit(Active Orbitals) + +MACRO-ITERATION 6: + --- Inactive Energy E0 = -44.72890337 Eh +CI-ITERATION 0: + -54.397609522 0.000000000000 ( 0.00) + CI-PROBLEM SOLVED + DENSITIES MADE + E(CAS)= -54.397609522 Eh DE= -7.825491e-09 + --- Energy gap subspaces: Ext-Act = 0.316 Act-Int = 14.684 + N(occ)= 2.00000 1.00000 1.00000 1.00000 + ||g|| = 5.710511e-05 Max(G)= 3.612727e-05 Rot=45,1 + ---- THE CAS-SCF ENERGY HAS CONVERGED ---- + ---- THE CAS-SCF GRADIENT HAS CONVERGED ---- + --- FINALIZING ORBITALS --- + ---- DOING ONE FINAL ITERATION FOR PRINTING ---- + --- Forming Natural Orbitals + --- Canonicalize Internal Space + --- Canonicalize External Space + +MACRO-ITERATION 7: + --- Inactive Energy E0 = -44.72890337 Eh + --- All densities will be recomputed +CI-ITERATION 0: + -54.397609522 0.000000000000 ( 0.00) + CI-PROBLEM SOLVED + DENSITIES MADE + E(CAS)= -54.397609522 Eh DE= -1.004565e-10 + --- Energy gap subspaces: Ext-Act = 0.311 Act-Int = 14.684 + N(occ)= 2.00000 1.00000 1.00000 1.00000 + ||g|| = 5.710508e-05 Max(G)= 3.643662e-05 Rot=45,1 +-------------- +CASSCF RESULTS +-------------- + +Final CASSCF energy : -54.397609522 Eh -1480.2342 eV + +---------------- +ORBITAL ENERGIES +---------------- + + NO OCC E(Eh) E(eV) + 0 2.0000 -15.630414 -425.3252 + 1 2.0000 -0.946888 -25.7661 + 2 1.0000 -0.180692 -4.9169 + 3 1.0000 -0.180692 -4.9169 + 4 1.0000 -0.180692 -4.9169 + 5 0.0000 0.129931 3.5356 + 6 0.0000 0.137198 3.7333 + 7 0.0000 0.137198 3.7333 + 8 0.0000 0.137198 3.7333 + 9 0.0000 0.464734 12.6461 + 10 0.0000 0.464734 12.6461 + 11 0.0000 0.464734 12.6461 + 12 0.0000 0.464734 12.6461 + 13 0.0000 0.464734 12.6461 + 14 0.0000 0.779518 21.2118 + 15 0.0000 0.779518 21.2118 + 16 0.0000 0.779518 21.2118 + 17 0.0000 1.009605 27.4727 + 18 0.0000 1.496268 40.7155 + 19 0.0000 1.496268 40.7155 + 20 0.0000 1.496268 40.7155 + 21 0.0000 1.496268 40.7155 + 22 0.0000 1.496268 40.7155 + 23 0.0000 1.496268 40.7155 + 24 0.0000 1.496268 40.7155 + 25 0.0000 1.559115 42.4257 + 26 0.0000 1.559115 42.4257 + 27 0.0000 1.559115 42.4257 + 28 0.0000 1.559115 42.4257 + 29 0.0000 1.559115 42.4257 + 30 0.0000 3.350863 91.1816 + 31 0.0000 3.350863 91.1816 + 32 0.0000 3.350863 91.1816 + 33 0.0000 4.877040 132.7110 + 34 0.0000 4.877040 132.7110 + 35 0.0000 4.877040 132.7110 + 36 0.0000 4.877040 132.7110 + 37 0.0000 4.877040 132.7110 + 38 0.0000 4.877040 132.7110 + 39 0.0000 4.877040 132.7110 + 40 0.0000 5.059015 137.6628 + 41 0.0000 5.059015 137.6628 + 42 0.0000 5.059015 137.6628 + 43 0.0000 5.059015 137.6628 + 44 0.0000 5.059015 137.6628 + 45 0.0000 6.334698 172.3759 + + +--------------------------------------------- +CAS-SCF STATES FOR BLOCK 1 MULT= 4 NROOTS= 1 +--------------------------------------------- + +ROOT 0: E= -54.3976095224 Eh + 1.00000 [ 3]: 2111 + + +-------------- +DENSITY MATRIX +-------------- + + 0 1 2 3 + 0 2.000000 0.000000 0.000000 0.000000 + 1 0.000000 1.000000 0.000000 0.000000 + 2 0.000000 0.000000 1.000000 0.000000 + 3 0.000000 0.000000 0.000000 1.000000 +Trace of the electron density: 5.000000 +Extracting Spin-Density from 2-RDM (MULT=4) ... done + +------------------- +SPIN-DENSITY MATRIX +------------------- + + 0 1 2 3 + 0 0.000000 0.000000 0.000000 0.000000 + 1 0.000000 1.000000 0.000000 0.000000 + 2 0.000000 0.000000 1.000000 0.000000 + 3 0.000000 0.000000 0.000000 1.000000 +Trace of the spin density: 3.000000 + +----------------- +ENERGY COMPONENTS +----------------- + +One electron energy : -73.937937606 Eh -2011.9536 eV +Two electron energy : 19.540328083 Eh 531.7194 eV +Nuclear repulsion energy : 0.000000000 Eh 0.0000 eV + ---------------- + -54.397609522 + +Kinetic energy : 54.383096271 Eh 1479.8393 eV +Potential energy : -108.780705794 Eh -2960.0735 eV +Virial ratio : -2.000266871 + ---------------- + -54.397609522 + +Core energy : -44.728903374 Eh -1217.1353 eV + + +---------------------------- +LOEWDIN ORBITAL-COMPOSITIONS +---------------------------- + + 0 1 2 3 4 5 + -15.63041 -0.94689 -0.18069 -0.18069 -0.18069 0.12993 + 2.00000 2.00000 1.00000 1.00000 1.00000 0.00000 + -------- -------- -------- -------- -------- -------- + 0 N s 100.0 100.0 0.0 0.0 0.0 100.0 + 0 N pz 0.0 0.0 98.7 1.3 0.0 0.0 + 0 N px 0.0 0.0 1.3 98.7 0.0 0.0 + 0 N py 0.0 0.0 0.0 0.0 100.0 0.0 + + 6 7 8 9 10 11 + 0.13720 0.13720 0.13720 0.46473 0.46473 0.46473 + 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 + -------- -------- -------- -------- -------- -------- + 0 N pz 0.6 28.8 70.6 0.0 0.0 0.0 + 0 N px 0.2 70.6 29.2 0.0 0.0 0.0 + 0 N py 99.2 0.6 0.2 0.0 0.0 0.0 + 0 N dz2 0.0 0.0 0.0 0.0 1.2 86.4 + 0 N dxz 0.0 0.0 0.0 69.8 23.3 0.0 + 0 N dyz 0.0 0.0 0.0 3.5 0.0 11.6 + 0 N dx2y2 0.0 0.0 0.0 12.1 66.6 0.9 + 0 N dxy 0.0 0.0 0.0 14.6 8.9 1.2 + + 12 13 14 15 16 17 + 0.46473 0.46473 0.77952 0.77952 0.77952 1.00960 + 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 + -------- -------- -------- -------- -------- -------- + 0 N s 0.0 0.0 0.0 0.0 0.0 100.0 + 0 N pz 0.0 0.0 0.0 27.3 72.7 0.0 + 0 N px 0.0 0.0 0.1 72.6 27.3 0.0 + 0 N py 0.0 0.0 99.9 0.0 0.0 0.0 + 0 N dz2 0.9 11.5 0.0 0.0 0.0 0.0 + 0 N dxz 3.6 3.3 0.0 0.0 0.0 0.0 + 0 N dyz 1.2 83.7 0.0 0.0 0.0 0.0 + 0 N dx2y2 19.3 1.1 0.0 0.0 0.0 0.0 + 0 N dxy 75.0 0.3 0.0 0.0 0.0 0.0 + + 18 19 20 21 22 23 + 1.49627 1.49627 1.49627 1.49627 1.49627 1.49627 + 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 + -------- -------- -------- -------- -------- -------- + 0 N f0 5.6 24.2 37.4 21.3 4.3 2.9 + 0 N f+1 46.0 0.9 0.5 24.9 1.5 4.7 + 0 N f-1 18.8 40.5 9.7 5.5 0.0 0.5 + 0 N f+2 2.5 2.5 11.3 4.0 70.8 8.9 + 0 N f-2 1.7 9.1 3.0 18.4 20.1 29.2 + 0 N f+3 22.5 3.1 31.4 24.5 0.5 17.9 + 0 N f-3 2.8 19.7 6.7 1.3 2.8 35.9 + + 24 25 26 27 28 29 + 1.49627 1.55912 1.55912 1.55912 1.55912 1.55912 + 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 + -------- -------- -------- -------- -------- -------- + 0 N dz2 0.0 5.6 15.9 74.3 1.7 2.5 + 0 N dxz 0.0 12.7 2.5 0.9 6.7 77.2 + 0 N dyz 0.0 5.3 37.5 20.9 35.1 1.2 + 0 N dx2y2 0.0 65.9 18.1 0.9 0.0 15.1 + 0 N dxy 0.0 10.6 26.0 3.0 56.4 4.0 + 0 N f0 4.2 0.0 0.0 0.0 0.0 0.0 + 0 N f+1 21.5 0.0 0.0 0.0 0.0 0.0 + 0 N f-1 25.0 0.0 0.0 0.0 0.0 0.0 + 0 N f-2 18.5 0.0 0.0 0.0 0.0 0.0 + 0 N f-3 30.8 0.0 0.0 0.0 0.0 0.0 + + 30 31 32 33 34 35 + 3.35086 3.35086 3.35086 4.87704 4.87704 4.87704 + 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 + -------- -------- -------- -------- -------- -------- + 0 N pz 23.6 12.5 63.8 0.0 0.0 0.0 + 0 N px 56.8 8.5 34.6 0.0 0.0 0.0 + 0 N py 19.5 78.9 1.6 0.0 0.0 0.0 + 0 N f0 0.0 0.0 0.0 5.7 0.4 27.9 + 0 N f+1 0.0 0.0 0.0 5.5 0.0 0.0 + 0 N f-1 0.0 0.0 0.0 0.5 2.4 0.5 + 0 N f+2 0.0 0.0 0.0 36.3 53.6 2.9 + 0 N f-2 0.0 0.0 0.0 5.6 1.5 55.0 + 0 N f+3 0.0 0.0 0.0 12.8 0.1 0.3 + 0 N f-3 0.0 0.0 0.0 33.6 42.0 13.5 + + 36 37 38 39 40 41 + 4.87704 4.87704 4.87704 4.87704 5.05902 5.05902 + 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 + -------- -------- -------- -------- -------- -------- + 0 N dz2 0.0 0.0 0.0 0.0 44.5 6.2 + 0 N dxz 0.0 0.0 0.0 0.0 1.2 0.0 + 0 N dyz 0.0 0.0 0.0 0.0 3.8 33.6 + 0 N dx2y2 0.0 0.0 0.0 0.0 47.3 7.1 + 0 N dxy 0.0 0.0 0.0 0.0 3.2 53.1 + 0 N f0 8.9 0.1 3.3 53.6 0.0 0.0 + 0 N f+1 10.6 64.8 19.1 0.0 0.0 0.0 + 0 N f-1 1.1 26.1 66.5 3.0 0.0 0.0 + 0 N f+2 5.1 0.8 0.1 1.3 0.0 0.0 + 0 N f-2 0.1 0.0 1.3 36.6 0.0 0.0 + 0 N f+3 66.4 8.1 7.1 5.2 0.0 0.0 + 0 N f-3 7.9 0.1 2.6 0.3 0.0 0.0 + + 42 43 44 45 + 5.05902 5.05902 5.05902 6.33470 + 0.00000 0.00000 0.00000 0.00000 + -------- -------- -------- -------- + 0 N s 0.0 0.0 0.0 100.0 + 0 N dz2 32.3 16.9 0.0 0.0 + 0 N dxz 1.5 0.1 97.2 0.0 + 0 N dyz 19.7 41.9 1.1 0.0 + 0 N dx2y2 5.9 39.0 0.8 0.0 + 0 N dxy 40.7 2.1 0.9 0.0 + +---------------------------- +LOEWDIN REDUCED ACTIVE MOs +---------------------------- + + 0 1 2 3 4 5 + -15.63041 -0.94689 -0.18069 -0.18069 -0.18069 0.12993 + 2.00000 2.00000 1.00000 1.00000 1.00000 0.00000 + -------- -------- -------- -------- -------- -------- + 0 N s 100.0 100.0 0.0 0.0 0.0 100.0 + 0 N pz 0.0 0.0 98.7 1.3 0.0 0.0 + 0 N px 0.0 0.0 1.3 98.7 0.0 0.0 + 0 N py 0.0 0.0 0.0 0.0 100.0 0.0 + +------------------------------------------------------------------------------ + ORCA POPULATION ANALYSIS +------------------------------------------------------------------------------ +Input electron density ... input.scfp +Input spin density ... input.scfr +BaseName (.gbw .S,...) ... input + + ******************************** + * MULLIKEN POPULATION ANALYSIS * + ******************************** + +------------------------------------------ +MULLIKEN ATOMIC CHARGES AND SPIN DENSITIES +------------------------------------------ + 0 N : -0.000000 3.000000 +Sum of atomic charges : -0.0000000 +Sum of atomic spin densities: 3.0000000 + +--------------------------------------------------- +MULLIKEN REDUCED ORBITAL CHARGES AND SPIN DENSITIES +--------------------------------------------------- +CHARGE + 0 N s : 4.000000 s : 4.000000 + pz : 1.000000 p : 3.000000 + px : 1.000000 + py : 1.000000 + dz2 : 0.000000 d : 0.000000 + dxz : 0.000000 + dyz : 0.000000 + dx2y2 : 0.000000 + dxy : 0.000000 + f0 : 0.000000 f : 0.000000 + f+1 : 0.000000 + f-1 : 0.000000 + f+2 : 0.000000 + f-2 : 0.000000 + f+3 : 0.000000 + f-3 : 0.000000 + +SPIN + 0 N s : 0.000000 s : 0.000000 + pz : 1.000000 p : 3.000000 + px : 1.000000 + py : 1.000000 + dz2 : 0.000000 d : 0.000000 + dxz : 0.000000 + dyz : 0.000000 + dx2y2 : 0.000000 + dxy : 0.000000 + f0 : 0.000000 f : 0.000000 + f+1 : 0.000000 + f-1 : 0.000000 + f+2 : 0.000000 + f-2 : 0.000000 + f+3 : 0.000000 + f-3 : 0.000000 + + + ******************************* + * LOEWDIN POPULATION ANALYSIS * + ******************************* + +----------------------------------------- +LOEWDIN ATOMIC CHARGES AND SPIN DENSITIES +----------------------------------------- + 0 N : -0.000000 3.000000 + +-------------------------------------------------- +LOEWDIN REDUCED ORBITAL CHARGES AND SPIN DENSITIES +-------------------------------------------------- +CHARGE + 0 N s : 4.000000 s : 4.000000 + pz : 1.000000 p : 3.000000 + px : 1.000000 + py : 1.000000 + dz2 : 0.000000 d : 0.000000 + dxz : 0.000000 + dyz : 0.000000 + dx2y2 : 0.000000 + dxy : 0.000000 + f0 : 0.000000 f : 0.000000 + f+1 : 0.000000 + f-1 : 0.000000 + f+2 : 0.000000 + f-2 : 0.000000 + f+3 : 0.000000 + f-3 : 0.000000 + +SPIN + 0 N s : 0.000000 s : 0.000000 + pz : 1.000000 p : 3.000000 + px : 1.000000 + py : 1.000000 + dz2 : 0.000000 d : 0.000000 + dxz : 0.000000 + dyz : 0.000000 + dx2y2 : 0.000000 + dxy : 0.000000 + f0 : 0.000000 f : 0.000000 + f+1 : 0.000000 + f-1 : 0.000000 + f+2 : 0.000000 + f-2 : 0.000000 + f+3 : 0.000000 + f-3 : 0.000000 + + + ***************************** + * MAYER POPULATION ANALYSIS * + ***************************** + + NA - Mulliken gross atomic population + ZA - Total nuclear charge + QA - Mulliken gross atomic charge + VA - Mayer's total valence + BVA - Mayer's bonded valence + FA - Mayer's free valence + + ATOM NA ZA QA VA BVA FA + 0 N 7.0000 7.0000 -0.0000 3.0000 0.0000 3.0000 + + + +Transition Dipole Moments (a.u.) with input orbitals: +MO 0: + MO 2: 0.074753310 ( 0.008585038, 0.000026009, -0.074258695) + MO 3: 0.074753310 ( -0.074258616, -0.000109345, -0.008585067) + MO 4: 0.074753310 ( -0.000111609, 0.074753225, 0.000013280) +MO 1: + MO 2: 0.777510748 ( 0.089293158, 0.000270525, -0.772366248) + MO 3: 0.777510748 ( -0.772365423, -0.001137300, -0.089293461) + MO 4: 0.777510748 ( -0.001160843, 0.777509869, 0.000138122) +MO 2: +MO 3: +MO 4: + newgto N + 0 18 + 1 11420.000000000000 0.000522768355 + 2 1712.000000000000 0.004043208403 + 3 389.300000000000 0.020765798413 + 4 110.000000000000 0.080691244693 + 5 35.570000000000 0.232970767719 + 6 12.540000000000 0.433308995327 + 7 4.644000000000 0.347318098976 + 8 0.511800000000 -0.008504231668 + 9 11420.000000000000 -0.000000607139 + 10 1712.000000000000 -0.000004725125 + 11 389.300000000000 -0.000024412268 + 12 110.000000000000 -0.000097818014 + 13 35.570000000000 -0.000302719511 + 14 12.540000000000 -0.000697291235 + 15 4.644000000000 -0.000910761311 + 16 0.511800000000 0.003167386147 + 17 1.293000000000 0.042437946502 + 18 0.178700000000 0.006072346930 + 0 18 + 1 11420.000000000000 0.000002720308 + 2 1712.000000000000 0.000021039475 + 3 389.300000000000 0.000108058121 + 4 110.000000000000 0.000419889672 + 5 35.570000000000 0.001212300289 + 6 12.540000000000 0.002254791986 + 7 4.644000000000 0.001807324738 + 8 11420.000000000000 0.000115506572 + 9 1712.000000000000 0.000898942453 + 10 389.300000000000 0.004644368606 + 11 110.000000000000 0.018609615382 + 12 35.570000000000 0.057591576877 + 13 12.540000000000 0.132657791513 + 14 4.644000000000 0.173269902282 + 15 0.511800000000 -0.602586738479 + 16 1.293000000000 -0.151583562870 + 17 0.178700000000 -0.380619025879 + 18 0.057600000000 -0.006167374158 + 1 6 + 1 26.630000000000 0.014646107832 + 2 5.948000000000 0.091614549360 + 3 1.742000000000 0.298196552532 + 4 0.555000000000 0.500982554894 + 5 0.172500000000 0.327306035784 + 6 0.049100000000 0.015517087267 + end + +------------------------------------------------------------- + Forming the transition density ... done in 0.000164 sec +------------------------------------------------------------- + + + +========================================== +CASSCF UV, CD spectra and dipole moments +========================================== +------------------- +ABSORPTION SPECTRUM +------------------- + +Center of mass = ( 0.0000, 0.0000, 0.0000) +Nuclear contribution to the dipole moment = 0.000000, 0.000000, 0.000000 au + +Calculating the Dipole integrals ... done +Transforming integrals ... done +Calculating the Linear Momentum integrals ... done +Transforming integrals ... done +Calculating the Angular Momentum integrals ... done +Transforming integrals ... done + +------------------------------------------------------------------------------ + DIPOLE MOMENTS +------------------------------------------------------------------------------ + Root Block TX TY TZ |T| + (Debye) (Debye) (Debye) (Debye) +------------------------------------------------------------------------------ + 0 0 0.00000 0.00000 0.00000 0.00000 + +-------------- +CASSCF TIMINGS +-------------- + +Total time ... 7.2 sec +Sum of individual times ... 3.1 sec ( 42.6%) + +Calculation of AO operators + F(Core) operator ... 1.4 sec ( 18.9%) + G(Act) operator ... 0.3 sec ( 4.1%) + J(AO) operators ... 0.0 sec ( 0.0%) +Calculation of MO transformed quantities + J(MO) operators ... 0.1 sec ( 1.2%) + (pq|rs) integrals ... 0.0 sec ( 0.0%) + AO->MO one electron integrals ... 0.0 sec ( 0.0%) +Configuration interaction steps + CI-setup phase ... 0.0 sec ( 0.0%) + CI-solution phase ... 0.4 sec ( 6.0%) + Generation of densities ... 0.0 sec ( 0.0%) +Orbital improvement steps + Orbital gradient ... 0.9 sec ( 12.4%) + O(1) converger ... 0.0 sec ( 0.0%) +Properties ... 0.0 sec ( 0.0%) + SOC integral calculation ... 0.0 sec ( 0.0%) + SSC RMEs (incl. integrals) ... 0.0 sec ( 0.0%) + SOC RMEs ... 0.0 sec ( 0.0%) + +Maximum memory used throughout the entire CASSCF-calculation: 117.8 MB +Warning: no block have been defined for MRCI - copying CASSCF information! + + + ************************************************************ + * Program running with 16 parallel MPI-processes * + * working on a common directory * + ************************************************************ + +------------------------------------------------------------------------------ + ORCA MRCI +------------------------------------------------------------------------------ + +Transformed one-electron integrals ... input.cih.tmp +Transformed RI-integrals ... input.rijt.tmp +Output vectors ... input.mrci + +---------------- +MRCI-SETUP PHASE +---------------- + +GBW-Name ... input.gbw +IVO-Name ... input.ivo +HName ... input.H.tmp +SName ... input.S.tmp +CIHName ... input.cih.tmp +CIFName ... input.cif.tmp +MRCIName ... input.mrci +IntFiles ... input.rijt.tmp +LocName ... input.loc +MRCIInput ... input.mrciinp +Basis dimension ... 46 +Improved Virtual Orbitals ... OFF +Orbital localization ... OFF + +Figured out Orbital ranges +Set data to blocks + +----------------------- +FROZEN CORE FOCK MATRIX +----------------------- + +Improved virtual orbitals (IVOs) WILL NOT be constructed +Orbital Range is before PREP ... Int= 1- 0 Act= 1- 4 Ext= 5- 45 +Calculating Frozen Core Matrices ... (look at input.lastciprep) +Warning: FirstInternal=1 LastInternal=0 NInternals=0 - setting LastInternal for FI=-1 + +------------------------------------------------------------------------------ + ORCA CI-PREPARATION +------------------------------------------------------------------------------ +Reading the GBW file ... done + + +One-Electron Matrix ... input.H.tmp +GBW-File ... input.gbw +First MO in the CI ... 1 +Integral package used ... LIBINT +Reading the GBW file ... done + +Reading the one-electron matrix ... done +Forming inactive density ... done +Forming Fock matrix/matrices ... +Nuclear repulsion ... 0.000000 +Core repulsion ... 0.000000 +One-electron energy ... -48.843003 +Fock-energy ... -40.614803 +Final value ... -44.728903 +done +Transforming integrals ... done +Storing passive energy ... done ( -44.72890337 Eh) +The internal FI matrix is equal to the CIH matrix; storing it as such! + .... done with the Frozen Core Fock matrices +Final Orbital Range is now ... Int= 1- 0 Act= 1- 4 Ext= 5- 45 + +------------------------------ +PARTIAL COULOMB TRANSFORMATION +------------------------------ + +Dimension of the basis ... 46 +Number of internal MOs ... 45 (1-45) +Pair cutoff ... 2.500e-12 Eh +Number of AO pairs included in the trafo ... 1081 +Total Number of distinct AO pairs ... 1081 +Memory devoted for trafo ... 3200 MB +Memory needed per MO pair ... 0 MB +Max. Number of MO pairs treated together ... 388002 +Memory needed per MO ... 0 MB +Max. Number of MOs treated per batch ... 45 +Number Format for Storage ... Double (8 Byte) +Integral package used ... LIBINT + + --->>> The Coulomb operators (i,j|mue,nue) will be calculated + +Starting integral evaluation: +: : 1575 b 0 skpd 0.002 s ( 0.001 ms/b) +: 2100 b 0 skpd 0.002 s ( 0.001 ms/b) +: 1575 b 0 skpd 0.001 s ( 0.001 ms/b) +: 1050 b 0 skpd 0.002 s ( 0.002 ms/b) +: 1050 b 0 skpd 0.001 s ( 0.001 ms/b) +: 1260 b 0 skpd 0.001 s ( 0.001 ms/b) +: 840 b 0 skpd 0.002 s ( 0.003 ms/b) + 630 b 0 skpd 0.002 s ( 0.003 ms/b) +: 630 b 0 skpd 0.003 s ( 0.005 ms/b) +: 315 b 0 skpd 0.004 s ( 0.014 ms/b) +Collecting buffer AOJ + ... done with AO integral generation +Closing buffer AOJ ( 0.00 GB; CompressionRatio= 1.77) +Number of MO pairs included in the trafo ... 1035 + ... Now sorting integrals +IBATCH = 1 of 2 +IBATCH = 2 of 2 +Closing buffer JAO ( 0.01 GB; CompressionRatio= 1.00) +TOTAL TIME for half transformation ... 0.030 sec +AO-integral generation ... 0.020 sec +Half transformation ... 0.003 sec +J-integral sorting ... 0.007 sec +Collecting buffer JAO + +------------------- +FULL TRANSFORMATION +------------------- + +Processing MO 10 +Processing MO 20 +Processing MO 30 +Processing MO 40 +Full transformation done +Number of integrals made ... 536130 +Number of integrals stored ... 261508 +Timings: +Time for first half transformation ... 0.032 sec +Time for second half transformation ... 0.002 sec +Total time ... 0.037 sec + +------------------ +CI-BLOCK STRUCTURE +------------------ + +Number of CI-blocks ... 1 + +=========== +CI BLOCK 1 +=========== +Multiplicity ... 4 +Irrep ... -1 +Number of reference defs ... 1 + Reference 1: CAS(5,4) + +Excitation type ... CISD +Excitation flags for singles: + 1 1 1 1 +Excitation flags for doubles: + 1 1 1 / 1 1 1 / 1 1 1 + + + + -------------------------------------------------------------------- + -------------------- ALL SETUP TASKS ACCOMPLISHED ------------------ + -------------------- ( 0.258 sec) ------------------ + -------------------------------------------------------------------- + + + + ################################################### + # # + # M R C I # + # # + # TSel = 1.000e-06 Eh # + # TPre = 1.000e-04 # + # TIntCut = 1.000e-10 Eh # + # Extrapolation to unselected MR-CI by full MP2 # + # DAVIDSON-1 Correction to full CI # + # # + ################################################### + + +--------------------- +INTEGRAL ORGANIZATION +--------------------- + +Reading the one-Electron matrix ... done +E0 read was -44.728903374198 +Reading the internal Fock matrix ... done +Preparing the integral list ... done +Loading the full integral list ... done +Making the simple integrals ... done + + *************************************** + * CI-BLOCK 1 * + *************************************** + +Configurations with insufficient # of SOMOs WILL be rejected +Building a CAS(5,4) for multiplicity 4 +Reference Space: + Initial Number of Configurations : 4 + Internal Orbitals : 1 - 0 + Active Orbitals : 1 - 4 + External Orbitals : 5 - 45 +The number of CSFs in the reference is 4 +Calling MRPT_Selection with N(ref)=4 +------------------ +REFERENCE SPACE CI +------------------ + + Pre-diagonalization threshold : 1.000e-04 +Warning: Setting NGuessMat to 512 +N(ref-CFG)=4 N(ref-CSF)=4 + + ****Iteration 0**** + Lowest Energy : -54.397609522415 + Maximum Energy change : 54.397609522415 (vector 0) + Maximum residual norm : 0.000000000000 + + *** CONVERGENCE OF RESIDUAL NORM REACHED *** +Reference space selection using TPre= 1.00e-04 + + ... found 1 reference configurations (1 CSFs) + ... now redoing the reference space CI ... + +Warning: Setting NGuessMat to 512 +N(ref-CFG)=1 N(ref-CSF)=1 + + ****Iteration 0**** + Lowest Energy : -54.397609522415 + Maximum Energy change : 54.397609522415 (vector 0) + Maximum residual norm : 0.000000000000 + + *** CONVERGENCE OF RESIDUAL NORM REACHED *** + +---------- +CI-RESULTS +---------- + +The threshold for printing is 0.30 percent +The weights of configurations will be printed. The weights are summed over +all CSFs that belong to a given configuration before printing + +STATE 0: Energy= -54.397609522 Eh RefWeight= 1.0000 0.00 eV 0.0 cm**-1 + 1.0000 : h---h---[2111] + +------------------------------ +MR-PT SELECTION TSel= 1.00e-06 +------------------------------ + + +Setting reference configurations WITHOUT use of symmetry +Building active patterns WITHOUT use of symmetry + +Selection will be done from 1 spatial configurations + ( 0) Refs : Sel: 1CFGs/ 1CSFs Gen: 1CFGs/ 1CSFs ( 0.000 sec) +Building active space densities ... 0.002 sec +Building active space Fock operators ... 0.000 sec + ( 1) (p,q)->(r,s): Sel: 3CFGs/ 3CSFs Gen: 3CFGs/ 3CSFs ( 0.001 sec) + ( 5) (p,-)->(a,-): Sel: 164CFGs/ 287CSFs Gen: 164CFGs/ 287CSFs ( 0.001 sec) + ( 6) (i,-)->(a,-): Sel: 0CFGs/ 0CSFs Gen: 0CFGs/ 0CSFs ( 0.001 sec) + ( 7) (i,j)->(p,a): Sel: 0CFGs/ 0CSFs Gen: 0CFGs/ 0CSFs ( 0.000 sec) + ( 8) (i,p)->(q,a): Sel: 0CFGs/ 0CSFs Gen: 0CFGs/ 0CSFs ( 0.001 sec) + ( 9) (p,q)->(r,a): Sel: 108CFGs/ 108CSFs Gen: 369CFGs/ 369CSFs ( 0.001 sec) + (10) (i,p)->(a,b): Sel: 0CFGs/ 0CSFs Gen: 0CFGs/ 0CSFs ( 0.001 sec) + (11) (p,q)->(a,b): Sel: 1279CFGs/ 3493CSFs Gen: 5904CFGs/ 15744CSFs ( 0.002 sec) + (12) (i,j)->(a,b): Sel: 0CFGs/ 0CSFs Gen: 0CFGs/ 0CSFs ( 2.945 sec) + +Selection results: +Total number of generated configurations: 6441 +Number of selected configurations : 1555 ( 24.1%) +Total number of generated CSFs : 16404 +Number of selected CSFS : 3892 ( 23.7%) + +The selected tree structure: +Number of selected Internal Portions : 4 +Number of selected Singly External Portions: 13 + average number of VMOs/Portion : 19.43 + percentage of selected singly externals : 50.94 +Number of selected Doubly External Portions: 7 + average number of VMOs/Portion : 159.88 + percentage of selected doubly externals : 22.28 + +Diagonal second order perturbation results: +State E(tot) E(0)+E(1) E2(sel) E2(unsel) + Eh Eh Eh Eh +---------------------------------------------------------------- + 0 -54.503566265 -54.397609522 -0.105685 -0.000272 + +Computing the reference space Hamiltonian ... done (DIM=1) +Storing the reference space Hamiltonian ... done +Finding start and stop indices ... done +Collecting additional information ... done +Entering the DIIS solver section +------------------------ +MULTIROOT DIIS CI SOLVER +------------------------ + +Number of CSFs ... 3892 +Number of configurations ... 1555 +Maximum number of DIIS vectors stored ... 5 +Level shift ... 0.20 +Convergence tolerance on energies ... 2.500e-07 +Convergence tolerance on residual ... 2.500e-07 +Partitioning used ... MOELLER-PLESSET + + + ****Iteration 0**** + State 0: E= -54.466179124 Ec=-0.068569602 R= 0.299648465 W0= 0.96521 + Max energy change = 6.8570e-02 Eh + Max Residual Norm = 2.9965e-01 + + ****Iteration 1**** + State 0: E= -54.512269425 Ec=-0.114659903 R= 0.002512143 W0= 0.95744 + Max energy change = 4.6090e-02 Eh + Max Residual Norm = 2.5121e-03 + + ****Iteration 2**** + State 0: E= -54.512978160 Ec=-0.115368637 R= 0.000325639 W0= 0.96224 + Max energy change = 7.0873e-04 Eh + Max Residual Norm = 3.2564e-04 + + ****Iteration 3**** + State 0: E= -54.513035558 Ec=-0.115426036 R= 0.000008152 W0= 0.96143 + Max energy change = 5.7399e-05 Eh + Max Residual Norm = 8.1520e-06 + + ****Iteration 4**** + State 0: E= -54.513039684 Ec=-0.115430162 R= 0.000001364 W0= 0.96186 + Max energy change = 4.1259e-06 Eh + Max Residual Norm = 1.3636e-06 + + ****Iteration 5**** + State 0: residual converged + State 0: E= -54.513040333 Ec=-0.115430811 R= 0.000000068 W0= 0.96184 + Max energy change = 0.0000e+00 Eh + Max Residual Norm = 6.7607e-08 + *** Convergence of energies reached *** + *** Convergence of residual reached *** + *** All vectors converged *** +Returned from DIIS section + +---------------------------------------------- +MULTI-REFERENCE/MULTI-ROOT DAVIDSON CORRECTION +---------------------------------------------- + + +Summary of multireference corrections: + +Root W(ref) E(MR-CI) E(ref) Delta-E None Davidson-1 Davidson-2 Siegbahn Pople +------------------------------------------------------------------------------------------------------------ + 0 0.962 -54.513040333 -54.397609522 0.115430811 0.000000 -0.004405 -0.004769 -0.004580 -0.002769 +------------------------------------------------------------------------------------------------------------ +Active option = Davidson-1 + +Unselected CSF estimate: +Full relaxed MR-MP2 calculation ... + +Selection will be done from 1 spatial configurations + +Selection will be done from 1 spatial configurations + +Selection will be done from 1 spatial configurations +done +Selected MR-MP2 energies ... + + Root= 0 E(unsel)= -0.000272010 + +---------- +CI-RESULTS +---------- + +The threshold for printing is 0.30 percent +The weights of configurations will be printed. The weights are summed over +all CSFs that belong to a given configuration before printing + +STATE 0: Energy= -54.517717250 Eh RefWeight= 0.9618 0.00 eV 0.0 cm**-1 + 0.9618 : h---h---[2111] +Now choosing densities with flags StateDens=3 and TransDens=1 NStates(total)=1 +State density of the lowest state in each block NStateDens= 2 +GS to excited state transition electron densities NTransDens=0 +NDens(total)=2 +All lowest density information prepared Cnt(Dens)=2 +GS to ES state electron density information prepared Cnt(Dens)=2 + +------------------ +DENSITY GENERATION +------------------ + + ... generating densities (input.mrci.vec0) ... o.k. +MRCI-Population analysis: looping over 2 densities +Found state electron-density state=0 block=0 +Found state spin-density state=0 block=0 +------------------------------------------------------------------------------ + ORCA POPULATION ANALYSIS +------------------------------------------------------------------------------ +Input electron density ... input.state_0_block_0.el.tmp +Input spin density ... input.state_0_block_0.spin.tmp +BaseName (.gbw .S,...) ... input + + ******************************** + * MULLIKEN POPULATION ANALYSIS * + ******************************** + +------------------------------------------ +MULLIKEN ATOMIC CHARGES AND SPIN DENSITIES +------------------------------------------ + 0 N : -0.000000 3.000000 +Sum of atomic charges : -0.0000000 +Sum of atomic spin densities: 3.0000000 + +--------------------------------------------------- +MULLIKEN REDUCED ORBITAL CHARGES AND SPIN DENSITIES +--------------------------------------------------- +CHARGE + 0 N s : 3.975014 s : 3.975014 + pz : 0.998985 p : 2.996924 + px : 0.998969 + py : 0.998970 + dz2 : 0.005285 d : 0.026369 + dxz : 0.005270 + dyz : 0.005265 + dx2y2 : 0.005292 + dxy : 0.005257 + f0 : 0.000241 f : 0.001693 + f+1 : 0.000239 + f-1 : 0.000253 + f+2 : 0.000241 + f-2 : 0.000236 + f+3 : 0.000234 + f-3 : 0.000251 + +SPIN + 0 N s : 0.021881 s : 0.021881 + pz : 0.984931 p : 2.954801 + px : 0.984937 + py : 0.984933 + dz2 : 0.004517 d : 0.022525 + dxz : 0.004496 + dyz : 0.004491 + dx2y2 : 0.004526 + dxy : 0.004496 + f0 : 0.000113 f : 0.000793 + f+1 : 0.000112 + f-1 : 0.000119 + f+2 : 0.000112 + f-2 : 0.000109 + f+3 : 0.000110 + f-3 : 0.000117 + + + ******************************* + * LOEWDIN POPULATION ANALYSIS * + ******************************* + +----------------------------------------- +LOEWDIN ATOMIC CHARGES AND SPIN DENSITIES +----------------------------------------- + 0 N : -0.000000 3.000000 + +-------------------------------------------------- +LOEWDIN REDUCED ORBITAL CHARGES AND SPIN DENSITIES +-------------------------------------------------- +CHARGE + 0 N s : 3.975014 s : 3.975014 + pz : 0.998985 p : 2.996924 + px : 0.998969 + py : 0.998970 + dz2 : 0.005285 d : 0.026369 + dxz : 0.005270 + dyz : 0.005265 + dx2y2 : 0.005292 + dxy : 0.005257 + f0 : 0.000241 f : 0.001693 + f+1 : 0.000239 + f-1 : 0.000253 + f+2 : 0.000241 + f-2 : 0.000236 + f+3 : 0.000234 + f-3 : 0.000251 + +SPIN + 0 N s : 0.021881 s : 0.021881 + pz : 0.984931 p : 2.954801 + px : 0.984937 + py : 0.984933 + dz2 : 0.004517 d : 0.022525 + dxz : 0.004496 + dyz : 0.004491 + dx2y2 : 0.004526 + dxy : 0.004496 + f0 : 0.000113 f : 0.000793 + f+1 : 0.000112 + f-1 : 0.000119 + f+2 : 0.000112 + f-2 : 0.000109 + f+3 : 0.000110 + f-3 : 0.000117 + + + ***************************** + * MAYER POPULATION ANALYSIS * + ***************************** + + NA - Mulliken gross atomic population + ZA - Total nuclear charge + QA - Mulliken gross atomic charge + VA - Mayer's total valence + BVA - Mayer's bonded valence + FA - Mayer's free valence + + ATOM NA ZA QA VA BVA FA + 0 N 7.0000 7.0000 -0.0000 3.1783 0.0000 3.1783 + + + + +--------------------- +CI-EXCITATION SPECTRA +--------------------- + +Center of mass = ( 0.0000, 0.0000, 0.0000) + +Nuclear contribution to the dipole moment= 0.000000, 0.000000, 0.000000 au + +Calculating the Dipole integrals ... done +Transforming integrals ... done +Calculating the Linear Momentum integrals ... done +Transforming integrals ... done +Calculating the Angular momentum integrals ... done +Transforming integrals ... done + +------------------------------------------------------------------------------------------ + ABSORPTION SPECTRUM +------------------------------------------------------------------------------------------ + States Energy Wavelength fosc T2 TX TY TZ + (cm-1) (nm) (D**2) (D) (D) (D) +------------------------------------------------------------------------------------------ + +------------------------------------------------------------------------------ + CD SPECTRUM +------------------------------------------------------------------------------ + States Energy Wavelength R*T RX RY RZ + (cm-1) (nm) (1e40*sgs) (au) (au) (au) +------------------------------------------------------------------------------ + +------------------------------------------------------------------------------ + STATE DIPOLE MOMENTS +------------------------------------------------------------------------------ + Root Block TX TY TZ |T| + (Debye) (Debye) (Debye) (Debye) +------------------------------------------------------------------------------ + 0 0 0.00000 0.00000 0.00000 0.00000 + +Maximum memory used throughout the entire MRCI-calculation: 76.9 MB + +------------------------- -------------------- +FINAL SINGLE POINT ENERGY -54.517717249721 +------------------------- -------------------- + + + *************************************** + * ORCA property calculations * + *************************************** + + --------------------- + Active property flags + --------------------- + (+) Dipole Moment + + +------------------------------------------------------------------------------ + ORCA ELECTRIC PROPERTIES CALCULATION +------------------------------------------------------------------------------ + +Dipole Moment Calculation ... on +Quadrupole Moment Calculation ... off +Polarizability Calculation ... off +GBWName ... input.gbw +Electron density ... input.scfp +The origin for moment calculation is the CENTER OF MASS = ( 0.000000, 0.000000 0.000000) + +------------- +DIPOLE MOMENT +------------- + X Y Z +Electronic contribution: 0.00000 0.00000 0.00000 +Nuclear contribution : 0.00000 0.00000 0.00000 + ----------------------------------------- +Total Dipole Moment : 0.00000 0.00000 0.00000 + ----------------------------------------- +Magnitude (a.u.) : 0.00000 +Magnitude (Debye) : 0.00000 + + + +-------------------- +Rotational spectrum +-------------------- + +Rotational constants in cm-1: 0.000000 0.000000 0.000000 +Rotational constants in MHz : 0.000000 0.000000 0.000000 + + Dipole components along the rotational axes: +x,y,z [a.u.] : 0.000000 0.000000 0.000000 +x,y,z [Debye]: 0.000000 0.000000 0.000000 + + + +Timings for individual modules: + +Sum of individual times ... 17.846 sec (= 0.297 min) +GTO integral calculation ... 0.534 sec (= 0.009 min) 3.0 % +SCF iterations ... 0.410 sec (= 0.007 min) 2.3 % +CASSCF iterations ... 9.882 sec (= 0.165 min) 55.4 % +Multireference CI module ... 7.020 sec (= 0.117 min) 39.3 % + ****ORCA TERMINATED NORMALLY**** +TOTAL RUN TIME: 0 days 0 hours 0 minutes 18 seconds 202 msec diff --git a/arkane/ess/adapter.py b/arkane/ess/adapter.py index 9b25b1e2c1..f0a30c932a 100644 --- a/arkane/ess/adapter.py +++ b/arkane/ess/adapter.py @@ -45,10 +45,11 @@ class ESSAdapter(ABC): An abstract ESS Adapter class """ - def __init__(self, path, check_for_errors=True): + def __init__(self, path, check_for_errors=True, scratch_directory=None): self.path = path if check_for_errors: self.check_for_errors() + self.scratch_directory = scratch_directory if scratch_directory is not None else os.path.join(os.path.abspath('.'), str('scratch')) @abstractmethod def check_for_errors(self): @@ -174,7 +175,7 @@ def get_symmetry_properties(self): coordinates, atom_numbers, _ = self.load_geometry() unique_id = '0' # Just some name that the SYMMETRY code gives to one of its jobs # Scratch directory that the SYMMETRY code writes its files in: - scr_dir = os.path.join(os.path.abspath('.'), str('scratch')) + scr_dir = self.scratch_directory if not os.path.exists(scr_dir): os.makedirs(scr_dir) try: diff --git a/arkane/ess/factory.py b/arkane/ess/factory.py index 8e50390093..ca0baee26c 100644 --- a/arkane/ess/factory.py +++ b/arkane/ess/factory.py @@ -61,6 +61,7 @@ def register_ess_adapter(ess: str, def ess_factory(fullpath: str, check_for_errors: bool = True, + scratch_directory: str = None, ) -> Type[ESSAdapter]: """ A factory generating the ESS adapter corresponding to ``ess_adapter``. @@ -106,4 +107,4 @@ def ess_factory(fullpath: str, raise InputError(f'The file at {fullpath} could not be identified as a ' f'Gaussian, Molpro, Orca, Psi4, QChem, or TeraChem log file.') - return _registered_ess_adapters[ess_name](path=fullpath, check_for_errors=check_for_errors) + return _registered_ess_adapters[ess_name](path=fullpath, check_for_errors=check_for_errors, scratch_directory=scratch_directory) diff --git a/arkane/ess/molpro.py b/arkane/ess/molpro.py index 35fcfbb00c..01be43adac 100644 --- a/arkane/ess/molpro.py +++ b/arkane/ess/molpro.py @@ -371,6 +371,9 @@ def load_energy(self, zpe_scale_factor=1.): if 'CCSD' in line and 'energy=' in line: e_elect = float(line.split()[-1]) break + if 'RS2C' in line and 'energy' in line: + e_elect = float(line.split()[-1]) + break if e_elect is None and mrci: # No Davidson correction is given, search for MRCI energy read_e_elect = False @@ -435,10 +438,10 @@ def load_negative_frequency(self): if len(freqs) == 1: return -float(freqs[0]) elif len(freqs) > 1: - logging.info('More than one imaginary frequency in Molpro output file {0}.'.format(self.path)) + logging.info(f'More than one imaginary frequency in Molpro output file {self.path}.') return -float(freqs[0]) else: - raise LogError('Unable to find imaginary frequency in Molpro output file {0}'.format(self.path)) + raise LogError(f'Unable to find imaginary frequency in Molpro output file {self.path}') def load_scan_energies(self): """ @@ -458,7 +461,8 @@ def get_T1_diagnostic(self): if 'T1 diagnostic: ' in line: items = line.split() return float(items[-1]) - raise LogError('Unable to find T1 diagnostic in energy file: {0}'.format(self.path)) + logging.warning(f'Unable to find T1 diagnostic in energy file: {self.path}') + return None def get_D1_diagnostic(self): """ @@ -472,7 +476,8 @@ def get_D1_diagnostic(self): if 'D1 diagnostic: ' in line: items = line.split() return float(items[-1]) - raise LogError('Unable to find D1 diagnostic in energy file: {0}'.format(self.path)) + logging.warning(f'Unable to find D1 diagnostic in energy file: {self.path}') + return None def load_scan_pivot_atoms(self): """Not implemented for Molpro""" diff --git a/arkane/ess/orca.py b/arkane/ess/orca.py index e80d5ad180..a538f4dea3 100644 --- a/arkane/ess/orca.py +++ b/arkane/ess/orca.py @@ -109,6 +109,9 @@ def load_force_constant_matrix(self): The units of the returned force constants are J/m^2. If no force constant matrix can be found, ``None`` is returned. """ + n_atoms = self.get_number_of_atoms() + if n_atoms == 1: + return None hess_files = list() for (_, _, files) in os.walk(os.path.dirname(self.path)): for file_ in files: @@ -196,7 +199,7 @@ def load_conformer(self, symmetry=None, spin_multiplicity=0, optical_isomers=Non you can use the `symmetry` parameter to substitute your own value; if not provided, the value in the Orca log file will be adopted. """ - freq, mmass, rot, unscaled_frequencies = [], [], [], [] + freq, mmass, rot, unscaled_frequencies, modes = [], [], [], [], [] e0 = 0.0 if optical_isomers is None or symmetry is None: @@ -230,7 +233,7 @@ def load_conformer(self, symmetry=None, spin_multiplicity=0, optical_isomers=Non symbols = [symbol_by_number[i] for i in number] inertia = get_principal_moments_of_inertia(coord, numbers=number, symbols=symbols) inertia = list(inertia[0]) - if len(inertia): + if len(inertia) and not all(i == 0.0 for i in inertia): if any(i == 0.0 for i in inertia): inertia.remove(0.0) rot.append(LinearRotor(inertia=(inertia, "amu*angstrom^2"), symmetry=symmetry)) @@ -241,7 +244,11 @@ def load_conformer(self, symmetry=None, spin_multiplicity=0, optical_isomers=Non mmass.append(translation) # Take only the last modes found (in the event of multiple jobs). - modes = [mmass[-1], rot[-1], freq[-1]] + modes = [mmass[-1]] + if len(rot): + modes.append(rot[-1]) + if len(freq): + modes.append(freq[-1]) return Conformer(E0=(e0 * 0.001, "kJ/mol"), modes=modes, diff --git a/documentation/source/users/rmg/input.rst b/documentation/source/users/rmg/input.rst index 38dead4517..fbbff65940 100644 --- a/documentation/source/users/rmg/input.rst +++ b/documentation/source/users/rmg/input.rst @@ -59,8 +59,8 @@ ThermoLibrary field must be with respect to the :file:`$RMG/RMG-database/input/t directory. .. note:: - Checks during the initialization are maid to avoid users to use "liquid thermo librairies" in gas phase simulations or to use - "liquid phase libraries" obtained in another solvent that the one defined in the input file in liquid phase simulations. + Checks during the initialization are made to avoid users using "liquid thermo libraries" in gas phase simulations or using + "liquid phase libraries" obtained in another solvent than the one defined in the input file in liquid phase simulations. .. _reactionlibraries: diff --git a/documentation/source/users/rmg/installation/anacondaDeveloper.rst b/documentation/source/users/rmg/installation/anacondaDeveloper.rst index 4a79244d0c..7dbcfb6677 100644 --- a/documentation/source/users/rmg/installation/anacondaDeveloper.rst +++ b/documentation/source/users/rmg/installation/anacondaDeveloper.rst @@ -4,26 +4,7 @@ Installation by Source Using Anaconda Environment for Unix-based Systems: Linux and Mac OSX ******************************************************************************************* -#. Install the `conda` package manager, if you do not already have it (or Anaconda). - Select one of the following options: - - a. Users of Fedora Linux and Red Hat derivatives (RHEL, CentOS Stream) may install from the official repositories and EPEL, respectively, with the command :: - - sudo dnf install conda - - b. All other users, download and install `Miniconda `_. - - The download will be a .sh file with a name like ``Miniconda3-latest-Linux-x86_64.sh``. - Open a terminal in the same directory as this file, and type the following to install Conda - (replace the name of your .sh file below). :: - - bash Miniconda3-latest-Linux-x86_64.sh - - **When prompted to append Anaconda to your PATH, select or type Yes**. - Install the Conda folder inside your home directory - (typically ``/home/YourUsername/`` in Linux and ``/Users/YourUsername`` in Mac). - - Note that you should reinitialize or restart your terminal in order for the changes to take effect, as the installer will tell you. +#. Install the `conda` package manager via `miniforge`, if you do not already have it (or Anaconda), by following the `Miniforge installation instructions `_. #. There are a few system-level dependencies which are required and should not be installed via Conda. These include `Git `_ for version control, `GNU Make `_, and the C and C++ compilers from the `GNU Compiler Collection (GCC) `_ for compiling RMG. diff --git a/documentation/source/users/rmg/installation/anacondaUser.rst b/documentation/source/users/rmg/installation/anacondaUser.rst index 1c42d02e28..286f77db14 100644 --- a/documentation/source/users/rmg/installation/anacondaUser.rst +++ b/documentation/source/users/rmg/installation/anacondaUser.rst @@ -5,26 +5,7 @@ Binary Installation Using Anaconda for Unix-Based Systems: Linux and Mac OSX **************************************************************************** -#. Install the `conda` package manager, if you do not already have it (or Anaconda). - Select one of the following options: - - a. Users of Fedora Linux and Red Hat derivatives (RHEL, CentOS Stream) may install from the official repositories and EPEL, respectively, with the command :: - - sudo dnf install conda - - b. All other users, download and install `Miniconda `_. - - The download will be a .sh file with a name like ``Miniconda3-latest-Linux-x86_64.sh``. - Open a terminal in the same directory as this file, and type the following to install Conda - (replace the name of your .sh file below). :: - - bash Miniconda3-latest-Linux-x86_64.sh - - **When prompted to append Anaconda to your PATH, select or type Yes**. - Install the Conda folder inside your home directory - (typically ``/home/YourUsername/`` in Linux and ``/Users/YourUsername`` in Mac). - - Note that you should reinitialize or restart your terminal in order for the changes to take effect, as the installer will tell you. +#. Install the `conda` package manager via `miniforge`, if you do not already have it (or Anaconda), by following the `Miniforge installation instructions `_. #. Install both RMG and the RMG-database binaries through the terminal. Dependencies will be installed automatically. It is safest to make a new conda environment for RMG and its dependencies. Type the following command into the terminal to create the new environment named 'rmg_env' containing the latest stable version of the RMG program and its database. :: diff --git a/environment.yml b/environment.yml index 48a4da34a3..da15b2dfe3 100644 --- a/environment.yml +++ b/environment.yml @@ -16,10 +16,10 @@ # made dependency list more explicit (@JacksonBurns). # - October 16, 2023 Switched RDKit and descripatastorus to conda-forge, # moved diffeqpy to pip and (temporarily) removed chemprop -# +# - April 17, 2024 Limit versions of cclib at advice of maintainers. +# - August 4, 2024 Restricted pyrms to <2 name: rmg_env channels: - - defaults - rmg - conda-forge - cantera @@ -44,7 +44,8 @@ dependencies: - coolprop - cantera::cantera=2.6 - conda-forge::mopac - - conda-forge::cclib >=1.6.3,<1.8.0 + # see https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2639#issuecomment-2050292972 + - conda-forge::cclib >=1.6.3,<1.9 - conda-forge::openbabel >= 3 - conda-forge::rdkit >=2022.09.1 @@ -88,7 +89,7 @@ dependencies: # packages we maintain - rmg::pydas >=1.0.3 - rmg::pydqed >=1.0.3 - - rmg::pyrms + - rmg::pyrms <2 - rmg::symmetry # packages we would like to stop maintaining (and why) @@ -100,8 +101,8 @@ dependencies: # Note that _some other_ dep. in this list requires diffeqpy in its recipe # which will cause it to be downloaded from the rmg conda channel -# conda mutex metapackage - - nomkl +# configure packages to use OpenBLAS instead of Intel MKL + - blas=*=openblas # additional packages that are required, but not specified here (and why) # pydqed, pydas, mopac, and likely others require a fortran compiler (specifically gfortran) diff --git a/rmgpy/molecule/draw.py b/rmgpy/molecule/draw.py index 6dd6c8b46b..e18611b92a 100644 --- a/rmgpy/molecule/draw.py +++ b/rmgpy/molecule/draw.py @@ -1644,6 +1644,7 @@ def __init__(self, options=None): self.options = MoleculeDrawer().options.copy() self.options.update({ 'arrowLength': 36, + 'drawReversibleArrow': True }) if options: self.options.update(options) @@ -1744,11 +1745,30 @@ def draw(self, reaction, file_format, path=None): rxn_cr.save() rxn_cr.set_source_rgba(0.0, 0.0, 0.0, 1.0) rxn_cr.set_line_width(1.0) - rxn_cr.move_to(rxn_x + 8, rxn_top + 0.5 * rxn_height) - rxn_cr.line_to(rxn_x + arrow_width - 8, rxn_top + 0.5 * rxn_height) - rxn_cr.move_to(rxn_x + arrow_width - 14, rxn_top + 0.5 * rxn_height - 3.0) - rxn_cr.line_to(rxn_x + arrow_width - 8, rxn_top + 0.5 * rxn_height) - rxn_cr.line_to(rxn_x + arrow_width - 14, rxn_top + 0.5 * rxn_height + 3.0) + if self.options['drawReversibleArrow'] and reaction.reversible: # draw double harpoons + TOP_HARPOON_Y = rxn_top + (0.5 * rxn_height - 1.75) + BOTTOM_HARPOON_Y = rxn_top + (0.5 * rxn_height + 1.75) + + # Draw top harpoon + rxn_cr.move_to(rxn_x + 8, TOP_HARPOON_Y) + rxn_cr.line_to(rxn_x + arrow_width - 8, TOP_HARPOON_Y) + rxn_cr.move_to(rxn_x + arrow_width - 14, TOP_HARPOON_Y - 3.0) + rxn_cr.line_to(rxn_x + arrow_width - 8, TOP_HARPOON_Y) + + # Draw bottom harpoon + rxn_cr.move_to(rxn_x + arrow_width - 8, BOTTOM_HARPOON_Y) + rxn_cr.line_to(rxn_x + 8, BOTTOM_HARPOON_Y) + rxn_cr.move_to(rxn_x + 14, BOTTOM_HARPOON_Y + 3.0) + rxn_cr.line_to(rxn_x + 8, BOTTOM_HARPOON_Y) + + + else: # draw forward arrow + rxn_cr.move_to(rxn_x + 8, rxn_top + 0.5 * rxn_height) + rxn_cr.line_to(rxn_x + arrow_width - 8, rxn_top + 0.5 * rxn_height) + rxn_cr.move_to(rxn_x + arrow_width - 14, rxn_top + 0.5 * rxn_height - 3.0) + rxn_cr.line_to(rxn_x + arrow_width - 8, rxn_top + 0.5 * rxn_height) + rxn_cr.line_to(rxn_x + arrow_width - 14, rxn_top + 0.5 * rxn_height + 3.0) + rxn_cr.stroke() rxn_cr.restore() rxn_x += arrow_width diff --git a/rmgpy/qm/molecule.py b/rmgpy/qm/molecule.py index 81d771781d..45cf457b67 100644 --- a/rmgpy/qm/molecule.py +++ b/rmgpy/qm/molecule.py @@ -408,19 +408,28 @@ def parse(self): parser = self.get_parser(self.output_file_path) parser.logger.setLevel( logging.ERROR - ) # cf. http://cclib.sourceforge.net/wiki/index.php/Using_cclib#Additional_information - parser.rotcons = ( + ) # cf. https://cclib.github.io/index.html#how-to-use-cclib + parser.molmass = None # give it an attribute and it won't delete it, leaving it on the parser object + parser.rotcons = ( # for cclib < 1.8.0 [] - ) # give it an attribute and it won't delete it, leaving it on the parser object - parser.molmass = None # give it an attribute and it won't delete it, leaving it on the parser object - cclib_data = parser.parse() + ) + parser.rotconsts = ( # for cclib >= 1.8.0 + [] + ) + cclib_data = parser.parse() # fills in either parser.rotcons or parser.rotconsts but not both + assert bool(parser.rotconsts) != bool(parser.rotcons) + if parser.rotcons: # for cclib < 1.8.0 + cclib_data.rotcons = ( + parser.rotcons + ) + else: # for cclib >= 1.8.0 + cclib_data.rotconsts = ( + parser.rotconsts + ) radical_number = self.molecule.get_radical_count() - cclib_data.rotcons = ( - parser.rotcons - ) # this hack required because rotcons not part of a default cclib data object cclib_data.molmass = ( parser.molmass - ) # this hack required because rotcons not part of a default cclib data object + ) # this hack required because molmass is not part of a default cclib data object qm_data = parse_cclib_data( cclib_data, radical_number + 1 ) # Should `radical_number+1` be `self.molecule.multiplicity` in the next line of code? It's the electronic ground state degeneracy. diff --git a/rmgpy/qm/qmdata.py b/rmgpy/qm/qmdata.py index 976649ddf7..6bf0b6a44e 100644 --- a/rmgpy/qm/qmdata.py +++ b/rmgpy/qm/qmdata.py @@ -98,7 +98,11 @@ def parse_cclib_data(cclib_data, ground_state_degeneracy): molecular_mass = None energy = (cclib_data.scfenergies[-1], 'eV/molecule') atomic_numbers = cclib_data.atomnos - rotational_constants = (cclib_data.rotcons[-1], 'cm^-1') + if hasattr(cclib_data, 'rotconsts'): + rotational_constants = (cclib_data.rotconsts[-1], 'cm^-1') + else: + rotational_constants = (cclib_data.rotcons[-1], 'cm^-1') + atom_coords = (cclib_data.atomcoords[-1], 'angstrom') frequencies = (cclib_data.vibfreqs, 'cm^-1') diff --git a/test/arkane/ess/molproTest.py b/test/arkane/ess/molproTest.py index fcc1c27ea8..d0b1b3c559 100644 --- a/test/arkane/ess/molproTest.py +++ b/test/arkane/ess/molproTest.py @@ -144,6 +144,14 @@ def test_load_non_f12_e0(self): e0 = molpro_log.load_energy() assert round(abs(e0 - -301585968.58196217), 7) == 0 + def test_load_rs2c_e0(self): + """ + Load E0 for RS2C from a molpro output file + """ + molpro_log = MolproLog(os.path.join(self.data_path, "HO2_RS2C.out")) + e0 = molpro_log.load_energy() + assert round(abs(e0 - -395663227.2323160), 6) == 0 + def test_load_mrci_e0(self): """ Load the MRCI and MRCI+Davidson energies from a molpro output file diff --git a/test/arkane/ess/orcaTest.py b/test/arkane/ess/orcaTest.py index bf9a0e878f..616fa80057 100644 --- a/test/arkane/ess/orcaTest.py +++ b/test/arkane/ess/orcaTest.py @@ -65,6 +65,8 @@ def test_number_of_atoms_from_orca_log(self): Uses Orca log files to test that number of atoms can be properly read. """ + log = OrcaLog(os.path.join(self.data_path, "N_MRCI.log")) + assert log.get_number_of_atoms() == 1 log = OrcaLog(os.path.join(self.data_path, "Orca_opt_freq_test.log")) assert log.get_number_of_atoms() == 3 log = OrcaLog(os.path.join(self.data_path, "Orca_dlpno_test.log")) @@ -144,6 +146,13 @@ def test_load_modes_from_orca_log(self): assert len([mode for mode in conformer.modes if isinstance(mode, HarmonicOscillator)]) == 1 assert len(unscaled_frequencies) == 3 + log = OrcaLog(os.path.join(self.data_path, "N_MRCI.log")) + conformer, unscaled_frequencies = log.load_conformer() + assert len([mode for mode in conformer.modes if isinstance(mode, IdealGasTranslation)]) == 1 + assert len([mode for mode in conformer.modes if isinstance(mode, NonlinearRotor)]) == 0 + assert len([mode for mode in conformer.modes if isinstance(mode, HarmonicOscillator)]) == 0 + assert len(unscaled_frequencies) == 0 + def test_spin_multiplicity_from_orca_log(self): """ Test that molecular degrees of freedom can be properly read. diff --git a/test/regression/minimal_surface/input.py b/test/regression/minimal_surface/input.py index ddfea2dd87..9054a32827 100644 --- a/test/regression/minimal_surface/input.py +++ b/test/regression/minimal_surface/input.py @@ -104,7 +104,8 @@ toleranceKeepInEdge=0.0, toleranceMoveToCore=1e-1, toleranceInterruptSimulation=0.1, - maximumEdgeSpecies=100000, + maximumEdgeSpecies=100, + maxNumSpecies=10, ) options( units='si',