From 8abb8cb5730263edae9a4d68c53dae0958170274 Mon Sep 17 00:00:00 2001 From: nwchemgit Date: Thu, 15 Jun 2023 02:15:53 +0000 Subject: [PATCH] website changes on Thu_Jun_15_02:15:52_2023 --- 1D-RISM.html | 6 ------ 404.html | 6 ------ ARMCI.html | 6 ------ Aba2.html | 6 ------ Abm2.html | 6 ------ Ama2.html | 6 ------ Amm2.html | 6 ------ Analysis.html | 6 ------ Archived-Forum.html | 6 ------ AvailableBasisSets.html | 6 ------ Basis.html | 6 ------ Benchmarks.html | 6 ------ Bq.html | 6 ------ C2.html | 6 ------ C222.html | 6 ------ C222_1.html | 6 ------ C2Sc.html | 6 ------ C2Sm.html | 6 ------ CCCA_method.html | 6 ------ CCSD.html | 6 ------ COSMO-Solvation-Model.html | 6 ------ Capabilities.html | 6 ------ Cartesian-coordinate-input.html | 6 ------ Cc.html | 6 ------ Ccc2.html | 6 ------ Ccca.html | 6 ------ Cccm.html | 6 ------ Charge.html | 6 ------ Citation.html | 6 ------ Classical-Methods.html | 6 ------ Cm.html | 6 ------ Cmc2_1.html | 6 ------ Cmca.html | 6 ------ Cmcm.html | 6 ------ Cmm2.html | 6 ------ Cmma.html | 6 ------ Cmmm.html | 6 ------ Compiling-NWChem.html | 6 ------ Constraints.html | 6 ------ Containers.html | 6 ------ Current_events.html | 6 ------ DNTMC.html | 6 ------ DPLOT.html | 6 ------ Density-Functional-Theory-for-Molecules.html | 6 ------ ...nctional-Theory-for-Molecules_bibtext.html | 6 ------ Developer.html | 6 ------ Developer_Team.html | 6 ------ Download.html | 6 ------ ECCE_PRINT.html | 6 ------ ECHO.html | 6 ------ ECP.html | 6 ------ EMSL_Arrows.html | 6 ------ EPR-pNMR.html | 6 ------ ESP.html | 6 ------ Electron-Transfer.html | 6 ------ Electronic-Structure-Analysis.html | 6 ------ Examples.html | 6 ------ Excited-State-Calculations.html | 6 ------ F-43c.html | 6 ------ F-43m.html | 6 ------ F222.html | 6 ------ F23.html | 6 ------ F432.html | 6 ------ F4_132.html | 6 ------ FAQ.html | 6 ------ FCIDUMP.html | 6 ------ Fd-3.html | 6 ------ Fd-3c.html | 6 ------ Fd-3m.html | 6 ------ Fdd2.html | 6 ------ Fddd.html | 6 ------ Fm-3.html | 6 ------ Fm-3c.html | 6 ------ Fm-3m.html | 6 ------ Fmm2.html | 6 ------ Fmmm.html | 6 ------ Format_of_MD_Files.html | 6 ------ Forum.html | 6 ------ Forum_search.html | 6 ------ Forum_search2.html | 6 ------ GW.html | 6 ------ Gaussian-Basis-AIMD.html | 6 ------ Geometry-Optimization.html | 6 ------ Geometry-examples.html | 6 ------ Geometry-load.html | 6 ------ Geometry.html | 6 ------ Getting-Started.html | 6 ------ Guidelines-for-Authors.html | 6 ------ Hartree-Fock-Theory-for-Molecules.html | 6 ------ Hessians-and-Vibrational-Frequencies.html | 6 ------ Home.html | 6 ------ Hybrid-Approaches.html | 6 ------ I-4.html | 6 ------ I-42d.html | 6 ------ I-42m.html | 6 ------ I-43d.html | 6 ------ I-43m.html | 6 ------ I-4c2.html | 6 ------ I-4m2.html | 6 ------ I222.html | 6 ------ I23.html | 6 ------ I2_12_12_1.html | 6 ------ I2_13.html | 6 ------ I4.html | 6 ------ I422.html | 6 ------ I432.html | 6 ------ I4Sm.html | 6 ------ I4Smcm.html | 6 ------ I4Smmm.html | 6 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Overview.html | 6 ------ P-1.html | 6 ------ P-3.html | 6 ------ P-31c.html | 6 ------ P-31m.html | 6 ------ P-3c1.html | 6 ------ P-3m1.html | 6 ------ P-4.html | 6 ------ P-42_1c.html | 6 ------ P-42_1m.html | 6 ------ P-42c.html | 6 ------ P-42m.html | 6 ------ P-43m.html | 6 ------ P-43n.html | 6 ------ P-4b2.html | 6 ------ P-4c2.html | 6 ------ P-4m2.html | 6 ------ P-4n2.html | 6 ------ P-6.html | 6 ------ P-62c.html | 6 ------ P-62m.html | 6 ------ P-6c2.html | 6 ------ P-6m2.html | 6 ------ P1.html | 6 ------ P2.html | 6 ------ P222.html | 6 ------ P222_1.html | 6 ------ P23.html | 6 ------ P2Sc.html | 6 ------ P2Sm.html | 6 ------ P2_1.html | 6 ------ P2_12_12.html | 6 ------ P2_12_12_1.html | 6 ------ P2_13.html | 6 ------ P2_1Sc.html | 6 ------ P2_1Sm.html | 6 ------ P3.html | 6 ------ P312.html | 6 ------ P31c.html | 6 ------ P31m.html | 6 ------ P321.html | 6 ------ P3_1.html | 6 ------ P3_112.html | 6 ------ P3_121.html | 6 ------ P3_2.html | 6 ------ P3_212.html | 6 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P4bm.html | 6 ------ P4cc.html | 6 ------ P4mm.html | 6 ------ P4nc.html | 6 ------ P6.html | 6 ------ P622.html | 6 ------ P6Sm.html | 6 ------ P6Smcc.html | 6 ------ P6Smmm.html | 6 ------ P6_1.html | 6 ------ P6_122.html | 6 ------ P6_2.html | 6 ------ P6_222.html | 6 ------ P6_3.html | 6 ------ P6_322.html | 6 ------ P6_3Sm.html | 6 ------ P6_3Smcm.html | 6 ------ P6_3Smmc.html | 6 ------ P6_3cm.html | 6 ------ P6_3mc.html | 6 ------ P6_4.html | 6 ------ P6_422.html | 6 ------ P6_5.html | 6 ------ P6_522.html | 6 ------ P6cc.html | 6 ------ P6mm.html | 6 ------ PDF.html | 6 ------ Pa-3.html | 6 ------ Pba2.html | 6 ------ Pbam.html | 6 ------ Pban.html | 6 ------ Pbca.html | 6 ------ Pbcm.html | 6 ------ Pbcn.html | 6 ------ Pc.html | 6 ------ Pca2_1.html | 6 ------ Pcc2.html | 6 ------ Pcca.html | 6 ------ Pccm.html | 6 ------ Pccn.html | 6 ------ Permanent_Dir.html | 6 ------ Plane-Wave-Density-Functional-Theory.html | 6 ------ Pm-3.html | 6 ------ Pm-3m.html | 6 ------ Pm-3n.html | 6 ------ Pm.html | 6 ------ Pma2.html | 6 ------ Pmc2_1.html | 6 ------ Pmm2.html | 6 ------ Pmma.html | 6 ------ Pmmm.html | 6 ------ Pmmn.html | 6 ------ Pmn2_1.html | 6 ------ Pmna.html | 6 ------ Pn-3.html | 6 ------ Pn-3m.html | 6 ------ Pn-3n.html | 6 ------ Pna2_1.html | 6 ------ Pnc2.html | 6 ------ Pnma.html | 6 ------ Pnn2.html | 6 ------ Pnna.html | 6 ------ Pnnm.html | 6 ------ Pnnn.html | 6 ------ Potential-Energy-Surface-Analysis.html | 6 ------ Prepare.html | 6 ------ Print_Noprint.html | 6 ------ Properties.html | 6 ------ Python.html | 6 ------ QMMM.html | 6 ------ QMMM_Appendix.html | 6 ------ QMMM_Dynamics.html | 6 ------ QMMM_ESP.html | 6 ------ QMMM_Excited_States.html | 6 ------ QMMM_FEP_Example.html | 6 ------ QMMM_Free_Energy.html | 6 ------ QMMM_Input_File.html | 6 ------ QMMM_MM_Parameters.html | 6 ------ QMMM_Parameters.html | 6 ------ QMMM_Preparation_Prerequisites.html | 6 ------ QMMM_QMMM_Parameters.html | 6 ------ QMMM_QM_Parameters.html | 6 ------ QMMM_References.html | 6 ------ QMMM_Restart_and_Topology_Files.html | 6 ------ QMMM_Transition_States.html | 6 ------ QM_Parameters.html | 6 ------ Qmmm_NEB_Calculations.html | 6 ------ Qmmm_convergence.html | 6 ------ Qmmm_density.html | 6 ------ Qmmm_freq.html | 6 ------ Qmmm_maxiter.html | 6 ------ Qmmm_ncycles.html | 6 ------ Qmmm_nsamples.html | 6 ------ Qmmm_optimization.html | 6 ------ Qmmm_preparation_basic.html | 6 ------ Qmmm_preparation_constraints.html | 6 ------ Qmmm_preparation_solvation.html | 6 ------ Qmmm_region.html | 6 ------ Qmmm_rename.html | 6 ------ Qmmm_xyz.html | 6 ------ Quantum-Mechanical-Methods.html | 6 ------ Quantum-Molecular-Dynamics.html | 6 ------ Quantum.html | 6 ------ R-3.html | 6 ------ R-3c.html | 6 ------ R-3m.html | 6 ------ R3.html | 6 ------ R32.html | 6 ------ R3c.html | 6 ------ R3m.html | 6 ------ RT-TDDFT.html | 6 ------ Relativistic-All-electron-Approximations.html | 6 ------ Running.html | 6 ------ SELCI.html | 6 ------ SET.html | 6 ------ SMD-Model.html | 6 ------ STOP.html | 6 ------ SYMMETRY----Symmetry-Group-Input.html | 6 ------ ...ttice-parameters-for-periodic-systems.html | 6 ------ Sample.html | 6 ------ Scratch_Dir.html | 6 ------ Software-supporting-NWChem.html | 6 ------ Solvation-Models.html | 6 ------ Start_Restart.html | 6 ------ Supplementary-Information.html | 6 ------ System-Description.html | 6 ------ TASK.html | 6 ------ TCE.html | 6 ------ TITLE.html | 6 ------ Top-level.html | 6 ------ Tutorial-Athens2018.html | 6 ------ Tutorial-Slides.html | 6 ------ Tutorials.html | 6 ------ UNSET.html | 6 ------ VEM-Model.html | 6 ------ VSCF.html | 6 ------ Vibration.html | 6 ------ ZCOORD-Forcing-internal-coordinates.html | 6 ------ ZMATRIX-Z-matrix-input.html | 6 ------ ZMATRIX.html | 6 ------ _Footer.html | 6 ------ _Sidebar.html | 6 ------ index.html | 14 ++++---------- mepgs.html | 6 ------ print_page.html | 14 ++++---------- projects.html | 6 ------ qmmm_bq_zone.html | 6 ------ qmmm_eref.html | 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--- a/SYMMETRY----Symmetry-Group-Input.html +++ b/SYMMETRY----Symmetry-Group-Input.html @@ -34,12 +34,6 @@ - - - - - - diff --git a/SYSTEM----Lattice-parameters-for-periodic-systems.html b/SYSTEM----Lattice-parameters-for-periodic-systems.html index cb8c8a0cce..bbf6a34d42 100644 --- a/SYSTEM----Lattice-parameters-for-periodic-systems.html +++ b/SYSTEM----Lattice-parameters-for-periodic-systems.html @@ -34,12 +34,6 @@ - - - - - - diff --git a/Sample.html b/Sample.html index b4176c69c8..5dbac62372 100644 --- a/Sample.html +++ b/Sample.html @@ -38,12 +38,6 @@ - - - - - - diff --git a/Scratch_Dir.html b/Scratch_Dir.html index 68606607fa..d898950cae 100644 --- a/Scratch_Dir.html +++ b/Scratch_Dir.html @@ -34,12 +34,6 @@ - - - - - - diff --git a/Software-supporting-NWChem.html b/Software-supporting-NWChem.html index fde5670942..639bf207ff 100644 --- a/Software-supporting-NWChem.html +++ b/Software-supporting-NWChem.html @@ -38,12 +38,6 @@ - - - - - - diff --git a/Solvation-Models.html b/Solvation-Models.html index 60fe81fabf..360f2c529e 100644 --- a/Solvation-Models.html +++ b/Solvation-Models.html @@ -38,12 +38,6 @@ - - - - - - diff --git a/Start_Restart.html b/Start_Restart.html index 39582fcd1f..6cbd00ddc4 100644 --- a/Start_Restart.html +++ b/Start_Restart.html @@ -34,12 +34,6 @@ - - - - - - diff --git a/Supplementary-Information.html b/Supplementary-Information.html index ac2b9ab2d7..19a3eaece7 100644 --- a/Supplementary-Information.html +++ b/Supplementary-Information.html @@ -34,12 +34,6 @@ - - - - - - diff --git a/System-Description.html b/System-Description.html index 7fd6704392..b3b1afc747 100644 --- a/System-Description.html +++ b/System-Description.html @@ -34,12 +34,6 @@ - - - - - - diff --git a/TASK.html b/TASK.html index 9bc7617e9a..66a5facf7c 100644 --- a/TASK.html +++ b/TASK.html @@ -34,12 +34,6 @@ - - - - - - diff --git a/TCE.html b/TCE.html index 216955c82d..6191e46146 100644 --- a/TCE.html +++ b/TCE.html @@ -38,12 +38,6 @@ - - - - - - diff --git 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diff --git a/_Footer.html b/_Footer.html index baf65f53d6..c277196fbc 100644 --- a/_Footer.html +++ b/_Footer.html @@ -34,12 +34,6 @@ - - - - - - diff --git a/_Sidebar.html b/_Sidebar.html index cb0457d5ac..964e0b1fa8 100644 --- a/_Sidebar.html +++ b/_Sidebar.html @@ -34,12 +34,6 @@ - - - - - - diff --git a/index.html b/index.html index 78958a571c..fcf3f42f4f 100644 --- a/index.html +++ b/index.html @@ -36,12 +36,6 @@ - - - - - - @@ -2358,10 +2352,10 @@

NWChem: Ope
  • Properties and relativistic effects

    • -

    NWChem is actively developed by a consortium of developers and -maintained by the The Environmental Molecular Sciences Laboratory (EMSL) located at the Pacific -Northwest National Laboratory (PNNL) in Washington -State. Researchers interested in contributing to NWChem should review +

    NWChem is actively developed by a consortium of developers and maintained by
    +The Environmental Molecular Sciences Laboratory (EMSL) located at the Pacific
    +Northwest National Laboratory (PNNL) in Washington State. Researchers interested +in contributing to NWChem should review the Developers page. The code is distributed as open-source under the terms of the Educational Community License diff --git a/mepgs.html b/mepgs.html index 570c3ffca3..9920d92586 100644 --- a/mepgs.html +++ b/mepgs.html @@ -34,12 +34,6 @@ - - - - - - diff --git a/print_page.html b/print_page.html index 91166803b2..eb2b915a9a 100644 --- a/print_page.html +++ b/print_page.html @@ -34,12 +34,6 @@ - - - - - - @@ -2848,10 +2842,10 @@

    Table of Contents

  • Properties and relativistic effects

    • -

    NWChem is actively developed by a consortium of developers and -maintained by the The Environmental Molecular Sciences Laboratory (EMSL) located at the Pacific -Northwest National Laboratory (PNNL) in Washington -State. Researchers interested in contributing to NWChem should review +

    NWChem is actively developed by a consortium of developers and maintained by
    +The Environmental Molecular Sciences Laboratory (EMSL) located at the Pacific
    +Northwest National Laboratory (PNNL) in Washington State. Researchers interested +in contributing to NWChem should review the Developers page. The code is distributed as open-source under the terms of the Educational Community License diff --git a/projects.html b/projects.html index f9761a080b..1d96462fc6 100644 --- a/projects.html +++ b/projects.html @@ -34,12 +34,6 @@ - - - - - - diff --git a/qmmm_bq_zone.html b/qmmm_bq_zone.html index f70a2f0d09..3d8afff524 100644 --- a/qmmm_bq_zone.html +++ b/qmmm_bq_zone.html @@ -34,12 +34,6 @@ - - - - - - diff --git a/qmmm_eref.html b/qmmm_eref.html index 225348d149..ceef47001a 100644 --- a/qmmm_eref.html +++ b/qmmm_eref.html @@ -34,12 +34,6 @@ - - - - - - diff --git a/qmmm_example3.html b/qmmm_example3.html index 55e6a15023..4d432159ac 100644 --- a/qmmm_example3.html +++ b/qmmm_example3.html @@ -34,12 +34,6 @@ - - - - - - diff --git a/qmmm_example6.html b/qmmm_example6.html index 93bf911a30..3ab7a54d83 100644 --- a/qmmm_example6.html +++ b/qmmm_example6.html @@ -34,12 +34,6 @@ - - - - - - diff --git a/qmmm_example7.html b/qmmm_example7.html index 204c8dd276..5b0e5b8a32 100644 --- a/qmmm_example7.html +++ b/qmmm_example7.html @@ -34,12 +34,6 @@ - - - - - - diff --git a/qmmm_introduction.html b/qmmm_introduction.html index 26d6ad37d9..2bec031d8b 100644 --- a/qmmm_introduction.html +++ b/qmmm_introduction.html @@ -38,12 +38,6 @@ - - - - - - diff --git a/qmmm_link_atoms.html b/qmmm_link_atoms.html index 38c8874660..f0f98f4f09 100644 --- a/qmmm_link_atoms.html +++ b/qmmm_link_atoms.html @@ -34,12 +34,6 @@ - - - - - - diff --git a/qmmm_link_ecp.html b/qmmm_link_ecp.html index 79ce72d9ab..bc4ff0c566 100644 --- a/qmmm_link_ecp.html +++ b/qmmm_link_ecp.html @@ -34,12 +34,6 @@ - - - - - - diff --git a/qmmm_load.html b/qmmm_load.html index 7e389c5bdc..888c93e678 100644 --- a/qmmm_load.html +++ b/qmmm_load.html @@ -34,12 +34,6 @@ - - - - - - diff --git a/qmmm_method.html b/qmmm_method.html index a67b8c5363..426cb11d56 100644 --- a/qmmm_method.html +++ b/qmmm_method.html @@ -34,12 +34,6 @@ - - - - - - diff --git a/qmmm_mm_charges.html b/qmmm_mm_charges.html index ea06278130..b7addebbac 100644 --- a/qmmm_mm_charges.html +++ b/qmmm_mm_charges.html @@ -34,12 +34,6 @@ - - - - - - diff --git a/qmmm_sp_energy.html b/qmmm_sp_energy.html index 829c284f17..64176e773e 100644 --- a/qmmm_sp_energy.html +++ b/qmmm_sp_energy.html @@ -38,12 +38,6 @@ - - - - - - diff --git a/qmmm_sp_property.html b/qmmm_sp_property.html index db062f89de..7e7083e9b6 100644 --- a/qmmm_sp_property.html +++ b/qmmm_sp_property.html @@ -38,12 +38,6 @@ - - - - - - diff --git a/search/search_index.json b/search/search_index.json index 92c73fc993..efab8b5588 100644 --- a/search/search_index.json +++ b/search/search_index.json @@ -1 +1 @@ -{"config":{"lang":["en"],"separator":"[\\s\\-]+","pipeline":["stopWordFilter"]},"docs":[{"location":"index.html","title":"NWChem: Open Source High-Performance Computational Chemistry","text":"

    The NWChem software contains computational chemistry tools that are scalable both in their ability to efficiently treat large scientific problems, and in their use of available computing resources from high-performance parallel supercomputers to conventional workstation clusters.

    NWChem can handle:

    NWChem is actively developed by a consortium of developers and maintained by the The Environmental Molecular Sciences Laboratory (EMSL) located at the Pacific Northwest National Laboratory (PNNL) in Washington State. Researchers interested in contributing to NWChem should review the Developers page. The code is distributed as open-source under the terms of the Educational Community License version 2.0 (ECL 2.0).

    The NWChem development strategy is focused on providing new and essential scientific capabilities to its users in the areas of kinetics and dynamics of chemical transformations, chemistry at interfaces and in the condensed phase, and enabling innovative and integrated research at EMSL. At the same time continued development is needed to enable NWChem to effectively utilize architectures of tens of petaflops and beyond.

    "},{"location":"index.html#latest-nwchem-release","title":"Latest NWChem release","text":"

    NWChem version 7.2.0 is the latest release available for download from the link https://github.com/nwchemgit/nwchem/releases.

    "},{"location":"index.html#emsl-arrows","title":"EMSL Arrows","text":"

    Are you just learning how to use NWChem and would like to have an easy way to generate input decks, check your output decks against a large database of calculations, perform simple thermochemistry calculations, calculate the NMR and IR spectra of a modest size molecule, or just try out nwchem before installing it? EMSL Arrows scientific service can help. A web api to EMSL Arrows is now available for alpha testing.

    for more information see EMSL Arrows - an easier way to use nwchem and EMSL Arrows

    EMSL Arrows API

    "},{"location":"index.html#nwchem-documentation","title":"NWChem Documentation","text":""},{"location":"index.html#nwchem-citation","title":"NWChem Citation","text":"

    Please cite the following reference when publishing results obtained with NWChem:

    E. Apr\u00e0, E. J. Bylaska, W. A. de Jong, N. Govind, K. Kowalski, T. P. Straatsma, M. Valiev, H. J. J. van Dam, Y. Alexeev, J. Anchell, V. Anisimov, F. W. Aquino, R. Atta-Fynn, J. Autschbach, N. P. Bauman, J. C. Becca, D. E. Bernholdt, K. Bhaskaran-Nair, S. Bogatko, P. Borowski, J. Boschen, J. Brabec, A. Bruner, E. Cau\u00ebt, Y. Chen, G. N. Chuev, C. J. Cramer, J. Daily, M. J. O. Deegan, T. H. Dunning Jr., M. Dupuis, K. G. Dyall, G. I. Fann, S. A. Fischer, A. Fonari, H. Fr\u00fcchtl, L. Gagliardi, J. Garza, N. Gawande, S. Ghosh, K. Glaesemann, A. W. G\u00f6tz, J. Hammond, V. Helms, E. D. Hermes, K. Hirao, S. Hirata, M. Jacquelin, L. Jensen, B. G. Johnson, H. J\u00f3nsson, R. A. Kendall, M. Klemm, R. Kobayashi, V. Konkov, S. Krishnamoorthy, M. Krishnan, Z. Lin, R. D. Lins, R. J. Littlefield, A. J. Logsdail, K. Lopata, W. Ma, A. V. Marenich, J. Martin del Campo, D. Mejia-Rodriguez, J. E. Moore, J. M. Mullin, T. Nakajima, D. R. Nascimento, J. A. Nichols, P. J. Nichols, J. Nieplocha, A. Otero-de-la-Roza, B. Palmer, A. Panyala, T. Pirojsirikul, B. Peng, R. Peverati, J. Pittner, L. Pollack, R. M. Richard, P. Sadayappan, G. C. Schatz, W. A. Shelton, D. W. Silverstein, D. M. A. Smith, T. A. Soares, D. Song, M. Swart, H. L. Taylor, G. S. Thomas, V. Tipparaju, D. G. Truhlar, K. Tsemekhman, T. Van Voorhis, \u00c1. V\u00e1zquez-Mayagoitia, P. Verma, O. Villa, A. Vishnu, K. D. Vogiatzis, D. Wang, J. H. Weare, M. J. Williamson, T. L. Windus, K. Woli\u0144ski, A. T. Wong, Q. Wu, C. Yang, Q. Yu, M. Zacharias, Z. Zhang, Y. Zhao, and R. J. Harrison, \u201cNWChem: Past, present, and future\u201d, The Journal of Chemical Physics 152, 184102 (2020). DOI: 10.1063/5.0004997

    "},{"location":"1D-RISM.html","title":"1-D RISM","text":""},{"location":"1D-RISM.html#overview","title":"Overview","text":"

    The 1D-RISM module in NWChem provides description of solvated systems following one-dimensional reference interaction site of model of Chandler and Anderson. Similar to ab-initio density-functional theory, 1D-RISM can be thought of as an approach where discrete particle representation of solvent degrees of freedom is replaced by average density field. Unlike traditional continuum solvation model, this density based representation is inherently inhomogenous and incorporates specific molecular features of the solvent. In the current implementation, 1D-RISM is not directly coupled to QM calculations but presumed to be used as a post processing step after QM calculations which provide ESP point charges for a given solute geometry.

    Then parameters for 1D-RISM calculations are defined in the rism input block

    rism\n\u00a0\u00a0solute\u00a0configuration\u00a0<filename>\n\u00a0\u00a0vdw\u00a0[rule\u00a0<arithmetic|geometric>\u00a0]\u00a0parameters\u00a0<filename>\n\u00a0\u00a0[temp\u00a0<float\u00a0default\u00a0298.15>]\n\u00a0\u00a0[closure\u00a0<hnc|kh>]\nend\n

    At this point energy task is supported, which is invoked using standard directive

    task\u00a0rism\u00a0energy\n
    7\n\nO1\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0-1.092111\u00a0\u00a0\u00a0\u00a00.733461\u00a0\u00a0\u00a0\u00a01.237573\u00a0\u00a0-1.104415\u00a0O\nO2\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a00.758765\u00a0\u00a0\u00a0-0.201687\u00a0\u00a0\u00a0\u00a00.473908\u00a0\u00a0-1.043019\u00a0O\nC1\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0-0.212954\u00a0\u00a0\u00a0\u00a01.568653\u00a0\u00a0\u00a0-0.833617\u00a0\u00a0-0.474263\u00a0C1\nC2\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0-0.174205\u00a0\u00a0\u00a0\u00a00.630432\u00a0\u00a0\u00a0\u00a00.357135\u00a0\u00a0\u00a01.276672\u00a0C2\nH1\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a00.360636\u00a0\u00a0\u00a0\u00a01.160405\u00a0\u00a0\u00a0-1.668859\u00a0\u00a0\u00a00.102898\u00a0H\nH2\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a00.242419\u00a0\u00a0\u00a0\u00a02.521128\u00a0\u00a0\u00a0-0.531952\u00a0\u00a0\u00a00.118979\u00a0H\nH3\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0-1.243967\u00a0\u00a0\u00a0\u00a01.772778\u00a0\u00a0\u00a0-1.139547\u00a0\u00a0\u00a00.123148\u00a0H\n
    #Van\u00a0der\u00a0Waals\u00a0parameters\u00a0file\u00a0for\u00a0RISM\u00a0\n#\u00a0type\u00a0\u00a0\u00a0sigma(Angstrom)\u00a0epsilon\u00a0(kj/mol)\nC\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a00.3400E+01\u00a0\u00a00.3601E+00\nH\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a00.2600E+01\u00a0\u00a00.0628E-00\n

    Upon completion of the run, the resulting radial distribution functions are saved into rdf_out.data file.

    The computed chemical potentials in both HNC and gaussian approximations are written in the output file.

    Here is the complete example input file for solvated calculation of acetic acid.

    echo\nstart\u00a0rism\n\nmemory\u00a0global\u00a040\u00a0mb\u00a0stack\u00a023\u00a0mb\u00a0heap\u00a05\u00a0mb\n\nrism\n\u00a0\u00a0closure\u00a0kh\n\u00a0\u00a0temp\u00a0298\n\u00a0\u00a0vdw\u00a0rule\u00a0arithmetic\u00a0parameters\u00a0vdw.par\n\u00a0\u00a0solute\u00a0configuration\u00a0solute2.data\nend\n\ntask\u00a0energy\u00a0rism\n

    solute2.data file

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    vdw.par file

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    "},{"location":"ARMCI.html","title":"Choosing the ARMCI Library","text":""},{"location":"ARMCI.html#overview","title":"Overview","text":"

    The Global Arrays parallel environment relies upon a one-sided communication runtime system. There are at least three options currently available:

    By default, Global Arrays will choose ARMCI or ComEx, based upon the environment variables selected by the user (see GA documentation for details). When a native implementation is available and works reliably, this is the best option for the NWChem user. However, in cases where an native implementation of ARMCI is not available or is not reliable, the user should consider using one of the MPI-based implementations.

    There are many different ways to use MPI as the communication runtime of Global Arrays:

    ARMCI_NETWORK Result Notes MPI-PR ARMCI with progress rank Recommended, except on Blue Gene/Q. MPI-PT ARMCI with progress thread Appropriate for Blue Gene/Q. MPI-MT ARMCI over multi-threaded MPI Do not use Open-MPI 1.x. MPI-TS ARMCI over MPI without data server MPI-SPAWN ARMCI using MPI dynamic processes Requires MPI_Comm_spawn support. ARMCI Uses ARMCI-MPI See the ARMCI-MPI NWChem page for details. (please use mpi3rma branch) requires EXTERNAL_ARMCI_PATH

    It is difficult to provide complete guidance to the user as to which option to choose. However, we observe the following:

    When using ARMCI-MPI, please make sure to use the most recent version of MPI (MPICH 3.2+, Cray MPI 7.2+, MVAPICH2 2.0+, Intel MPI 5.1+, Open-MPI 2.0+). Older versions of MPI are known to have bugs in the MPI-3 RMA features that affect the correctness of NWChem.

    "},{"location":"ARMCI.html#support","title":"Support","text":"

    Global Arrays, ARMCI and ComEx are developed and supported by PNNL. The user list for support is hpctools@googlegroups.com.

    ARMCI-MPI is developed by Argonne and Intel. All ARMCI-MPI questions should be directed to armci-discuss@lists.mpich.org. ARMCI-MPI is not an Intel product.

    "},{"location":"ARMCI.html#automated-installation-of-armci-mpi","title":"Automated installation of ARMCI-MPI","text":"

    If you wish to use ARMCI-MPI, a script is available to automatically install it:

    cd\u00a0$NWCHEM_TOP/tools\u00a0&&\u00a0./install-armci-mpi\n
    "},{"location":"Aba2.html","title":"Aba2","text":"
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    "},{"location":"Abm2.html","title":"Abm2","text":"
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    "},{"location":"Ama2.html","title":"Ama2","text":"
    group\u00a0number\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0=\u00a040\ngroup\u00a0name\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0=\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0Ama2\ncrystal\u00a0system\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0=\u00a0Orthorhombic\nsetting\u00a0number\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0=\u00a01\nnumber\u00a0of\u00a0symmetry\u00a0operators\u00a0=\u00a08\n\n+x,+y,+z\n-x,-y,+z\n+x+1/2,-y,+z\n-x+1/2,+y,+z\n+x,+y+1/2,+z+1/2\n-x,-y+1/2,+z+1/2\n+x+1/2,-y+1/2,+z+1/2\n-x+1/2,+y+1/2,+z+1/2\n\n=\u00a0operator\u00a01\u00a0=\n\u00a01.0\u00a00.0\u00a00.0\u00a00.0\n\u00a00.0\u00a01.0\u00a00.0\u00a00.0\n\u00a00.0\u00a00.0\u00a01.0\u00a00.0\n\n=\u00a0operator\u00a02\u00a0=\n\u00a0-1.0\u00a00.0\u00a00.0\u00a00.0\n\u00a00.0\u00a0-1.0\u00a00.0\u00a00.0\n\u00a00.0\u00a00.0\u00a01.0\u00a00.0\n\n=\u00a0operator\u00a03\u00a0=\n\u00a01.0\u00a00.0\u00a00.0\u00a00.5\n\u00a00.0\u00a0-1.0\u00a00.0\u00a00.0\n\u00a00.0\u00a00.0\u00a01.0\u00a00.0\n\n=\u00a0operator\u00a04\u00a0=\n\u00a0-1.0\u00a00.0\u00a00.0\u00a00.5\n\u00a00.0\u00a01.0\u00a00.0\u00a00.0\n\u00a00.0\u00a00.0\u00a01.0\u00a00.0\n\n=\u00a0operator\u00a05\u00a0=\n\u00a01.0\u00a00.0\u00a00.0\u00a00.0\n\u00a00.0\u00a01.0\u00a00.0\u00a00.5\n\u00a00.0\u00a00.0\u00a01.0\u00a00.5\n\n=\u00a0operator\u00a06\u00a0=\n\u00a0-1.0\u00a00.0\u00a00.0\u00a00.0\n\u00a00.0\u00a0-1.0\u00a00.0\u00a00.5\n\u00a00.0\u00a00.0\u00a01.0\u00a00.5\n\n=\u00a0operator\u00a07\u00a0=\n\u00a01.0\u00a00.0\u00a00.0\u00a00.5\n\u00a00.0\u00a0-1.0\u00a00.0\u00a00.5\n\u00a00.0\u00a00.0\u00a01.0\u00a00.5\n\n=\u00a0operator\u00a08\u00a0=\n\u00a0-1.0\u00a00.0\u00a00.0\u00a00.5\n\u00a00.0\u00a01.0\u00a00.0\u00a00.5\n\u00a00.0\u00a00.0\u00a01.0\u00a00.5 \n
    "},{"location":"Amm2.html","title":"Amm2","text":"
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    "},{"location":"Analysis.html","title":"Analysis","text":"

    The analysis module is used to analyze molecular trajectories generated by the NWChem molecular dynamics module, or partial charges generated by the NWChem electrostatic potential fit module. This module should not de run in parallel mode.

    Directives for the analysis module are read from an input deck,

    analysis\n ...\nend\n

    The analysis is performed as post-analysis of trajectory files through using the task directive

    task analysis\n

    or

    task analyze\n
    "},{"location":"Analysis.html#system-specification","title":"System specification","text":"
    system <string systemid>_<string calcid>\n

    where the strings systemid and calcid are user defined names for the chemical system and the type of calculation to ber performed, respectively. These names are used to derive the filenames used for the calculation. The topoly file used will be systemid.top, while all other files are named systemid_calcid.ext.

    "},{"location":"Analysis.html#reference-coordinates","title":"Reference coordinates","text":"

    Most analyses require a set of reference coordinates. These coordinates are read from a NWChem restart file by the directive,

    reference <string filename>\n

    where filename is the name of an existing restart file. This input directive is required.

    "},{"location":"Analysis.html#file-specification","title":"File specification","text":"

    The trajectory file(s) to be analyzed are specified with

    file  <string filename>  [ <integer firstfile>   <integer lastfile> ]\n

    where filename is an existing trj trajectory file. If firstfile and lastfile are specified, the specified filename needs to have a ? wildcard character that will be substituted by the 3-character integer number from firstfile to lastfile, and the analysis will be performed on the series of files. For example,

    file tr_md?.trj 3 6\n

    will instruct the analysis to be performed on files tr_md003.trj, tr_md004.trj, tr_md005.trj and tr_md006.trj.

    From the specified files the subset of frames to be analyzed is specified by

    frames [ <integer firstframe default 1> ]  <integer lastframe>  \\\n\n       [ <integer frequency default 1> ]\n

    For example, to analyze the first 100 frames from the specified trajectory files, use

    frames 100\n

    To analyze every 10-th frame between frames 200 and 400 recorded on the specified trajectory files, use

    frames 200 400 10\n

    A time offset can be specified with

    time <real timoff>\n

    Solute coordinates of the reference set and ech subsequent frame read from a trajectory file are translated to have the center of geometry of the specified solute molecule at the center of the simulation box. After this translation all molecules are folded back into the box according to the periodic boundary conditions. The directive for this operation is

    center  <integer imol>  [ <integer jmol default imol> ]\n

    Coordinates of each frame read from a trajectory file can be rotated using

    rotate ( off | x | y | z ) <real angle units degrees>\n

    If center was defined, rotation takes place after the system has been centered. The rotate directives only apply to frames read from the trajectory files, and not to the reference coordinates. Up to 100 rotate directives can be specified, which will be carried out in the order in which they appear in the input deck. rotate off cancels all previously defined rotate directives.

    To perform a hydrogen bond analysis:

    hbond [distance [[<real rhbmin default 0.0>] <real rhbmin>]] \\\n      [angle [<real hbdmin> [ <real hbdmax default pi>]]] \\\n      [solvent [<integer numwhb>]]\n
    "},{"location":"Analysis.html#selection","title":"Selection","text":"

    Analyses can be applied to a selection of solute atoms and solvent molecules. The selection is determined by

    select ( [ super ] [ { <string atomlist> } ] |\n   solvent <real range> | save <string filename> | read <string filename> )\n

    where {atomlist} is the set of atom names selected from the specified residues. By default all solute atoms are selected. When keyword super is specified the selecion applies to the superimposition option.

    The selected atoms are specified by the string atomlist which takes the form

    [{isgm [ - jsgm ] [,]} [:] [{aname[,]}]\n

    where isgm and jsgm are the first and last residue numbers, and aname is an atom name. In the atomname a question mark may be used as a wildcard character.

    For example, all protein backbone atoms are selected by

    select _N,_CA,_C\n

    To select the backbone atoms in residues 20 to 80 and 90 to 100 only, use

    select 20-80,90-100:_N,_CA,_C\n

    This selection is reset to apply to all atoms after each file directive.

    Solvent molecules within range nm from any selected solute atom are selected by

    select solvent <real range>\n

    After solvent selection, the solute atom selection is reset to being all selected.

    The current selection can be saved to, or read from a file using the save and read keywords, respectively.

    Some analysis are performed on groups of atoms. These groups of atoms are defined by

    define <integer igroup> [<real rsel>] [solvent] { <string atomlist> }\n

    The string atom in this definitions again takes the form

    [{isgm [ - jsgm ] [,]} [:] [{aname[,]}]\n

    where isgm and jsgm are the first and last residue numbers, and aname is an atom name. In the atomname a question mark may be used as a wildcard character.

    Multiple define directive can be used to define a single set of atoms.

    "},{"location":"Analysis.html#coordinate-analysis","title":"Coordinate analysis","text":"

    To analyze the root mean square deviation from the specified reference coordinates:

    rmsd\n

    To analyze protein \u03c6-\u03c8 and backbone hydrogen bonding:

    ramachandran\n

    To define a distance:

    distance <integer ibond> <string atomi> <string atomj>\n

    To define an angle:

    angle <integer iangle> <string atomi> <string atomj> <string atomk>\n

    To define a torsion:

    torsion <integer itorsion> <string atomi> <string atomj> \\\n                      <string atomk> <string atoml>\n

    To define a vector:

    vector <integer ivector> <string atomi> <string atomj>\n

    The atom string in these definitions takes the form

    <integer segment>:<string atomname> | w<integer molecule>:<string atomname>\n

    for solute and solvent atom specification, respectively.

    To define charge distribution in z-direction:

    charge_distribution <integer bins>\n

    Analyses on atoms in a predefined group are specified by

    group [<integer igroup> [periodic <integer ipbc>] \\\n      ( local [<real rsel default 0.0>] [<real rval default rsel>]\n        <string function> )\n

    where igroup specifies the group of atoms defined with a define directive. Keyword periodic can be used to specify the periodicity, ipbc=1 for periodicity in z, ipbc=2 for periodicity in x and y, and ipbc=3 for periodicity in x, y and z. Currently the only option is local which prints all selected solute atom with a distance between rsel and rval from the atoms defined in igroup. The actual analysis is done by the scan deirective. A formatted report is printed from group analyses using

    report <string filename> local\n

    Analyses on pairs of atoms in predefined groups are specified by

    groups [<integer igroup> [<integer jgroup>]] [periodic [<integer ipbc default 3>]] \\ \n       <string function> [<real value1> [<real value2>]] [<string filename>]\n

    where igroup and jgroup are groups of atoms defined with a define directive. Keyword periodic specifies that periodic boundary conditions need to be applied in ipbc dimensions. The type of analysis is define by function, value1 and value2. If filename is specified, the analysis is applied to the reference coordinates and written to the specified file. If no filename is given, the analysis is applied to the specified trajectory and performed as part of the scan directive. Implemented analyses defined by <string function> [<real value1> [<real value2>]] include

    Coordinate histograms are specified by

    histogram <integer idef> [<integer length>] zcoordinate <string filename>\n

    where idef is the atom group definition number, length is the size of the histogram, zcoordinate is the currently only histogram option, and filename is the filname to which the histogram is written.

    Order parameters are evalated using

    order <integer isel> <integer jsel> <string atomi> <string atomj>\n

    This is an experimental feature.

    To write the average coordinates of a trajectory

    average [super] <string filename>\n

    To perform the coordinate analysis:

    scan [ super ] <string filename>\n

    which will create, depending on the specified analysis options files filename.rms and filename.ana. After the scan directive previously defined coordinate analysis options are all reset. Optional keyword super specifies that frames read from the trajectory file(s) are superimposed to the reference structure before the analysis is performed.

    "},{"location":"Analysis.html#essential-dynamics-analysis","title":"Essential dynamics analysis","text":"

    Essential dynamics analysis is performed by

    essential\n

    This can be followed by one or more

    project <integer vector> <string filename>\n

    to project the trajectory onto the specified vector. This will create files filename with extensions frm or trj, val, vec, _min.pdb and _max.pdb, with the projected trajectory, the projection value, the eigenvector, and the minimum and maximum projection structure.

    For example, an essential dynamics analysis with projection onto the first vector generating files firstvec.{trj, val, vec, _min.pdb, _max.pdb} is generated by

    essential\nproject 1 firstvec\n
    "},{"location":"Analysis.html#trajectory-format-conversion","title":"Trajectory format conversion","text":"

    To write a single frame in PDB or XYZ format, use

    write [<integer number default 1>] [super] [solute] <string filename>\n

    To copy the selected frames from the specified trejctory file(s), onto a new file, use

    copy  [solute] [rotate <real tangle>] <string filename>\n

    To superimpose the selected atoms for each specified frame to the reference coordinates before copying onto a new file, use

    super [solute] [rotate <real tangle>] <string filename>\n

    The rotate directive specifies that the structure will make a full ratation every tangle ps. This directive only has effect when writing povray files.

    The format of the new file is determined from the extension, which can be one of

    If no extension is specified, a trj formatted file will be written.

    A special tag can be added to frm and pov formatted files using

    label <integer itag> <string tag>  [ <real rval default 1.0> ] \\\\\n      [ <integer iatag> [ <integer jatag default iatag> ] [ <real rtag default 0.0> ] ]\n      [ <string anam> ]\n

    where tag number itag is set to the string tag for all atoms anam within a distance rtag from segments iatag through jatag. A question mark can be used in anam as a wild card character.

    Atom rendering is specified using

    render ( cpk | stick )  [ <real rval default 1.0> ] \\\\\n       [ <integer iatag> [ <integer jatag default iatag> ] [ <real rtag default 0.0> ] ]\n       [ <string anam> ]\n

    for all atoms anam within a distance rtag from segments iatag through jatag, and a scaling factor of rval. A question mark can be used in anam as a wild card character.

    Atom color is specified using

    color ( <string color> | atom ) \\\\\n\n      [ <integer iatag> [ <integer jatag default iatag> ] [ <real rtag default 0.0> ] ]\n\n      [ <string anam> ]\n

    for all atoms anam within a distance rtag from segments iatag through jatag. A question mark can be used in anam as a wildcard character.

    For example, to display all carbon atoms in segments 34 through 45 in green and rendered cpk in povray files can be specified with

    render cpk 34 45 _C??\ncolor green 34 45 _C??\n

    Coordinates written to a pov file can be scaled using

    scale <real factor>\n

    A zero or negative scaling factor will scale the coordinates to lie within [-1,1] in all dimensions.

    The cpk rendering in povray files can be scaled by

    cpk <real factor default 1.0>\n

    The stick rendering in povray files can be scaled by

    stick <real factor default 1.0>\n

    The initial sequence number of esp related files is defined by

    index <integer index default 1>\n

    A sequence of trajectory files with unequal lengths can be converted to files with all nclean frames using

    clean <integer nclean>\n
    "},{"location":"Analysis.html#electrostatic-potentials","title":"Electrostatic potentials","text":"

    A file in plt format of the electrostatic potential resulting from partial charges generated by the ESP module is generated by the command

    esp  [ <integer spacing default 10> ] \\\n     [ <real rcut default 1.0> ] [periodic [<integer iper default 3>]] \\\n     [ <string xfile> [ <string pltfile> ] ]\n

    The input coordinates are taken from the xyzq file that can be generated from a rst by the prepare module. Parameter spacing specifies the number of gridpoints per nm, rcut specifies extent of the charge grid beyond the molecule. Periodic boundaries will be used if periodic is specified. If iper is set to 2, periodic boundary conditions are applied in x and y dimensions only. If periodic is specified, a negative value of rcut will extend the grid in the periodic dimensions by abs(rcut), otherwise this value will be ignored in the periodic dimensions. The resulting plt formatted file pltfile can be viewed with the gOpenMol program. The resulting electrostatic potential grid is in units of . If no files are specified, only the parameters are set. This analysis applies to solute(s) only.

    The electrostatic potential at specific point are evaluated using 

    esp_points [<string filpin> [<string filhol> [<string filpou> [<string filavg>]]]]\n
    "},{"location":"Archived-Forum.html","title":"Archived Forum","text":"

    Clicking the link below will bring you to the archived forum entries from the old NWChem website

    NWChem\u2019s Corner

    You can use the form below to search the entries of the archived forum

    "},{"location":"AvailableBasisSets.html","title":"Gaussian basis sets","text":" "},{"location":"AvailableBasisSets.html#gaussian-basis-sets-with-ecps","title":"Gaussian basis sets with ECPs","text":" "},{"location":"AvailableBasisSets.html#relativistic-douglas-kroll-optimized-basis-sets","title":"Relativistic Douglas-Kroll optimized basis sets","text":" "},{"location":"AvailableBasisSets.html#relativistic-zora-basis-sets","title":"Relativistic ZORA basis sets","text":""},{"location":"AvailableBasisSets.html#relativistic-nesc-basis-sets","title":"Relativistic NESC basis sets","text":" "},{"location":"AvailableBasisSets.html#resolution-of-identity-ri-basis-sets","title":"Resolution-of-identity (RI) basis sets","text":" "},{"location":"AvailableBasisSets.html#fitting-basis-sets","title":"Fitting basis sets","text":" "},{"location":"AvailableBasisSets.html#polarization-basis-functions","title":"Polarization basis functions","text":" "},{"location":"AvailableBasisSets.html#diffuse-basis-functions","title":"Diffuse basis functions","text":" "},{"location":"AvailableBasisSets.html#tight-basis-functions","title":"Tight basis functions","text":" "},{"location":"Basis.html","title":"Basis sets","text":""},{"location":"Basis.html#overview","title":"Overview","text":"

    NWChem currently supports basis sets consisting of generally contracted Cartesian Gaussian functions up to a maximum angular momentum of six (h functions), and also sp (or L) functions. The BASIS directive is used to define these, and also to specify use of an Effective Core Potential that is associated with a basis set.

    The basis functions to be used for a given calculation can be drawn from a standard set in the Basis set library that is included in the release of NWChem. Alternatively, the user can specify particular functions explicitly in the input, to define a particular basis set.

    "},{"location":"Basis.html#basis-directive","title":"BASIS directive","text":"

    The general form of the BASIS directive is as follows:

     BASIS [<string name default \"ao basis\">] \\  \n       [(spherical || cartesian) default cartesian] \\  \n       [(print || noprint) default print]  \\\n       [rel] [bse] \n    <string tag> library [<string tag_in_lib>] \\  \n                 <string standard_set> [file <filename>] \\  \n                 [except <string tag list>] [rel]  \n       ...  \n    <string tag> <string shell_type> [rel]  \n       <real exponent> <real list_of_coefficients>  \n       ...  \n END\n

    The following sections examine the keywords on the first line of the BASIS directive:

    "},{"location":"Basis.html#basis-set-name","title":"Basis set NAME","text":"

    NAME : By default, the basis set is stored in the database with the name \u201cao basis\u201d. Another name may be specified in the BASIS directive, thus, multiple basis sets may be stored simultaneously in the database. Also, the DFT and RI-MP2 modules and the Dyall-modified-Dirac relativistic method require multiple basis sets with specific names. The user can associate the \u201cao basis\u201d with another named basis using the SET directive (see SET).

    "},{"location":"Basis.html#spherical-or-cartesian","title":"SPHERICAL or CARTESIAN","text":"

    SPHERICAL || CARTESIAN : The keywords spherical and cartesian offer the option of using either spherical-harmonic (5 d, 7 f, 9 g, \u2026) or Cartesian (6 d, 10 f, 15 g, \u2026) angular functions. The default is Cartesian. Note that the correlation-consistent basis sets were designed using spherical harmonics and to use these, the spherical keyword should be present in the BASIS directive. The use of spherical functions also helps eliminate problems with linear dependence.

    Cartesian Spherical 1 s s 1 px px 2 py py 3 pz pz 1 dxx dxy 2 dxy dyz 3 dxz dz2-x2-y2 4 dyy dxz 5 dyz dx2-y2 6 dzz 1 fxxx fxxy-yyy 2 fxxy fxyz 3 fxxz fyzz-xxy-yyy 4 fxyy fzzz-xxz-yyz 5 fxyz f-xzz+xxx+xyy 6 fxzz fxxz-yyz 7 fyyy fxyy-xxx 8 fyyz 9 fyzz 10 fzzz

    Order of functions.

    "},{"location":"Basis.html#print-keyword","title":"PRINT keyword","text":"

    PRINT or NOPRINT : The default is for the input module to print all basis sets encountered. Specifying the keyword noprint allows the user to suppress this output.

    "},{"location":"Basis.html#rel-keyword","title":"REL keyword","text":"

    REL : This keyword marks the entire basis as a relativistic basis for the purposes of the Dyall-modified-Dirac relativistic integral code. The marking of the basis set is necessary for the code to make the proper association between the relativistic shells in the ao basis and the shells in the large and/or small component basis. This is only necessary for basis sets which are to be used as the ao basis. The user is referred to the section on Dyall\u2019s modified Dirac-Hamiltonian approximation for more details.

    "},{"location":"Basis.html#bse-keyword","title":"BSE keyword","text":"

    BSE New in NWChem 7.2.0: This keyword loads the basis set library using data in $NWCHEM_TOP/src/basis/libraries.bse from basisetexchanger.org. CAVEAT: use of this keyword will also use the spherical/cartesian keywords from the basis library files.

    "},{"location":"Basis.html#basis-sets-tags","title":"Basis sets tags","text":"

    Basis sets are associated with centers by using the tag of a center in a geometry that has either been input by the user or is available elsewhere. Each atom or center with the same tag will have the same basis set. All atoms must have basis functions assigned to them \u2013 only dummy centers (X or Bq) may have no basis functions. To facilitate the specification of the geometry and the basis set for any chemical system, the matching process of a basis set tag to a geometry tag first looks for an exact match. If no match is found, NWChem will attempt to match, ignoring case, the name or symbol of the element. E.g., all hydrogen atoms in a system could be labeled \u201cH1\u201d, \u201cH2\u201d, \u2026, in the geometry but only one basis set specification for \u201cH\u201d or \u201chydrogen\u201d is necessary. If desired, a special basis may be added to one or more centers (e.g., \u201cH1\u201d) by providing a basis for that tag. If the matching mechanism fails then NWChem stops with an appropriate error message.

    A special set of tags, \u201c*\u201d and tags ending with a \u201c*\u201d (E.g. \u201cH*\u201d) can be used in combination with the keyword library. These tags facilitate the definition of a certain type of basis set of all atoms, or a group of atoms, in a geometry using only a single or very few basis set entries. The \u201c*\u201d tag will not place basis sets on dummy atoms, Bq* can be used for that if necessary.

    Examined next is how to reference standard basis sets in the basis set library, and finally, how to define a basis set using exponents and coefficients.

    "},{"location":"Basis.html#basis-set-library","title":"Basis set library","text":"

    The keyword library associated with each specific tag entry specifies that the calculation will use the standard basis set in NWChem for that center. The string <standard_set> is the name that identifies the functions in the library. The names of standard basis sets are not case sensitive. For a complete list of basis sets and associated ECPs in the NWChem library see the available basis sets or the Basis Set Exchange for naming conventions and their specifications.

    The general form of the input line requesting basis sets from the NWChem basis set library is:

        <string tag> library [<string tag_in_lib>] \\  \n                 <string standard set> [file < filename> \\  \n                 [except <string tag list>] [rel] \n       ...\n

    For example, the NWChem basis set library contains the Dunning cc-pvdz basis set. These may be used as follows

     basis  \n   oxygen library cc-pvdz  \n   hydrogen library cc-pvdz  \n end\n

    A default path of the NWChem basis set libraries is provided on installation of the code, but a different path can be defined by specifying the keyword file, and one can explicitly name the file to be accessed for the basis functions. For example,

     basis \n   o  library 3-21g file /usr/d3g681/nwchem/library \n   si library 6-31g file /usr/d3g681/nwchem/libraries/  \n end\n

    This directive tells the code to use the basis set 3-21g in the file /usr/d3g681/nwchem/library for atom o and to use the basis set 6-31g in the directory /usr/d3g681/nwchem/libraries/ for atom si, rather than look for them in the default libraries. When a directory is defined the code will search for the basis set in a file with the name 6-31g.

    The \u201c*\u201d tag can be used to efficiently define basis set input directives for large numbers of atoms. An example is:

     basis  \n   *  library 3-21g \n end\n

    This directive tells the code to assign the basis sets 3-21g to all the atom tags defined in the geometry. If one wants to place a different basis set on one of the atoms defined in the geometry, the following directive can be used:

     basis  \n   *  library 3-21g except H \n end\n

    This directive tells the code to assign the basis sets 3-21g to all the atoms in the geometry, except the hydrogen atoms. Remember that the user will have to explicitly define the hydrogen basis set in this directive! One may also define tags that end with a \u201c*\u201d:

     basis  \n   oxy*  library 3-21g   \n end\n

    This directive tells the code to assign the basis sets 3-21g to all atom tags in the geometry that start with \u201coxy\u201d.

    If standard basis sets are to be placed upon a dummy center, the variable <tag_in_lib> must also be entered on this line, to identify the correct atom type to use from the basis function library (see the ghost atom example in SET and below). For example: To specify the cc-pvdz basis for a calculation on the water monomer in the dimer basis, where the dummy oxygen and dummy hydrogen centers have been identified as bqo and bqh respectively, the BASIS directive is as follows:

     basis  \n   o   library cc-pvdz  \n   h   library cc-pvdz  \n   bqo library o cc-pvdz  \n   bqh library h cc-pvdz  \n end\n

    A special dummy center tag is bq*, which will assign the same basis set to all bq centers in the geometry. Just as with the * tag, the except list can be used to assign basis sets to unique dummy centers.

    The library basis sets can also be marked as relativistic by adding the rel keyword to the tag line. See the section on relativistic all-electron approximations for more details. The correlation consistent basis sets have been contracted for relativistic effects and are included in the standard library.

    There are also contractions in the standard library for both a point nucleus and a finite nucleus of Gaussian shape. These are usually distinguished by the suffix _pt and _fi. It is the user\u2019s responsibility to ensure that the contraction matches the nuclear type specified in the geometry object. The specification of a finite nucleus basis set does NOT automatically set the nuclear type for that atom to be finite. See Geometries for information.

    "},{"location":"Basis.html#how-to-use-basis-files-from-httpswwwbasissetexchangeorg-new-in-2019","title":"How to use basis files from https://www.basissetexchange.org (NEW in 2019)","text":"

    In order to ensure compatibility with the existing basis libraries available in NWChem, we suggest the user to select the \u201cAdvanced Options\u201d menu and tick the boxes \u201cOptimize General Contractions\u201d and \u201cUncontract General\u201d, as in the image below, when downloading basis files from www.basissetexchange.org

    As an alternative, basis set files downloaded from the basissetexchange.org website are available in the NWChem source code (after release 7.0.0). In order to switch from the default basis libraries to the library formed by files downloaded from www.basissetexchange.org, the following environment variable setting is required

    NWCHEM_BASIS_LIBRARY=$NWCHEM_TOP/src/basis/libraries.bse/\n
    "},{"location":"Basis.html#explicit-basis-set-definition","title":"Explicit basis set definition","text":"

    If the basis sets in the library or available in other external files are not suitable for a given calculation, the basis set may be explicitly defined. A generally contracted Gaussian basis function is associated with a center using an input line of the following form:

        <string tag> <string shell_type> [rel]  \n       <real exponent> <real list_of_coefficients>  \n       ...\n

    The variable identifies the angular momentum of the shell, s, p, d, .... NWChem is configured to handle up to h shells. The keyword rel marks the shell as relativistic \u2013 see the Section on relativistic all-electron approximations for more details. Subsequent lines define the primitive function exponents and contraction coefficients. General contractions are specified by including multiple columns of coefficients.

    The following example defines basis sets for the water molecule:

     basis spherical   \n   oxygen s  \n     11720.0000    0.000710  -0.000160  \n      1759.0000    0.005470  -0.001263  \n       400.8000    0.027837  -0.006267  \n       113.7000    0.104800  -0.025716  \n        37.0300    0.283062  -0.070924  \n        13.2700    0.448719  -0.165411  \n         5.0250    0.270952  -0.116955  \n         1.0130    0.015458   0.557368  \n         0.3023   -0.002585   0.572759  \n   oxygen s                  \n         0.3023    1.000000  \n   oxygen p                  \n        17.7000    0.043018  \n         3.8540    0.228913  \n         1.0460    0.508728  \n         0.2753    0.460531  \n   oxygen p                  \n         0.2753    1.000000  \n   oxygen d  \n         1.1850    1.000000  \n   hydrogen s  \n        13.0100    0.019685  \n         1.9620    0.137977  \n         0.4446    0.478148  \n         0.1220    0.501240  \n   hydrogen s    \n         0.1220    1.000000  \n   hydrogen p    \n         0.7270    1.000000  \n   oxygen s  \n         0.01      1.0  \n   hydrogen s  \n         0.02974   1.0  \n   hydrogen p  \n         0.141      1.0  \n end\n

    Explicit basis set specifications are available from the basis set exchange.

    "},{"location":"Basis.html#combinations-of-library-and-explicit-basis-set-input","title":"Combinations of library and explicit basis set input","text":"

    The user can use a mixture of library basis and explicit basis set input to define the basis sets used on the various atoms.

    For example, the following BASIS directive augments the Dunning cc-pvdz basis set for the water molecule with a diffuse s-shell on oxygen and adds the aug-cc-pVDZ diffuse functions onto the hydrogen.

     basis spherical   \n   oxygen library cc-pvdz  \n   hydrogen library cc-pvdz  \n   oxygen s  \n     0.01 1.0  \n   hydrogen library \"aug-cc-pVDZ Diffuse\"  \n end\n

    The resulting basis set defined is identical to the one defined above in the explicit basis set input.

    "},{"location":"Benchmarks.html","title":"Benchmarks performed with NWChem","text":"

    This page contains a suite of benchmarks performed with NWChem. The benchmarks include a variety of computational chemistry methods on a variety of high performance computing platforms. The list of benchmarks available will evolve continuously as new data becomes available. If you have benchmark information you would like to add for your computing system, please contact one of the developers.

    "},{"location":"Benchmarks.html#hybrid-density-functional-calculation-on-the-c240-buckyball","title":"Hybrid density functional calculation on the C240 Buckyball","text":"

    Performance of the Gaussian basis set DFT module in NWChem. This calculation involved performing a PBE0 calculation (in direct mode) on the on C240 system with the 6-31G* basis set (3600 basis functions) without symmetry. These calculations were performed on the Cascade supercomputer located at PNNL. Input and output files are available.

    "},{"location":"Benchmarks.html#parallel-performance-of-ab-initio-molecular-dynamics-using-plane-waves","title":"Parallel performance of Ab initio Molecular Dynamics using plane waves","text":"

    AIMD Parallel timings for +122O. These calculations were performed on the Franklin Cray-XT4 computer system at NERSC.

    AIMD and AIMD/MM Parallel Timings for +64O (unit cell parameters SC=12.4 Angs. and cutoff energy =100Ry). These calculations were performed on the Chinook HP computer system at MSCF EMSL, PNNL. Exact exchange timings \u2013 80 atom cell of hematite (cutoff energy=100Ry). These calculations were performed on the Franklin Cray-XT4 computer system at NERSC. Exact exchange timings \u2013 576 atom cell of water (cutoff energy=100Ry). These calculations were performed on the Hopper Cray-XE6 computer system at NERSC.

    "},{"location":"Benchmarks.html#parallel-performance-of-the-cr-eomccsdt-method-triples-part","title":"Parallel performance of the CR-EOMCCSD(T) method (triples part)","text":"

    An example of the scalability of the triples part of the CR-EOMCCSD(T) approach for Green Fluorescent Protein Chromophore (GFPC) described by cc-pVTZ basis set (648 basis functions) as obtained from NWChem. Timings were determined from calculations on the Franklin Cray-XT4 computer system at NERSC. See the input file for details.

    And more recent scalability test of the CR-EOMCCSD(T) formalism (Jaguar Cray XT5 at ORNL, see K. Kowalski, S. Krishnamoorthy, R.M. Olson, V. Tipparaju, E. Apr\u00e0 , SC2011, for details).

    "},{"location":"Benchmarks.html#parallel-performance-of-the-multireference-coupled-cluster-mrcc-methods","title":"Parallel performance of the multireference coupled cluster (MRCC) methods","text":"

    In collaboration with Dr. Jiri Pittner\u2019s group from Heyrovsky Institute of Physical Chemistry implementations of two variants of state-specific MRCC approaches have been developed. During his internship at PNNL Jirka Brabec, using novel processor-group-based algorithms, implemented Brillouin-Wigner and Mukherjee MRCC models with singles and doubles. The scalabililty tests for the Brillouin-Wigner MRCCSD approach have been performed on Jaguar XT5 system at ORNL for -carotene in 6-31 basis set (472 orbitals, 216 correlated electrons, 20 reference functions; see J.Brabec, J. Pittner, H.J.J. van Dam, E. Apr\u00e0, K. Kowalski, JCTC 2012, 8(2), pp 487\u2013497). The input file and output files for runs at 6000 cores, at 12000 cores and at 24000 cores are available.

    Former PNNL postdoctoral fellow Dr. Kiran Bhaskaran Nair developed perturbative MRCCSD(T) approaches, which accounts for the effect of triple excitations. Scaling of the triples part of the BW-MRCCSD(T) method for \u201d -carotene in 6-31 basis set (JCP 137, 094112 (2012)). The scalability tests of the BW-MRCCSD(T) implementation of NWChem have been performed on the Jaguar Cray-XK6 computer system of the National Center for Computational Sciences at Oak Ridge National Laboratory.

    "},{"location":"Benchmarks.html#timings-of-ccsdeomccsd-for-the-oligoporphyrin-dimer","title":"Timings of CCSD/EOMCCSD for the oligoporphyrin dimer","text":"

    CCSD/EOMCCSD timings for oligoporphyrin dimer (942 basis functions, 270 correlated electrons, D2h symmetry, excited-state calculations were performed for state of b1g symmetry, in all test calculation convergence threshold was relaxed, 1024 cores were used). See the input file for details.

    --------------------------------------------------------\n\u00a0Iter          Residuum       Correlation     Cpu    Wall\n --------------------------------------------------------\n   1   0.7187071521175  -7.9406033677717   640.9   807.7\n   ......\n MICROCYCLE DIIS UPDATE: 10 5\n  11   0.0009737920958  -7.9953441809574   691.1   822.2\n --------------------------------------------------------\n Iterations converged\n CCSD correlation energy / hartree =        -7.995344180957357\n CCSD total energy / hartree       =     -2418.570838364838890\n\n EOM-CCSD right-hand side iterations\n --------------------------------------------------------------\n      Residuum       Omega / hartree  Omega / eV    Cpu    Wall\n --------------------------------------------------------------\n......\nIteration   2 using    6 trial vectors\n  0.1584284659595   0.0882389635508    2.40111   865.3  1041.2\nIteration   3 using    7 trial vectors\n  0.0575982107592   0.0810948687618    2.20670   918.0  1042.2\n
    "},{"location":"Benchmarks.html#performance-tests-of-the-gpu-implementation-of-non-iterative-part-of-the-ccsdt-approach","title":"Performance tests of the GPU implementation of non-iterative part of the CCSD(T) approach","text":"

    Recent tests of the GPU CCSD(T) implementation performed on Titan Cray XK7 1 system at ORNL (C22H14, 378 basis set functions, C1 symmetry; 98 nodes: 8 cores per node + 1GPU)

    Using 8 CPU cores

    Using CUDA CCSD(T) code \nUsing 0 device(s) per node \nCCSD[T] correction energy / hartree = -0.150973754992986 \nCCSD[T] correlation energy / hartree = -3.067917061062492 \nCCSD[T] total energy / hartree = -844.403376796441080 \nCCSD(T) correction energy / hartree = -0.147996460406684 \nCCSD(T) correlation energy / hartree = -3.064939766476190 \nCCSD(T) total energy / hartree = -844.400399501854849 \nCpu & wall time / sec 9229.9 9240.3 \n

    Using 7 CPU cores and one GPU

    Using CUDA CCSD(T) code \nUsing 1 device(s) per node  \nCCSD[T] correction energy / hartree = -0.150973754993019 \nCCSD[T] correlation energy / hartree = -3.067917061062597 \nCCSD[T] total energy / hartree = -844.403376796441307 \nCCSD(T) correction energy / hartree = -0.147996460406693 \nCCSD(T) correlation energy / hartree = -3.064939766476270 \nCCSD(T) total energy / hartree = -844.400399501854963 \nCpu & wall time / sec 1468.0 1630.7 \n

    Using 1 CPU core and one GPU

    Using CUDA CCSD(T) code\nUsing 1 device(s) per node\nCCSD[T] correction energy / hartree = -0.150973754993069\nCCSD[T] correlation energy / hartree = -3.067917061063028\nCCSD[T] total energy / hartree =  -844.***************\nCCSD(T) correction energy / hartree = -0.147996460406749\nCCSD(T) correlation energy / hartree = -3.064939766476708\nCCSD(T) total energy / hartree = -844.400399501861216\nCpu & wall time / sec 1410.9 1756.5\n

    Without GPU 9240.3 sec. With GPU 1630.7 sec.

    Next release: GPU implementation of non-iterative part of the MRCCSD(T) approach (K. Bhaskarsan-Nair, W. Ma, S. Krishnamoorthy, O. Villa, H. van Dam, E. Apr\u00e0, K. Kowalski, J. Chem. Theory Comput. 9, 1949 (2013))

    "},{"location":"Benchmarks.html#performance-tests-of-the-xeon-phi-implementation-of-non-iterative-part-of-the-ccsdt-approach","title":"Performance tests of the Xeon Phi implementation of non-iterative part of the CCSD(T) approach","text":"

    Tests of the Xeon Phi CCSD(T) implementation performed on the EMSL cascade system at PNNL

    Apr\u00e0, E.; Klemm, M.; Kowalski, K., \u201cEfficient Implementation of Many-Body Quantum Chemical Methods on the Intel\u00ae Xeon Phi Coprocessor,\u201d High Performance Computing, Networking, Storage and Analysis, SC14: International Conference for , vol., no., pp.674-684, 16-21 Nov. 2014 http://dx.doi.org/10.1109/SC.2014.60

    (Triplet state of Si4C3N2H12, 706 basis set functions, C1 symmetry)

    "},{"location":"Benchmarks.html#non-iterative-part-of-the-ccsdt-approach-comparing-xeon-phi-and-nvidia-k20x-performance","title":"Non-iterative part of the CCSD(T) approach: Comparing Xeon Phi and NVidia K20X performance","text":"

    Wall time to solution (in seconds) of non-iterative triples part of the single-reference CCSD(T) approach for the pentacene molecule using Intel MIC and Nvidia GPU implementations. Tests were performed using 96 compute nodes on the Cascade system at EMSL (Intel\u00ae Xeon\u2122 Phi 5110P) and Titan system at ORNL (NVIDIA Tesla\u00ae K20X).

    ( input file)

    Tilesize Intel Xeon Phi 5110P Nvidia K20X 18 1806.4 1824.9 21 1652.2 1699.3 24 1453.3 1554.4"},{"location":"Benchmarks.html#current-developments-for-high-accuracy-alternative-task-schedulers-ats","title":"Current developments for high accuracy: alternative task schedulers (ATS)","text":"

    Currently various development efforts are underway for high accuracy methods that will be available in future releases of NWChem. The examples below shows the first results of the performance of the triples part of Reg-CCSD(T) on GPGPUs (left two examples) and of using alternative task schedules for the iterative CCSD and EOMCCSD.

    Scalability of the triples part of the Reg-CCSD(T) approach for Spiro cation described by the Sadlej\u2019s TZ basis set (POL1). The calculations were performed using Barracuda cluster at EMSL. Speedup of GPU over CPU of the (T) part of the (T) part of the Reg-CCSD(T) approach as a function of the tile size for the uracil molecule. The calculations were performed using Barracuda cluster at EMSL. *Comparison of the CCSD/EOMCCSD iteration times for BacterioChlorophyll (BChl, Mg O6 N4 C 36 H38) for various tile sizes. Calculations were performed for 3-21G basis set (503 basis functions, C1 symmetry, 240 correlated electrons, 1020 cores).

    *Time per CCSD iteration for BChl in 6-311G basis set (733 basis functions, C1 symmetry, 240 correlated electrons, 1020 cores) as a function of tile size. Scalability of the CCSD/EOMCCSD codes for BChl in 6-311G basis set (733 basis functions; tilesize=40, C1 symmetry, 240 correlated electrons).

    Other tests:

    The impact of the tilesize on the CCSD(ATS) timings: All tests have been performed for uracil trimer (6-31G* basis set; all core electrons frozen) on Hopper using 25 nodes (600 cores). One can observe almost 10-fold speedup of the CCSD(ATS) code for tilesize=40 compared to standard TCE CCSD implementation using tilesize=12.

    Performance tests for water clusters

    Luciferin (aug-cc-pVDZ basis set; RHF reference; frozen core) - time per CCSD iteration ( input file)

     tilesize = 30 \n   256 cores      644 sec.\n   512            378 sec.\n   664            314 sec.\n  1020            278 sec.\n  1300            237 sec.\n
     tilesize = 40\n    128             998 sec.\n    256             575 sec.\n

    Sucrose (6-311G** basis set; RHF reference; frozen core) - time per CCSD iteration ( input file)

    tilesize = 40\n   256 cores   1486 sec. \n   512          910 sec.\n  1024          608 sec.\n

    Cytosine-OH (POL1; UHF reference; frozen core) - time per EOMCCSD iteration ( input file)

     tilesize = 30\n 256 cores    44.5 sec.\n
     tilesize = 40\n 128 cores    55.6 sec.\n
    "},{"location":"Benchmarks.html#density-functional-calculation-of-a-zeolite-fragment","title":"Density functional calculation of a zeolite fragment","text":"

    Benchmark results with NWChem 7.0.0 for LDA calculations (energy plus gradient) on a 533 atoms siosi8 zeolite fragment. The input uses an atomic orbital basis set with 7108 functions and a charge density fitting basis with 16501 functions. The input file is available at this link.

    computer # nodes cores/node total # cores Wall time (seconds) cascade 9 16 144 1247 cascade 20 16 320 703 tahoma 4 36 144 927 tahoma 9 36 324 524

    Hardware used:

    "},{"location":"Bq.html","title":"Point charges","text":""},{"location":"Bq.html#overview","title":"Overview","text":"

    The Bq module provides a way to perform QM calculations in the presence of point charges or Bq\u2019s, (as typically referred to in quantum chemistry community). Using Bq module versus geometry block is a recommended way to include point charges in your calculations, in particular if number of charges are big.

    The format for including external point charges using the Bq module is shown below, supporting both explicit charge definition in the body of the block and/or loading from external files.

     bq [units au|nm|pm|ang...] [namespace]  \n   [clear] \n   [force|noforce]  \n   [load <file> [charges <chargefile>] [format ix iy iz iq] [units au|nm|pm|ang|...] [ scale <factor> ]]  \n   x  y  z  q\n   ...  \nend  \n
    set bq <namespace>\n

    Here is an example that illustrates this 

     ...  \n #store point charge in namespace \"foo\"  \n bq \"foo\"\n  ...  \n end  \n\n #perform calculation without actually loading charges in foo  \n task dft energy  \n\n #activate charges in foo  \n set bq foo  \n # now DFT calculation will performed in the presence of charges in foo  \n task dft energy\n