From 7bdf591662220f3c9789cff731c32fd7e39a3b9b Mon Sep 17 00:00:00 2001 From: Yuri Victorovich Date: Sun, 14 Mar 2021 07:38:07 +0000 Subject: [PATCH] science/votca: Update 1.6.3 -> 2021 Reported by: portscout --- science/votca/Makefile | 39 +++++---- science/votca/distinfo | 30 +++---- science/votca/pkg-plist | 171 ++++++++++++++++++++-------------------- 3 files changed, 119 insertions(+), 121 deletions(-) diff --git a/science/votca/Makefile b/science/votca/Makefile index a7aed59bac09..656efc9abb30 100644 --- a/science/votca/Makefile +++ b/science/votca/Makefile @@ -2,7 +2,7 @@ PORTNAME= votca DISTVERSIONPREFIX= v -DISTVERSION= 1.6.3 +DISTVERSION= 2021 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org @@ -16,41 +16,46 @@ BUILD_DEPENDS= bash:shells/bash \ lmp:science/lammps RUN_DEPENDS= bash:shells/bash LIB_DEPENDS= libboost_program_options.so:devel/boost-libs \ + libecpint.so:science/libecpint \ libexpat.so:textproc/expat2 \ libfftw3.so:math/fftw3 \ libgromacs_d.so:science/gromacs \ libhdf5.so:science/hdf5 \ + libint2.so:science/libint2 \ libsz.so:science/szip \ libxc.so:science/libxc USES= cmake compiler:c++14-lang eigen:3 perl5 pkgconfig python:run \ shebangfix -SHEBANG_GLOB= *.sh *.pl *.py -SHEBANG_FILES= csg/scripts/csg_call.in csg/scripts/csg_inverse.in tools/scripts/votca_compare.in \ - xtp/scripts/xtp_update_mapfile.in xtp/scripts/xtp_basisset.in xtp/scripts/xtp_makeauxbasis.in xtp/share/benchmark/xtp_benchmark.in \ - csg-manual/scripts/tex2eps -USE_GITHUB= yes USE_LDCONFIG= yes + +USE_GITHUB= yes GH_TUPLE= \ - votca:csg:efaa34c7f148c85493a3d15bf8cc800918d7111f:votca_csg/csg \ - votca:csg-manual:16d27d55248fe7d2f3d78dcb2483f723ba3e38fe:votca_csg_manual/csg-manual \ - votca:csg-tutorials:6819ffd5735cd253d55beffe1be61f0d49e6dd5e:votca_csg_tutorials/csg-tutorials \ - votca:csgapps:4e40d2b92a5d33db2d750efa1dacdf1d502e7447:votca_csgapps/csgapps \ - votca:tools:377b8487df371862de793dfe38287f4ce1cbafb8:votca_tools/tools \ - votca:xtp:5879ed8d006471d37cc0b19dcbb557eac60cf898:votca_xtp/xtp \ - votca:xtp-tutorials:b4b25d570fef22b8806e2efb2fdcc844ad8acb7e:votca_xtp_tutorials/xtp-tutorials + votca:tools:6c83772:tools/tools \ + votca:csg:253f1e5:csg/csg \ + votca:xtp:9df5eb4:xtp/xtp \ + votca:csg-tutorials:0bbe9db:csg_tutorials/csg-tutorials \ + votca:xtp-tutorials:4e36006:xtp_tutorials/xtp-tutorials + +SHEBANG_GLOB= *.sh *.pl *.py +SHEBANG_FILES= csg/scripts/csg_call.in csg/scripts/csg_inverse.in \ + tools/scripts/votca_compare.in tools/scripts/votca_help2doc.in \ + xtp/scripts/xtp_update_mapfile.in xtp/scripts/xtp_basisset.in xtp/share/benchmark/xtp_benchmark.in xtp/scripts/xtp_autogen_mapping.in \ + xtp/scripts/xtp_qmmm2qm.in CMAKE_ON= BUILD_XTP -OPTIONS_DEFINE= APPS DOCS +OPTIONS_DEFINE= APPS OPTIONS_DEFAULT= APPS OPTIONS_SUB= yes APPS_DESC= Build applications APPS_CMAKE_BOOL= BUILD_CSGAPPS -DOCS_CMAKE_BOOL= BUILD_CSG_MANUAL -DOCS_BUILD_DEPENDS= txt2tags:textproc/txt2tags -DOCS_USE= TEX=latex,dvipsk:build +do-test: + @cd ${BUILD_WRKSRC} && \ + ${SETENV} ${CONFIGURE_ENV} ${CMAKE_BIN} ${CMAKE_ARGS} -DENABLE_TESTING:BOOL=ON ${CMAKE_SOURCE_PATH} && \ + ${SETENV} ${MAKE_ENV} ${MAKE_CMD} ${MAKE_ARGS} ${ALL_TARGET} && \ + ${SETENV} ${MAKE_ENV} ${MAKE_CMD} ${MAKE_ARGS} test .include diff --git a/science/votca/distinfo b/science/votca/distinfo index 93726e03fdd0..7cd8b10aaeb7 100644 --- a/science/votca/distinfo +++ b/science/votca/distinfo @@ -1,17 +1,13 @@ -TIMESTAMP = 1608264233 -SHA256 (votca-votca-v1.6.3_GH0.tar.gz) = 26edb3590ae77cc5f7ed49126189825ed091014c2645c4cb7db535359e4c38e5 -SIZE (votca-votca-v1.6.3_GH0.tar.gz) = 23898 -SHA256 (votca-csg-efaa34c7f148c85493a3d15bf8cc800918d7111f_GH0.tar.gz) = 71f791ed5177b56bd2857ac1a64ddab4b1342558e8ad3ac60203e7f2746f3698 -SIZE (votca-csg-efaa34c7f148c85493a3d15bf8cc800918d7111f_GH0.tar.gz) = 523385 -SHA256 (votca-csg-manual-16d27d55248fe7d2f3d78dcb2483f723ba3e38fe_GH0.tar.gz) = 50ee82b378f2663693e70eb6a0f19fb5629ea40afc24399f66384f3830b2fdfc -SIZE (votca-csg-manual-16d27d55248fe7d2f3d78dcb2483f723ba3e38fe_GH0.tar.gz) = 3574272 -SHA256 (votca-csg-tutorials-6819ffd5735cd253d55beffe1be61f0d49e6dd5e_GH0.tar.gz) = 127b70810e8264729b730a729811a66b5603eb25df4de25c17a9ff2439a5357d -SIZE (votca-csg-tutorials-6819ffd5735cd253d55beffe1be61f0d49e6dd5e_GH0.tar.gz) = 5946873 -SHA256 (votca-csgapps-4e40d2b92a5d33db2d750efa1dacdf1d502e7447_GH0.tar.gz) = ccbc18a48161b75ba9c918f3f846db4d45b057a065e9171341e479513361c998 -SIZE (votca-csgapps-4e40d2b92a5d33db2d750efa1dacdf1d502e7447_GH0.tar.gz) = 19603 -SHA256 (votca-tools-377b8487df371862de793dfe38287f4ce1cbafb8_GH0.tar.gz) = f71c4587d321024f7b3954b87bce73230717378edff1d8bb9c31606c24d8718d -SIZE (votca-tools-377b8487df371862de793dfe38287f4ce1cbafb8_GH0.tar.gz) = 109914 -SHA256 (votca-xtp-5879ed8d006471d37cc0b19dcbb557eac60cf898_GH0.tar.gz) = 1e7cc6b8eacd00fccd5303cfc655727b559857f8f672ae74258aff95197d5f85 -SIZE (votca-xtp-5879ed8d006471d37cc0b19dcbb557eac60cf898_GH0.tar.gz) = 1406530 -SHA256 (votca-xtp-tutorials-b4b25d570fef22b8806e2efb2fdcc844ad8acb7e_GH0.tar.gz) = 81b8c8c06b43497ce2c188b861c22179eb89716c1cf9ab8cd584ed945dcf6361 -SIZE (votca-xtp-tutorials-b4b25d570fef22b8806e2efb2fdcc844ad8acb7e_GH0.tar.gz) = 46194733 +TIMESTAMP = 1615703868 +SHA256 (votca-votca-v2021_GH0.tar.gz) = c3ada008b51cd3c96904a75eb502c67790feda14b8b27ff132c8864171cdd472 +SIZE (votca-votca-v2021_GH0.tar.gz) = 43489 +SHA256 (votca-tools-6c83772_GH0.tar.gz) = e07fe43baea7113cd92eb7a942f877976204075a968d69db81a55fec3e392891 +SIZE (votca-tools-6c83772_GH0.tar.gz) = 114796 +SHA256 (votca-csg-253f1e5_GH0.tar.gz) = 5395e0dcf088497fdfe8ac72e3544cda971b9398744a533eb61b4c073aab7f52 +SIZE (votca-csg-253f1e5_GH0.tar.gz) = 4301555 +SHA256 (votca-xtp-9df5eb4_GH0.tar.gz) = 15801909f517f401e616fbd37988f8ddcb786d9fd01fef86d1e4a6bc34f8da47 +SIZE (votca-xtp-9df5eb4_GH0.tar.gz) = 2249637 +SHA256 (votca-csg-tutorials-0bbe9db_GH0.tar.gz) = 6e4457f9b6741c443ff0b004c8c6b1eea4f8a83cfdc71d5a755597ae80c9de24 +SIZE (votca-csg-tutorials-0bbe9db_GH0.tar.gz) = 5945729 +SHA256 (votca-xtp-tutorials-4e36006_GH0.tar.gz) = 81ad6fe78c7ff3601ad5f6c570dc0369dd418f24d1e4db262239802c985cca78 +SIZE (votca-xtp-tutorials-4e36006_GH0.tar.gz) = 46207064 diff --git a/science/votca/pkg-plist b/science/votca/pkg-plist index dfdbf438f0f0..732bc06c16a3 100644 --- a/science/votca/pkg-plist +++ b/science/votca/pkg-plist @@ -1,5 +1,4 @@ bin/VOTCARC.bash -bin/VOTCARC.csh bin/csg_boltzmann bin/csg_call bin/csg_density @@ -22,15 +21,12 @@ bin/csg_sphericalorder bin/csg_stat bin/csg_traj_force bin/votca_compare +bin/votca_help2doc bin/votca_property -bin/xtp_basisset -bin/xtp_dump -bin/xtp_makeauxbasis bin/xtp_map bin/xtp_parallel bin/xtp_run bin/xtp_tools -bin/xtp_update_mapfile include/votca/csg/basebead.h include/votca/csg/bead.h include/votca/csg/beadlist.h @@ -41,7 +37,6 @@ include/votca/csg/beadpair.h include/votca/csg/beadstructure.h include/votca/csg/beadstructurealgorithms.h include/votca/csg/beadtriple.h -include/votca/csg/beadtype.h include/votca/csg/boundarycondition.h include/votca/csg/cgengine.h include/votca/csg/cgmoleculedef.h @@ -69,13 +64,13 @@ include/votca/csg/potentialfunctionlj126.h include/votca/csg/potentialfunctionljg.h include/votca/csg/residue.h include/votca/csg/topology.h -include/votca/csg/topologyitem.h include/votca/csg/topologymap.h include/votca/csg/topologyreader.h include/votca/csg/trajectoryreader.h include/votca/csg/trajectorywriter.h include/votca/csg/triclinicbox.h include/votca/csg/triplelist.h +include/votca/csg/units.h include/votca/csg/version.h include/votca/csg/xyzreader.h include/votca/csg/xyzwriter.h @@ -92,6 +87,7 @@ include/votca/tools/datacollection.h include/votca/tools/edge.h include/votca/tools/edgecontainer.h include/votca/tools/eigen.h +include/votca/tools/eigenio_matrixmarket.h include/votca/tools/eigensystem.h include/votca/tools/elements.h include/votca/tools/filesystem.h @@ -128,22 +124,24 @@ include/votca/tools/tokenizer.h include/votca/tools/types.h include/votca/tools/unitconverter.h include/votca/tools/version.h -include/votca/tools/votca_config.h +include/votca/tools/votca_tools_config.h include/votca/xtp/ERIs.h +include/votca/xtp/GaussianQuadratureBase.h +include/votca/xtp/ImaginaryAxisIntegration.h include/votca/xtp/IndexParser.h include/votca/xtp/adiis.h include/votca/xtp/adiis_costfunction.h include/votca/xtp/amplitude_integration.h +include/votca/xtp/anderson_mixing.h include/votca/xtp/aobasis.h include/votca/xtp/aomatrix.h -include/votca/xtp/aomatrix3d.h include/votca/xtp/aopotential.h include/votca/xtp/aoshell.h include/votca/xtp/aotransform.h include/votca/xtp/atom.h include/votca/xtp/atomcontainer.h include/votca/xtp/basisset.h -include/votca/xtp/bfgs-trm.h +include/votca/xtp/bfgs_trm.h include/votca/xtp/bse.h include/votca/xtp/bse_operator.h include/votca/xtp/bse_population.h @@ -169,7 +167,6 @@ include/votca/xtp/dftengine.h include/votca/xtp/diis.h include/votca/xtp/dipoledipoleinteraction.h include/votca/xtp/ecpaobasis.h -include/votca/xtp/ecpaoshell.h include/votca/xtp/ecpbasisset.h include/votca/xtp/eeinteractor.h include/votca/xtp/eigen.h @@ -177,10 +174,9 @@ include/votca/xtp/energy_costfunction.h include/votca/xtp/energy_terms.h include/votca/xtp/esp2multipole.h include/votca/xtp/espfit.h -include/votca/xtp/extractorfactory.h include/votca/xtp/filterfactory.h include/votca/xtp/forces.h -include/votca/xtp/fourcenter.h +include/votca/xtp/gaussianwriter.h include/votca/xtp/geometry_optimization.h include/votca/xtp/glink.h include/votca/xtp/gnode.h @@ -200,13 +196,17 @@ include/votca/xtp/jobcalculatorfactory.h include/votca/xtp/jobtopology.h include/votca/xtp/kmccalculator.h include/votca/xtp/logger.h +include/votca/xtp/make_libint_work.h include/votca/xtp/matrixfreeoperator.h include/votca/xtp/md2qmengine.h include/votca/xtp/mmregion.h +include/votca/xtp/molden.h include/votca/xtp/nbo.h include/votca/xtp/newton_rapson.h +include/votca/xtp/openmp_cuda.h include/votca/xtp/optimiser_costfunction.h include/votca/xtp/orbitals.h +include/votca/xtp/orbreorder.h include/votca/xtp/paircalculator.h include/votca/xtp/parallelxjobcalc.h include/votca/xtp/polarregion.h @@ -226,6 +226,7 @@ include/votca/xtp/qmregion.h include/votca/xtp/qmstate.h include/votca/xtp/qmthread.h include/votca/xtp/qmtool.h +include/votca/xtp/quadrature_factory.h include/votca/xtp/radial_euler_maclaurin_rule.h include/votca/xtp/rate_engine.h include/votca/xtp/region.h @@ -234,7 +235,9 @@ include/votca/xtp/rpa.h include/votca/xtp/segid.h include/votca/xtp/segment.h include/votca/xtp/segmentmapper.h +include/votca/xtp/settings.h include/votca/xtp/sigma_base.h +include/votca/xtp/sigma_cda.h include/votca/xtp/sigma_exact.h include/votca/xtp/sigma_ppm.h include/votca/xtp/sphere_lebedev_rule.h @@ -251,7 +254,7 @@ include/votca/xtp/topology.h include/votca/xtp/trustregion.h include/votca/xtp/vc2index.h include/votca/xtp/version.h -include/votca/xtp/votca_config.h +include/votca/xtp/votca_xtp_config.h include/votca/xtp/vxc_functionals.h include/votca/xtp/vxc_grid.h include/votca/xtp/vxc_potential.h @@ -260,39 +263,51 @@ lib/cmake/VOTCA_CSG/VOTCA_CSGConfig.cmake lib/cmake/VOTCA_CSG/VOTCA_CSGConfigVersion.cmake lib/cmake/VOTCA_CSG/VOTCA_CSG_Targets-%%CMAKE_BUILD_TYPE%%.cmake lib/cmake/VOTCA_CSG/VOTCA_CSG_Targets.cmake +lib/cmake/VOTCA_TOOLS/FindFFTW3.cmake lib/cmake/VOTCA_TOOLS/VOTCA_TOOLSConfig.cmake lib/cmake/VOTCA_TOOLS/VOTCA_TOOLSConfigVersion.cmake lib/cmake/VOTCA_TOOLS/VOTCA_TOOLS_Targets-%%CMAKE_BUILD_TYPE%%.cmake lib/cmake/VOTCA_TOOLS/VOTCA_TOOLS_Targets.cmake +lib/cmake/VOTCA_XTP/VOTCA_XTPConfig.cmake +lib/cmake/VOTCA_XTP/VOTCA_XTPConfigVersion.cmake +lib/cmake/VOTCA_XTP/VOTCA_XTP_Targets-%%CMAKE_BUILD_TYPE%%.cmake +lib/cmake/VOTCA_XTP/VOTCA_XTP_Targets.cmake lib/libvotca_csg.so -lib/libvotca_csg.so.6 +lib/libvotca_csg.so.2022 lib/libvotca_tools.so -lib/libvotca_tools.so.6 +lib/libvotca_tools.so.2022 lib/libvotca_xtp.so -lib/libvotca_xtp.so.6 -%%DOCS%%man/man1/csg_boltzmann.1.gz -%%DOCS%%man/man1/csg_call.1.gz -%%DOCS%%man/man1/csg_density.1.gz -%%DOCS%%man/man1/csg_dlptopol.1.gz -%%DOCS%%man/man1/csg_dump.1.gz -%%DOCS%%man/man1/csg_fmatch.1.gz -%%DOCS%%man/man1/csg_gmxtopol.1.gz -%%DOCS%%man/man1/csg_imc_solve.1.gz -%%DOCS%%man/man1/csg_inverse.1.gz -%%DOCS%%man/man1/csg_map.1.gz -%%DOCS%%man/man1/csg_property.1.gz -%%DOCS%%man/man1/csg_resample.1.gz -%%DOCS%%man/man1/csg_reupdate.1.gz -%%DOCS%%man/man1/csg_stat.1.gz +lib/libvotca_xtp.so.2022 +man/man1/csg_boltzmann.1.gz +man/man1/csg_call.1.gz +man/man1/csg_density.1.gz +man/man1/csg_dlptopol.1.gz +man/man1/csg_dump.1.gz +man/man1/csg_fluctuations.1.gz +man/man1/csg_fmatch.1.gz +man/man1/csg_gmxtopol.1.gz +man/man1/csg_imc_solve.1.gz +man/man1/csg_inverse.1.gz +man/man1/csg_map.1.gz +man/man1/csg_orientcorr.1.gz +man/man1/csg_part_dist.1.gz +man/man1/csg_partial_rdf.1.gz +man/man1/csg_property.1.gz +man/man1/csg_radii.1.gz +man/man1/csg_resample.1.gz +man/man1/csg_reupdate.1.gz +man/man1/csg_sphericalorder.1.gz +man/man1/csg_stat.1.gz +man/man1/csg_traj_force.1.gz +man/man1/votca_compare.1.gz +man/man1/votca_help2doc.1.gz man/man1/votca_property.1.gz -man/man1/xtp_dump.1.gz man/man1/xtp_map.1.gz man/man1/xtp_parallel.1.gz man/man1/xtp_run.1.gz man/man1/xtp_tools.1.gz -%%DOCS%%man/man7/votca-csg.7.gz +man/man7/votca-csg.7.gz man/man7/votca-tools.7.gz -%%PORTDOCS%%%%DOCSDIR%%/manual.pdf %%DATADIR%%/csg-tutorials/LJ1-LJ2/imc/LJ1-LJ1.dist.tgt %%DATADIR%%/csg-tutorials/LJ1-LJ2/imc/LJ1-LJ2.dist.tgt %%DATADIR%%/csg-tutorials/LJ1-LJ2/imc/LJ2-LJ2.dist.tgt @@ -305,8 +320,8 @@ man/man7/votca-tools.7.gz %%DATADIR%%/csg-tutorials/LJ1-LJ2/imc/svd.py %%DATADIR%%/csg-tutorials/LJ1-LJ2/imc/table.xvg %%DATADIR%%/csg-tutorials/LJ1-LJ2/imc/topol.top -%%DATADIR%%/csg-tutorials/README -%%DATADIR%%/csg-tutorials/guide/README.md +%%DATADIR%%/csg-tutorials/README.rst +%%DATADIR%%/csg-tutorials/guide/README.rst %%DATADIR%%/csg-tutorials/hexane/atomistic/Extract_Energies.sh %%DATADIR%%/csg-tutorials/hexane/atomistic/boltzmann_cmds %%DATADIR%%/csg-tutorials/hexane/atomistic/conf.gro @@ -909,9 +924,10 @@ man/man7/votca-tools.7.gz %%DATADIR%%/xml/csg_defaults.xml %%DATADIR%%/xml/mapping.xml %%DATADIR%%/xml/topol.xml +%%DATADIR%%/xtp-tutorials/GROMACS/KMC_Methane/GROMACS_KMC.ipynb %%DATADIR%%/xtp-tutorials/GROMACS/KMC_Methane/change_energy.py %%DATADIR%%/xtp-tutorials/GROMACS/KMC_Methane/lifetimes.xml -%%DATADIR%%/xtp-tutorials/GROMACS/KMC_Methane/run.sh +%%DATADIR%%/xtp-tutorials/GROMACS/KMC_Methane/xml_editor.py %%DATADIR%%/xtp-tutorials/GROMACS/Methane/MD_FILES/conf.gro %%DATADIR%%/xtp-tutorials/GROMACS/Methane/MD_FILES/topol.tpr %%DATADIR%%/xtp-tutorials/GROMACS/Methane/MP_FILES/Methane_e.mps @@ -919,32 +935,13 @@ man/man7/votca-tools.7.gz %%DATADIR%%/xtp-tutorials/GROMACS/Methane/MP_FILES/Methane_n.mps %%DATADIR%%/xtp-tutorials/GROMACS/Methane/MP_FILES/Methane_n2s1.mps %%DATADIR%%/xtp-tutorials/GROMACS/Methane/MP_FILES/Methane_s1.mps -%%DATADIR%%/xtp-tutorials/GROMACS/Methane/OPTIONFILES/qmmm_mm.xml -%%DATADIR%%/xtp-tutorials/GROMACS/Methane/QC_FILES/g09/anion_geo/.ls -%%DATADIR%%/xtp-tutorials/GROMACS/Methane/QC_FILES/g09/anion_geo/neutral/system.com -%%DATADIR%%/xtp-tutorials/GROMACS/Methane/QC_FILES/g09/anion_geo/polar/log2mps.xml -%%DATADIR%%/xtp-tutorials/GROMACS/Methane/QC_FILES/g09/anion_geo/polar/molpol.xml -%%DATADIR%%/xtp-tutorials/GROMACS/Methane/QC_FILES/g09/anion_geo/polar/output.xml -%%DATADIR%%/xtp-tutorials/GROMACS/Methane/QC_FILES/g09/anion_geo/polar/system.com -%%DATADIR%%/xtp-tutorials/GROMACS/Methane/QC_FILES/g09/anion_geo/system.com -%%DATADIR%%/xtp-tutorials/GROMACS/Methane/QC_FILES/g09/cation_geo/.ls -%%DATADIR%%/xtp-tutorials/GROMACS/Methane/QC_FILES/g09/cation_geo/neutral/system.com -%%DATADIR%%/xtp-tutorials/GROMACS/Methane/QC_FILES/g09/cation_geo/polar/log2mps.xml -%%DATADIR%%/xtp-tutorials/GROMACS/Methane/QC_FILES/g09/cation_geo/polar/molpol.xml -%%DATADIR%%/xtp-tutorials/GROMACS/Methane/QC_FILES/g09/cation_geo/polar/output.xml -%%DATADIR%%/xtp-tutorials/GROMACS/Methane/QC_FILES/g09/cation_geo/polar/system.com -%%DATADIR%%/xtp-tutorials/GROMACS/Methane/QC_FILES/g09/cation_geo/system.com -%%DATADIR%%/xtp-tutorials/GROMACS/Methane/QC_FILES/g09/neutral_geo/anion/system.com -%%DATADIR%%/xtp-tutorials/GROMACS/Methane/QC_FILES/g09/neutral_geo/cation/system.com -%%DATADIR%%/xtp-tutorials/GROMACS/Methane/QC_FILES/g09/neutral_geo/log2mps.xml -%%DATADIR%%/xtp-tutorials/GROMACS/Methane/QC_FILES/g09/neutral_geo/polar/log2mps.xml -%%DATADIR%%/xtp-tutorials/GROMACS/Methane/QC_FILES/g09/neutral_geo/polar/molpol.xml -%%DATADIR%%/xtp-tutorials/GROMACS/Methane/QC_FILES/g09/neutral_geo/polar/output.xml -%%DATADIR%%/xtp-tutorials/GROMACS/Methane/QC_FILES/g09/neutral_geo/polar/system.com -%%DATADIR%%/xtp-tutorials/GROMACS/Methane/QC_FILES/g09/neutral_geo/system.com %%DATADIR%%/xtp-tutorials/GROMACS/Methane/QC_FILES/methane.xyz -%%DATADIR%%/xtp-tutorials/GROMACS/Methane/run.sh +%%DATADIR%%/xtp-tutorials/GROMACS/Methane/QMMM_GROMACS.ipynb +%%DATADIR%%/xtp-tutorials/GROMACS/Methane/qmmm.xml +%%DATADIR%%/xtp-tutorials/GROMACS/Methane/qmmm_mm.xml %%DATADIR%%/xtp-tutorials/GROMACS/Methane/system.xml +%%DATADIR%%/xtp-tutorials/GROMACS/Methane/xml_editor.py +%%DATADIR%%/xtp-tutorials/LAMMPS/KMC_Thiophene/LAMMPS_KMC.ipynb %%DATADIR%%/xtp-tutorials/LAMMPS/KMC_Thiophene/MD_FILES/MD_Input/molecule_in_vacuum.data %%DATADIR%%/xtp-tutorials/LAMMPS/KMC_Thiophene/MD_FILES/MD_Input/molecule_in_vacuum.in %%DATADIR%%/xtp-tutorials/LAMMPS/KMC_Thiophene/MD_FILES/MD_Input/molecule_in_vacuum.in.init @@ -1992,7 +1989,6 @@ man/man7/votca-tools.7.gz %%DATADIR%%/xtp-tutorials/LAMMPS/KMC_Thiophene/MP_FILES/thiophene_e.mps %%DATADIR%%/xtp-tutorials/LAMMPS/KMC_Thiophene/MP_FILES/thiophene_h.mps %%DATADIR%%/xtp-tutorials/LAMMPS/KMC_Thiophene/MP_FILES/thiophene_n.mps -%%DATADIR%%/xtp-tutorials/LAMMPS/KMC_Thiophene/OPTIONFILES/mapchecker.xml %%DATADIR%%/xtp-tutorials/LAMMPS/KMC_Thiophene/OPTIONFILES/qmmm_mm.xml %%DATADIR%%/xtp-tutorials/LAMMPS/KMC_Thiophene/QC_FILES/GS_opt/system.engrad %%DATADIR%%/xtp-tutorials/LAMMPS/KMC_Thiophene/QC_FILES/GS_opt/system.gbw @@ -2072,6 +2068,7 @@ man/man7/votca-tools.7.gz %%DATADIR%%/xtp-tutorials/LAMMPS/KMC_Thiophene/run.sh %%DATADIR%%/xtp-tutorials/LAMMPS/KMC_Thiophene/state.hdf5 %%DATADIR%%/xtp-tutorials/LAMMPS/KMC_Thiophene/system.xml +%%DATADIR%%/xtp-tutorials/LAMMPS/KMC_Thiophene/xml_editor.py %%DATADIR%%/xtp-tutorials/LAMMPS/Thiophene/MD_FILES/MD_Input/molecule_in_vacuum.data %%DATADIR%%/xtp-tutorials/LAMMPS/Thiophene/MD_FILES/MD_Input/molecule_in_vacuum.in %%DATADIR%%/xtp-tutorials/LAMMPS/Thiophene/MD_FILES/MD_Input/molecule_in_vacuum.in.init @@ -2119,8 +2116,6 @@ man/man7/votca-tools.7.gz %%DATADIR%%/xtp-tutorials/LAMMPS/Thiophene/MP_FILES/thiophene_e.mps %%DATADIR%%/xtp-tutorials/LAMMPS/Thiophene/MP_FILES/thiophene_h.mps %%DATADIR%%/xtp-tutorials/LAMMPS/Thiophene/MP_FILES/thiophene_n.mps -%%DATADIR%%/xtp-tutorials/LAMMPS/Thiophene/OPTIONFILES/qmmm.xml -%%DATADIR%%/xtp-tutorials/LAMMPS/Thiophene/OPTIONFILES/qmmm_mm.xml %%DATADIR%%/xtp-tutorials/LAMMPS/Thiophene/QC_FILES/GS_opt/system.engrad %%DATADIR%%/xtp-tutorials/LAMMPS/Thiophene/QC_FILES/GS_opt/system.gbw %%DATADIR%%/xtp-tutorials/LAMMPS/Thiophene/QC_FILES/GS_opt/system.inp @@ -2190,21 +2185,27 @@ man/man7/votca-tools.7.gz %%DATADIR%%/xtp-tutorials/LAMMPS/Thiophene/QC_FILES/thiophene_e.xyz %%DATADIR%%/xtp-tutorials/LAMMPS/Thiophene/QC_FILES/thiophene_h.xyz %%DATADIR%%/xtp-tutorials/LAMMPS/Thiophene/QC_FILES/thiophene_n.xyz +%%DATADIR%%/xtp-tutorials/LAMMPS/Thiophene/QMMM_LAMMPS.ipynb %%DATADIR%%/xtp-tutorials/LAMMPS/Thiophene/plotting_scripts/make_spectrum.sh %%DATADIR%%/xtp-tutorials/LAMMPS/Thiophene/plotting_scripts/qmmm_spectra.py %%DATADIR%%/xtp-tutorials/LAMMPS/Thiophene/plotting_scripts/spectra.gp %%DATADIR%%/xtp-tutorials/LAMMPS/Thiophene/qmmm.jobs -%%DATADIR%%/xtp-tutorials/LAMMPS/Thiophene/run.sh +%%DATADIR%%/xtp-tutorials/LAMMPS/Thiophene/qmmm.xml +%%DATADIR%%/xtp-tutorials/LAMMPS/Thiophene/qmmm_mm.xml %%DATADIR%%/xtp-tutorials/LAMMPS/Thiophene/system.xml -%%DATADIR%%/xtp-tutorials/LICENSE -%%DATADIR%%/xtp-tutorials/README.md -%%DATADIR%%/xtp-tutorials/guide/HOW_TO_PREPARE_INPUTS.md -%%DATADIR%%/xtp-tutorials/guide/TUTORIAL.md +%%DATADIR%%/xtp-tutorials/LAMMPS/Thiophene/xml_editor.py +%%DATADIR%%/xtp-tutorials/LICENSE.rst +%%DATADIR%%/xtp-tutorials/README.rst +%%DATADIR%%/xtp-tutorials/clean_notebooks.sh +%%DATADIR%%/xtp-tutorials/python_tools/xml_editor.py +%%DATADIR%%/xtp-tutorials/share/doc/XTP-TUTORIAL.rst +%%DATADIR%%/xtp-tutorials/share/doc/help.rst +%%DATADIR%%/xtp-tutorials/tools/dftgwbse_CH4/DFTGWBSE_ENERGY.ipynb %%DATADIR%%/xtp-tutorials/tools/dftgwbse_CH4/methane.xyz -%%DATADIR%%/xtp-tutorials/tools/dftgwbse_CH4/plot_spectrum.gp -%%DATADIR%%/xtp-tutorials/tools/dftgwbse_CH4/run.sh +%%DATADIR%%/xtp-tutorials/tools/dftgwbse_CH4/xml_editor.py %%DATADIR%%/xtp-tutorials/tools/dftgwbse_CO_geoopt/CO.xyz -%%DATADIR%%/xtp-tutorials/tools/dftgwbse_CO_geoopt/run.sh +%%DATADIR%%/xtp-tutorials/tools/dftgwbse_CO_geoopt/DFTGWBSE_OPTIMIZATION.ipynb +%%DATADIR%%/xtp-tutorials/tools/dftgwbse_CO_geoopt/xml_editor.py %%DATADIR%%/xtp/basis_sets/3-21G.xml %%DATADIR%%/xtp/basis_sets/6-311++G(2p,2d).xml %%DATADIR%%/xtp/basis_sets/6-311++G.xml @@ -2240,15 +2241,19 @@ man/man7/votca-tools.7.gz %%DATADIR%%/xtp/basis_sets/cc-pvdz.xml %%DATADIR%%/xtp/basis_sets/cc-pvqz.xml %%DATADIR%%/xtp/basis_sets/cc-pvtz.xml +%%DATADIR%%/xtp/basis_sets/def2-qzvp-ecp.xml %%DATADIR%%/xtp/basis_sets/def2-qzvp.xml %%DATADIR%%/xtp/basis_sets/def2-qzvpd.xml +%%DATADIR%%/xtp/basis_sets/def2-qzvpp-ecp.xml %%DATADIR%%/xtp/basis_sets/def2-qzvpp.xml %%DATADIR%%/xtp/basis_sets/def2-qzvppd.xml %%DATADIR%%/xtp/basis_sets/def2-sv(p).xml %%DATADIR%%/xtp/basis_sets/def2-svp.xml %%DATADIR%%/xtp/basis_sets/def2-svpd.xml +%%DATADIR%%/xtp/basis_sets/def2-tzvp-ecp.xml %%DATADIR%%/xtp/basis_sets/def2-tzvp.xml %%DATADIR%%/xtp/basis_sets/def2-tzvpd.xml +%%DATADIR%%/xtp/basis_sets/def2-tzvpp-ecp.xml %%DATADIR%%/xtp/basis_sets/def2-tzvpp.xml %%DATADIR%%/xtp/basis_sets/def2-tzvppd.xml %%DATADIR%%/xtp/basis_sets/optaux-aug-cc-pvdz.xml @@ -2290,24 +2295,17 @@ man/man7/votca-tools.7.gz %%DATADIR%%/xtp/benchmark/gwbse.xml %%DATADIR%%/xtp/benchmark/xtp_benchmark %%DATADIR%%/xtp/benchmark/xtpdft.xml +%%DATADIR%%/xtp/data/orca_functional_names.xml +%%DATADIR%%/xtp/data/qmpackage_defaults.xml %%DATADIR%%/xtp/ecps/CRENBL_ECP.xml %%DATADIR%%/xtp/ecps/ECP2SDF.xml %%DATADIR%%/xtp/ecps/SBKJC_ECP.xml %%DATADIR%%/xtp/ecps/corelevels.xml +%%DATADIR%%/xtp/ecps/def2-ecp.xml %%DATADIR%%/xtp/ecps/ecp.xml -%%DATADIR%%/xtp/packages/bsecoupling.xml -%%DATADIR%%/xtp/packages/esp2multipole.xml -%%DATADIR%%/xtp/packages/gaussian.xml -%%DATADIR%%/xtp/packages/gaussian_iqm_pair.xml -%%DATADIR%%/xtp/packages/gwbse.xml -%%DATADIR%%/xtp/packages/gwbse_iqm_pair.xml -%%DATADIR%%/xtp/packages/nwchem.xml -%%DATADIR%%/xtp/packages/orca.xml -%%DATADIR%%/xtp/packages/orca_iqm_pair.xml -%%DATADIR%%/xtp/packages/polar.xml -%%DATADIR%%/xtp/packages/xtpdft.xml %%DATADIR%%/xtp/xml/apdft.xml %%DATADIR%%/xtp/xml/coupling.xml +%%DATADIR%%/xtp/xml/densityanalysis.xml %%DATADIR%%/xtp/xml/dftgwbse.xml %%DATADIR%%/xtp/xml/eanalyze.xml %%DATADIR%%/xtp/xml/einternal.xml @@ -2316,18 +2314,17 @@ man/man7/votca-tools.7.gz %%DATADIR%%/xtp/xml/gencube.xml %%DATADIR%%/xtp/xml/ianalyze.xml %%DATADIR%%/xtp/xml/iexcitoncl.xml -%%DATADIR%%/xtp/xml/iimport.xml %%DATADIR%%/xtp/xml/iqm.xml %%DATADIR%%/xtp/xml/kmclifetime.xml %%DATADIR%%/xtp/xml/kmcmultiple.xml %%DATADIR%%/xtp/xml/log2mps.xml -%%DATADIR%%/xtp/xml/map.xml %%DATADIR%%/xtp/xml/mapchecker.xml +%%DATADIR%%/xtp/xml/mol2orb.xml %%DATADIR%%/xtp/xml/molpol.xml %%DATADIR%%/xtp/xml/neighborlist.xml -%%DATADIR%%/xtp/xml/options.xml +%%DATADIR%%/xtp/xml/orb2fchk.xml +%%DATADIR%%/xtp/xml/orb2mol.xml %%DATADIR%%/xtp/xml/partialcharges.xml %%DATADIR%%/xtp/xml/qmmm.xml -%%DATADIR%%/xtp/xml/sandbox.xml %%DATADIR%%/xtp/xml/spectrum.xml %%DATADIR%%/xtp/xml/vaverage.xml