science/votca: Update 1.6.3 -> 2021

Reported by:	portscout


git-svn-id: http://svn.freebsd.org/ports/head@568364 35697150-7ecd-e111-bb59-0022644237b5

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 <bsd.port.mk>
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