Accepting request 1126770 from science
OBS-URL: https://build.opensuse.org/request/show/1126770 OBS-URL: https://build.opensuse.org/package/show/openSUSE:Factory/votca?expand=0&rev=9
This commit is contained in:
Ana Guerrero
Git OBS Bridge
commit
e0a7acf0cf
44
1083.patch
44
1083.patch
@ -1,44 +0,0 @@
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diff --git a/xtp/src/libxtp/calculators/kmclifetime.cc b/xtp/src/libxtp/calculators/kmclifetime.cc
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index f6a1093ff..56730bce9 100644
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--- a/xtp/src/libxtp/calculators/kmclifetime.cc
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+++ b/xtp/src/libxtp/calculators/kmclifetime.cc
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@@ -21,7 +21,7 @@
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// Third party includes
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#include <boost/format.hpp>
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-#include <boost/progress.hpp>
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+#include <boost/timer/progress_display.hpp>
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// VOTCA includes
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#include <votca/tools/constants.h>
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@@ -290,7 +290,7 @@ void KMCLifetime::RunVSSM() {
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// determine where it will jump to
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ResetForbiddenlist(forbiddendests);
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- boost::progress_display progress(insertions_);
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+ boost::timer::progress_display progress(insertions_);
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while (true) {
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// LEVEL 2
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diff --git a/xtp/src/libxtp/calculators/neighborlist.cc b/xtp/src/libxtp/calculators/neighborlist.cc
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index ce18af288..0b4bcc61b 100644
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--- a/xtp/src/libxtp/calculators/neighborlist.cc
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+++ b/xtp/src/libxtp/calculators/neighborlist.cc
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@@ -17,7 +17,7 @@
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// Third party includes
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#include <boost/format.hpp>
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-#include <boost/progress.hpp>
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+#include <boost/timer/progress_display.hpp>
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// Local private VOTCA includes
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#include "neighborlist.h"
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@@ -124,7 +124,7 @@ bool Neighborlist::Evaluate(Topology& top) {
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top.NBList().Cleanup();
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- boost::progress_display progress(segs.size());
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+ boost::timer::progress_display progress(segs.size());
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// cache approx sizes
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std::vector<double> approxsize = std::vector<double>(segs.size(), 0.0);
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#pragma omp parallel for
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74
1093.patch
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74
1093.patch
Normal file
@ -0,0 +1,74 @@
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From e1e568942fef46f63cfae0317a72f86cf4bddf46 Mon Sep 17 00:00:00 2001
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From: Christoph Junghans <junghans@votca.org>
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Date: Wed, 15 Nov 2023 19:56:20 -0700
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Subject: [PATCH] py: fix all shebangs
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---
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tools/scripts/extract_xml_metadata.py | 2 +-
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xtp-tutorials/pyxtp/scripts/run_energy.py | 2 +-
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xtp-tutorials/pyxtp/scripts/run_gradient.py | 2 +-
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xtp-tutorials/pyxtp/scripts/run_mapchecker.py | 2 +-
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xtp-tutorials/pyxtp/scripts/run_optimization.py | 2 +-
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xtp/src/pyxtp/pyxtp/capture_standard_output.py | 2 +-
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6 files changed, 6 insertions(+), 6 deletions(-)
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diff --git a/tools/scripts/extract_xml_metadata.py b/tools/scripts/extract_xml_metadata.py
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index 413fb81f07..fde43f5ec3 100755
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--- a/tools/scripts/extract_xml_metadata.py
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+++ b/tools/scripts/extract_xml_metadata.py
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@@ -1,4 +1,4 @@
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-#!/usr/bin/env python
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+#!/usr/bin/env python3
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#
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# Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org)
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#
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diff --git a/xtp-tutorials/pyxtp/scripts/run_energy.py b/xtp-tutorials/pyxtp/scripts/run_energy.py
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index bf585b91e8..dbc8d2b9d0 100644
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--- a/xtp-tutorials/pyxtp/scripts/run_energy.py
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+++ b/xtp-tutorials/pyxtp/scripts/run_energy.py
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@@ -1,4 +1,4 @@
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-#!/usr/bin/env python
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+#!/usr/bin/env python3
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"""Example to compute energies using XTP."""
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from pyxtp import xtp, Visualization
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from ase import Atoms
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diff --git a/xtp-tutorials/pyxtp/scripts/run_gradient.py b/xtp-tutorials/pyxtp/scripts/run_gradient.py
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index 30bfbf0472..16aa6c8730 100644
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--- a/xtp-tutorials/pyxtp/scripts/run_gradient.py
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+++ b/xtp-tutorials/pyxtp/scripts/run_gradient.py
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@@ -1,4 +1,4 @@
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-#!/usr/bin/env python
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+#!/usr/bin/env python3
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"""Example to perform a gradient calculation."""
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from pyxtp import xtp
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from ase import Atoms
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diff --git a/xtp-tutorials/pyxtp/scripts/run_mapchecker.py b/xtp-tutorials/pyxtp/scripts/run_mapchecker.py
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index 41db246465..f53783ce68 100755
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--- a/xtp-tutorials/pyxtp/scripts/run_mapchecker.py
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+++ b/xtp-tutorials/pyxtp/scripts/run_mapchecker.py
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@@ -1,4 +1,4 @@
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-#!/usr/bin/env python
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+#!/usr/bin/env python3
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"""Examples to show xtp_binds usage."""
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from pyxtp import xtp_binds
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from pathlib import Path
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diff --git a/xtp-tutorials/pyxtp/scripts/run_optimization.py b/xtp-tutorials/pyxtp/scripts/run_optimization.py
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index 3a624e35b5..c4301b43af 100644
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--- a/xtp-tutorials/pyxtp/scripts/run_optimization.py
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+++ b/xtp-tutorials/pyxtp/scripts/run_optimization.py
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@@ -1,4 +1,4 @@
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-#!/usr/bin/env python
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+#!/usr/bin/env python3
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"""Example to optimize the geometry of CO"""
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from pyxtp import xtp
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from ase.io import write
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diff --git a/xtp/src/pyxtp/pyxtp/capture_standard_output.py b/xtp/src/pyxtp/pyxtp/capture_standard_output.py
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index 5cc5e14c2d..ec5514ac33 100644
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--- a/xtp/src/pyxtp/pyxtp/capture_standard_output.py
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+++ b/xtp/src/pyxtp/pyxtp/capture_standard_output.py
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@@ -1,4 +1,4 @@
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-#!/usr/bin/env python
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+#!/usr/bin/env python3
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"""Examples to show xtp_binds usage."""
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import io
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from contextlib import redirect_stdout
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@ -1,3 +0,0 @@
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version https://git-lfs.github.com/spec/v1
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oid sha256:4710a7552f94789936324d76d2e0830b576de8d3f1c605748e2d20947d018100
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size 61692029
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3
votca-2023.tar.gz
Normal file
3
votca-2023.tar.gz
Normal file
@ -0,0 +1,3 @@
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version https://git-lfs.github.com/spec/v1
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oid sha256:ac78d2eb5a6694b76878d2ab1ec86bb161765143a447cc23905cdcb2bb6743be
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size 38975119
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@ -1,3 +1,62 @@
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-------------------------------------------------------------------
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Thu Nov 16 04:24:41 UTC 2023 - Christoph Junghans <junghans@votca.org>
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- Drop 1083.patch - merged upstream
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- Add 1093.patch from upstream to fix python shebang
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- Update to 2023
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- fix pyxtp option restart ([gh#votca/votca#1074])
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- fix Changelog check ([gh#votca/votca#1070])
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- add python bindings for xtp ([gh#votca/votca#1061])
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- replaced pointers in MD2QM mapping ([gh#votca/votca#1075])
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- fixed typo in esp2multipole option ([gh#votca/votca#1076])
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- update MKL detection to MKL config ([gh#votca/votca#1053])
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- remove geometry optimization ([gh#votca/votca#1077])
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- remove all references to old pdf manual ([gh#votca/votca#1081])
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- replaced deprecated boost::progress headers ([gh#votca/votca#1083])
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- drop intel classic builds from CI ([gh#votca/votca#1085])
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- disable some libint2 warning and CI clean up ([gh#votca/votca#1088])
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- fix population analysis for embedded DFT ([gh#votca/votca#1089])
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- fix pyxtp xtp-tutorials ([gh#votca/votca#1090])
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- add note on gmx build for install ([gh#votca/votca#1052])
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- fix typos in esp2multipole options ([gh#votca/votca#1054])
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- Used sharedable lock in xtp ([gh#votca/votca#1057])
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- Make votca tests compile without OpenMP ([gh#votca/votca#1065])
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- increase tolerance for diabatization test ([gh#votca/votca#1039],
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[gh#votca/votca#1043])
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- removed boost::filesystem ([gh#votca/votca#1041])
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- clean up C++ defines ([gh#votca/votca#1044])
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- drop gmx-2022 builds from CI ([gh#votca/votca#1046])
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- update ccaching in CI ([gh#votca/votca#1048], [gh#votca/votca#1050])
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- add support for gmx-2023 api ([gh#votca/votca#1059])
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- updated formatting ([gh#votca/votca#1062])
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- remove stable branch workflow ([gh#votca/votca#1066])
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- Refactor changelog actions ([gh#votca/votca#1068])
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- fix CI build with icpx ([gh#votca/votca#1018])
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- implemented projection-based DFT embedding ([gh#votca/votca#964])
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- Added LMO energy output and cube file generation ([gh#votca/votca#970])
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- fix typos in csg-tutorials xml files ([gh#votca/votca#980])
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- unitary optimization for localization of orbitals ([gh#votca/votca#971])
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- separate option for density max convergence tolerance in qmmm
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([gh#votca/votca#987])
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- Correct ECP charges added in Orca Molden reader ([gh#votca/votca#990])
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- Implemented truncated basis for embedded DFT ([gh#votca/votca#991])
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- Implemented ER diabatization for BSE ([gh#votca/votca#988])
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- update esp++ spce tutorial to py3 ([gh#votca/votca#997])
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- Truncated GW-in-DFT embedded in static/polar MM implemeted
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([gh#votca/votca#1003])
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- reducing XTP tutorial size ([gh#votca/votca#1020], [gh#votca/votca#1025])
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- Clean up 3body Stillinger-Weber implement, docs and tutorial
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([gh#votca/votca#1012])
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- fixed options handling in xtp_autogen_mapping ([gh#votca/votca#1024])
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- Major CMake refactor ([gh#votca/votca#950], [gh#votca/votca#1022])
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- Fix all doxygen warnings ([gh#votca/votca#1026])
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- basis and auxbasis are written to QMMM checkpoint file
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([gh#votca/votca#1030])
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- iterations_max can now be zero ([gh#votca/votca#1033])
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- add an XML check to csg_inverse ([gh#votca/votca#1031])
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- fix propane/imc and add propane/imc-ibiintra to csg-tutorials
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([gh#votca/votca#821])
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-------------------------------------------------------------------
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Mon Nov 13 23:26:43 UTC 2023 - Christoph Junghans <junghans@votca.org>
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12
votca.spec
12
votca.spec
@ -25,17 +25,17 @@
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%endif
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Name: votca
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Version: 2022.1
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Version: 2023
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Release: 0
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%define uversion %{version}
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%define sover 2022
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%define sover 2023
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Summary: Versatile Object-oriented Toolkit for Coarse-graining Applications
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License: Apache-2.0
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Group: Productivity/Scientific/Chemistry
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URL: https://www.votca.org
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Source0: https://github.com/votca/votca/archive/v%{uversion}.tar.gz#/%{name}-%{uversion}.tar.gz
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# PATCH-FIX-UPSTREAM 1083.patch -- based on upsteam PR 1083, fix build with boost-1.82
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Patch0: 1083.patch
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# PATCH-FIX-UPSTREAM 1093.patch -- fix python shebang
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Patch0: 1093.patch
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BuildRequires: cmake >= 3.13
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BuildRequires: eigen3-devel
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@ -196,7 +196,7 @@ This package contains the bash completion support for votca.
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%install
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%cmake_install
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sed -i '1s@env @@' %{buildroot}/%{_bindir}/votca_{compare,help2doc} \
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sed -i '1s@env @@' \
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%{buildroot}/%{_datadir}/votca/scripts/inverse/{iie,cma_processor,table_smooth_at_cut_off}.py \
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%{buildroot}/%{_datadir}/votca/csg-tutorials/LJ1-LJ2/imc/svd.py \
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%{buildroot}/%{_datadir}/votca/csg-tutorials/spce/ibi*/spce.py
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@ -207,7 +207,7 @@ sed -i '1s@env @@' %{buildroot}/%{_bindir}/xtp_* %{buildroot}/%{_datadir}/votca/
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# Move bash completion file to correct location
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mkdir -p %{buildroot}%{_datadir}/bash_completion.d
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cp %{buildroot}%{_datadir}/votca/rc/csg-completion.bash %{buildroot}%{_datadir}/bash_completion.d/votca
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cp %{__builddir}/csg/scripts/csg-completion.bash %{buildroot}%{_datadir}/bash_completion.d/votca
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%fdupes %{buildroot}%{_prefix}
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