Script 'mail_helper' called by obssrc
Hello community,
here is the log from the commit of package votca-xtp for openSUSE:Factory
checked in at 2021-01-15 19:46:22
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Comparing /work/SRC/openSUSE:Factory/votca-xtp (Old)
and /work/SRC/openSUSE:Factory/.votca-xtp.new.28504 (New)
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Package is "votca-xtp"
Fri Jan 15 19:46:22 2021 rev:7 rq:863158 version:1.6.4
Changes:
--------
--- /work/SRC/openSUSE:Factory/votca-xtp/votca-xtp.changes 2020-08-25
09:37:19.704160773 +0200
+++ /work/SRC/openSUSE:Factory/.votca-xtp.new.28504/votca-xtp.changes
2021-01-15 19:46:32.398049664 +0100
@@ -1,0 +2,19 @@
+Tue Jan 12 23:50:49 UTC 2021 - Christoph Junghans <jungh...@votca.org>
+
+- Update to 1.6.4
+ - fix build on openSUSE ([gh#votca/xtp#622])
+ - Refactored logger ([gh#votca/xtp#625])
+
+-------------------------------------------------------------------
+Wed Dec 9 20:28:07 UTC 2020 - Christoph Junghans <jungh...@votca.org>
+
+- Update to 1.6.3
+ - switch to ghcr.io for CI ([gh#votca/xtp#555])
+ - fixing Gaussian guess read keyword ([gh#votca/xtp#562],
+ [gh#votca/xtp#563])
+ - improved kmc output ([gh#votca/xtp#575])
+ - use master .clang-format in format action ([gh#votca/xtp#582],
+ [gh#votca/xtp#584])
+ - strip windows line endings in readers ([gh#votca/xtp#596])
+
+-------------------------------------------------------------------
Old:
----
votca-xtp-1.6.2.tar.gz
New:
----
votca-xtp-1.6.4.tar.gz
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Other differences:
------------------
++++++ votca-xtp.spec ++++++
--- /var/tmp/diff_new_pack.rR8fUb/_old 2021-01-15 19:46:33.054050641 +0100
+++ /var/tmp/diff_new_pack.rR8fUb/_new 2021-01-15 19:46:33.058050646 +0100
@@ -1,8 +1,8 @@
#
# spec file for package votca-xtp
#
-# Copyright (c) 2020 SUSE LLC
-# Copyright (c) 2018-2020 Christoph Junghans
+# Copyright (c) 2021 SUSE LLC
+# Copyright (c) 2018-2021 Christoph Junghans
#
# All modifications and additions to the file contributed by third parties
# remain the property of their copyright owners, unless otherwise agreed
@@ -18,7 +18,7 @@
Name: votca-xtp
-Version: 1.6.2
+Version: 1.6.4
Release: 0
%define uversion %{version}
%define sover 6
@@ -28,8 +28,6 @@
URL: http://www.votca.org
Source0:
https://github.com/votca/xtp/archive/v%{uversion}.tar.gz#/%{name}-%{uversion}.tar.gz
-BuildRoot: %{_tmppath}/%{name}-%{version}-build
-
BuildRequires: cmake >= 2.8.4
BuildRequires: fdupes
BuildRequires: gcc-c++
++++++ votca-xtp-1.6.2.tar.gz -> votca-xtp-1.6.4.tar.gz ++++++
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore'
old/xtp-1.6.2/.github/workflows/continuous-integration-workflow.yml
new/xtp-1.6.4/.github/workflows/continuous-integration-workflow.yml
--- old/xtp-1.6.2/.github/workflows/continuous-integration-workflow.yml
2020-08-22 15:31:18.000000000 +0200
+++ new/xtp-1.6.4/.github/workflows/continuous-integration-workflow.yml
2021-01-12 19:26:43.000000000 +0100
@@ -7,10 +7,10 @@
jobs:
CI:
- continue-on-error: ${{ matrix.distro == 'ubuntu_devel' || matrix.distro ==
'fedora_rawhide' || matrix.continue-on-error == true }}
+ continue-on-error: ${{ matrix.distro == 'ubuntu:devel' || matrix.distro ==
'opensuse:latest' || matrix.distro == 'fedora:rawhide' ||
matrix.continue-on-error == true }}
strategy:
matrix:
- distro: [latest, fedora_rawhide, opensuse, ubuntu, ubuntu_devel,
ubuntu_rolling, ubuntu_18.04, intel]
+ distro: ['fedora:latest', 'fedora:rawhide', 'opensuse:latest',
'ubuntu:latest', 'ubuntu:devel', 'ubuntu:rolling', 'ubuntu:18.04',
'fedora:intel']
toolchain: [gnu, clang]
cmake_build_type: [Release, Debug]
minimal: [false]
@@ -19,13 +19,13 @@
coverage: [false]
no_regression_testing: [true]
include:
- - distro: latest
+ - distro: 'fedora:latest'
toolchain: gnu
cmake_build_type: Release
module_build: true
no_regression_testing: true
runs-on: ubuntu-latest
- container: votca/buildenv:${{ matrix.distro }}
+ container: ghcr.io/votca/buildenv/${{ matrix.distro }}
steps:
- uses: actions/checkout@v2.2.0
with:
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/xtp-1.6.2/.github/workflows/format.yml
new/xtp-1.6.4/.github/workflows/format.yml
--- old/xtp-1.6.2/.github/workflows/format.yml 2020-08-22 15:31:18.000000000
+0200
+++ new/xtp-1.6.4/.github/workflows/format.yml 2021-01-12 19:26:43.000000000
+0100
@@ -7,7 +7,7 @@
name: clang-format
if: ${{ github.event.comment.body == '@votca-bot format' }}
runs-on: ubuntu-latest
- container: votca/buildenv:format
+ container: ghcr.io/votca/buildenv/format:latest
steps:
- name: Check if message comes from PR
uses: octokit/request-action@v2.x
@@ -35,7 +35,9 @@
token: ${{ secrets.VOTCA_BOT_TOKEN }}
- name: Run clang-format
if: ${{ fromJSON(steps.issue_info.outputs.data).pull_request }}
- run: find . -type f -regex ".*\.\(c\|h\|cc\|cpp\|hpp\)" -print0 |
xargs -0 clang-format -i -style=file
+ run: |
+ curl -OL https://github.com/votca/votca/raw/master/.clang-format
+ find . -type f -regex ".*\.\(c\|h\|cc\|cpp\|hpp\)" -print0 | xargs
-0 clang-format -i -style=file
- name: Commit and push
if: ${{ fromJSON(steps.issue_info.outputs.data).pull_request }}
run: |
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/xtp-1.6.2/.gitlab-ci.yml new/xtp-1.6.4/.gitlab-ci.yml
--- old/xtp-1.6.2/.gitlab-ci.yml 2020-08-22 15:31:18.000000000 +0200
+++ new/xtp-1.6.4/.gitlab-ci.yml 1970-01-01 01:00:00.000000000 +0100
@@ -1,66 +0,0 @@
-stages:
- - build
-
-.build_script:
- retry:
- max: 2
- variables:
- CCACHE_DIR: "${CI_PROJECT_DIR}/ccache"
- stage: build
- artifacts:
- paths:
- - ${CI_PROJECT_DIR}/votca
- when: always
- dependencies: []
- cache:
- paths:
- - ccache/
- script:
- - ccache -z
- - j="$(grep -c processor /proc/cpuinfo 2>/dev/null)" || j=0; ((j++))
- - git branch commit_of_build_${CI_BUILD_ID} ${CI_COMMIT_SHA}
- - git clone https://github.com/votca/votca
- - pushd votca
- - if [[ ${CI_COMMIT_TAG} = v[12].[0-9]* ]]; then
- git checkout -b ${CI_COMMIT_TAG} ${CI_COMMIT_TAG};
- elif [[ ( ${CI_COMMIT_REF_NAME} =~ ^for/([^/]*)/.* ||
${CI_COMMIT_REF_NAME} =~ ^(stable)$ ) && ${BASH_REMATCH[1]} != master ]]; then
- git checkout -b ${BASH_REMATCH[1]} origin/${BASH_REMATCH[1]};
- fi
- - git submodule update --recursive --init
- - git -C ${CI_PROJECT_NAME} fetch ${CI_PROJECT_DIR}
commit_of_build_${CI_BUILD_ID}
- - git -C ${CI_PROJECT_DIR} branch -d commit_of_build_${CI_BUILD_ID}
- - git -C ${CI_PROJECT_NAME} checkout -f ${CI_COMMIT_SHA}
- - mkdir -p build
- - pushd build
- - cmake .. -DCMAKE_VERBOSE_MAKEFILE=ON -DENABLE_TESTING=ON -DBUILD_XTP=ON
-DENABLE_WERROR=ON
- -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
- ${CMAKE_GENERATOR:+-G${CMAKE_GENERATOR}}
- -DMODULE_BUILD=${MODULE_BUILD}
${MODULE_BUILD:+-DCMAKE_INSTALL_PREFIX=/home/votca/votca.install}
- -DCMAKE_DISABLE_FIND_PACKAGE_MKL=${DISABLE_MKL}
- -DUSE_CUDA=${USE_CUDA}
- - cmake --build . --parallel 2
- - ctest --output-on-failure
- - test -z "${MODULE_BUILD}" && DESTDIR=${PWD}/install cmake --install . &&
rm -rf ${PWD}/install/usr && rmdir ${PWD}/install
- - sudo cmake --install .
- - if [[ ${CLANG_FORMAT} ]]; then cmake --build . --target format && git -C
${CI_PROJECT_DIR}/votca/${CI_PROJECT_NAME} diff --exit-code; fi
- - ccache -s
-
-.build:
- variables:
- DISTRO: "latest"
- image: votca/buildenv:${DISTRO}
- extends: .build_script
-
-Debug GPU Ubuntu:
- variables:
- CC: "gcc"
- CXX: "g++"
- CMAKE_BUILD_TYPE: "Debug"
- USE_CUDA: "yes"
- DISABLE_MKL: "yes"
- before_script:
- - source /opt/gromacs-2019/bin/GMXRC.bash
- extends: .build_script
- allow_failure: true
- tags:
- - gpu
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/xtp-1.6.2/CHANGELOG.md new/xtp-1.6.4/CHANGELOG.md
--- old/xtp-1.6.2/CHANGELOG.md 2020-08-22 15:31:18.000000000 +0200
+++ new/xtp-1.6.4/CHANGELOG.md 2021-01-12 19:26:43.000000000 +0100
@@ -1,7 +1,18 @@
For more detailed information about the changes see the history of the
[repository](https://github.com/votca/xtp/commits/master).
-## Version 1.6.2 (released 22.08.20)
+## Version 1.6.4 (released 12.01.21)
+* fix build on openSUSE (#622)
+* Refactored logger (#625)
+
+## Version 1.6.3 (released 09.12.20)
+* switch to ghcr.io for CI (#555)
+* fixing Gaussian guess read keyword (#562, #563)
+* improved kmc output (#575)
+* use master .clang-format in format action (#582, #584)
+* strip windows line endings in readers (#596)
+
+## Version 1.6.2 _SuperGitta_ (released 22.08.20)
* move CI to GitHub Actions (#512, #514, #516, #519)
* add more checks to the dft_parse_part (#521)
* make unit tests work in parallel (#530)
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/xtp-1.6.2/CMakeLists.txt new/xtp-1.6.4/CMakeLists.txt
--- old/xtp-1.6.2/CMakeLists.txt 2020-08-22 15:31:18.000000000 +0200
+++ new/xtp-1.6.4/CMakeLists.txt 2021-01-12 19:26:43.000000000 +0100
@@ -2,7 +2,7 @@
project(votca-xtp)
-set(PROJECT_VERSION "1.6.2")
+set(PROJECT_VERSION "1.6.4")
set(PROJECT_CONTACT "b...@votca.org")
string(REGEX REPLACE "^[1-9]+\\.([1-9]+).*$" "\\1" SOVERSION
"${PROJECT_VERSION}")
if (NOT ${SOVERSION} MATCHES "[1-9]+")
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/xtp-1.6.2/include/votca/xtp/logger.h
new/xtp-1.6.4/include/votca/xtp/logger.h
--- old/xtp-1.6.2/include/votca/xtp/logger.h 2020-08-22 15:31:18.000000000
+0200
+++ new/xtp-1.6.4/include/votca/xtp/logger.h 2021-01-12 19:26:43.000000000
+0100
@@ -42,7 +42,7 @@
/*
* Custom buffer to store messages
*/
-class LogBuffer : public std::stringbuf {
+class LogBuffer final : public std::stringbuf {
public:
LogBuffer() : std::stringbuf() { _LogLevel = Log::current_level; }
@@ -105,7 +105,7 @@
bool _writePreface = true;
protected:
- int sync() override {
+ int sync() {
std::ostringstream _message;
@@ -165,35 +165,30 @@
}
public:
- Logger() : std::ostream(new LogBuffer()), _ReportLevel(Log::current_level) {
+ Logger() : std::ostream(&_buffer), _ReportLevel(Log::current_level) {
setMultithreading(_maverick);
}
Logger(Log::Level ReportLevel)
- : std::ostream(new LogBuffer()), _ReportLevel(ReportLevel) {
+ : std::ostream(&_buffer), _ReportLevel(ReportLevel) {
setMultithreading(_maverick);
}
- ~Logger() final {
- delete rdbuf();
- rdbuf(nullptr);
- }
-
Logger &operator()(Log::Level LogLevel) {
- dynamic_cast<LogBuffer *>(rdbuf())->setLogLevel(LogLevel);
+ _buffer.setLogLevel(LogLevel);
return *this;
}
void setReportLevel(Log::Level ReportLevel) { _ReportLevel = ReportLevel; }
void setMultithreading(bool maverick) {
_maverick = maverick;
- dynamic_cast<LogBuffer *>(rdbuf())->setMultithreading(_maverick);
+ _buffer.setMultithreading(_maverick);
}
bool isMaverick() const { return _maverick; }
Log::Level getReportLevel() const { return _ReportLevel; }
void setPreface(Log::Level level, const std::string &preface) {
- dynamic_cast<LogBuffer *>(rdbuf())->setPreface(level, preface);
+ _buffer.setPreface(level, preface);
}
void setCommonPreface(const std::string &preface) {
@@ -203,22 +198,19 @@
setPreface(Log::warning, preface);
}
- void EnablePreface() { dynamic_cast<LogBuffer *>(rdbuf())->EnablePreface(); }
+ void EnablePreface() { _buffer.EnablePreface(); }
- void DisablePreface() {
- dynamic_cast<LogBuffer *>(rdbuf())->DisablePreface();
- }
+ void DisablePreface() { _buffer.DisablePreface(); }
private:
+ LogBuffer _buffer;
// at what level of detail output messages
Log::Level _ReportLevel = Log::error;
// if true, only a single processor job is executed
bool _maverick = false;
- std::string Messages() {
- return dynamic_cast<LogBuffer *>(rdbuf())->Messages();
- }
+ std::string Messages() { return _buffer.Messages(); }
};
/**
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/xtp-1.6.2/src/libxtp/calculators/kmclifetime.cc
new/xtp-1.6.4/src/libxtp/calculators/kmclifetime.cc
--- old/xtp-1.6.2/src/libxtp/calculators/kmclifetime.cc 2020-08-22
15:31:18.000000000 +0200
+++ new/xtp-1.6.4/src/libxtp/calculators/kmclifetime.cc 2021-01-12
19:26:43.000000000 +0100
@@ -1,5 +1,5 @@
/*
- * Copyright 2009-2019 The VOTCA Development Team (http://www.votca.org)
+ * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org)
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
@@ -379,9 +379,10 @@
time_t now = time(nullptr);
tm* localtm = localtime(&now);
+
XTP_LOG(Log::error, _log)
<< " KMCLIFETIME finished at:" << asctime(localtm) << std::flush;
-
+ std::cout << _log << std::flush;
return true;
}
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/xtp-1.6.2/src/libxtp/calculators/kmcmultiple.cc
new/xtp-1.6.4/src/libxtp/calculators/kmcmultiple.cc
--- old/xtp-1.6.2/src/libxtp/calculators/kmcmultiple.cc 2020-08-22
15:31:18.000000000 +0200
+++ new/xtp-1.6.4/src/libxtp/calculators/kmcmultiple.cc 2021-01-12
19:26:43.000000000 +0100
@@ -1,5 +1,5 @@
/*
- * Copyright 2009-2019 The VOTCA Development Team (http://www.votca.org)
+ * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org)
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
@@ -458,7 +458,7 @@
LoadGraph(top);
RunVSSM();
-
+ std::cout << _log << std::flush;
return true;
}
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/xtp-1.6.2/src/libxtp/calculators/vaverage.cc
new/xtp-1.6.4/src/libxtp/calculators/vaverage.cc
--- old/xtp-1.6.2/src/libxtp/calculators/vaverage.cc 2020-08-22
15:31:18.000000000 +0200
+++ new/xtp-1.6.4/src/libxtp/calculators/vaverage.cc 2021-01-12
19:26:43.000000000 +0100
@@ -1,5 +1,5 @@
/*
- * Copyright 2009-2019 The VOTCA Development Team
+ * Copyright 2009-2020 The VOTCA Development Team
* (http://www.votca.org)
*
* Licensed under the Apache License, Version 2.0 (the "License")
@@ -17,6 +17,8 @@
*
*/
+#include <votca/tools/getline.h>
+
#include "vaverage.h"
#include "votca/xtp/topology.h"
@@ -44,7 +46,7 @@
Index id = 0;
while (intt.good()) {
- std::getline(intt, line);
+ tools::getline(intt, line);
std::vector<std::string> split;
tools::Tokenizer toker(line, " \t");
toker.ToVector(split);
@@ -77,7 +79,7 @@
std::string line;
while (intt.good()) {
- std::getline(intt, line);
+ tools::getline(intt, line);
std::vector<std::string> split;
tools::Tokenizer toker(line, " \t");
toker.ToVector(split);
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/xtp-1.6.2/src/libxtp/classicalsegment.cc
new/xtp-1.6.4/src/libxtp/classicalsegment.cc
--- old/xtp-1.6.2/src/libxtp/classicalsegment.cc 2020-08-22
15:31:18.000000000 +0200
+++ new/xtp-1.6.4/src/libxtp/classicalsegment.cc 2021-01-12
19:26:43.000000000 +0100
@@ -1,5 +1,5 @@
/*
- * Copyright 2016 The VOTCA Development Team
+ * Copyright 2016-2020 The VOTCA Development Team
* (http://www.votca.org)
*
* Licensed under the Apache License, Version 2.0 (the "License")
@@ -21,6 +21,7 @@
#include "votca/xtp/atomcontainer.h"
#include <boost/format.hpp>
#include <votca/tools/elements.h>
+#include <votca/tools/getline.h>
#include <votca/tools/tokenizer.h>
namespace votca {
@@ -47,7 +48,7 @@
}
while (intt.good()) {
- std::getline(intt, line);
+ tools::getline(intt, line);
tools::Tokenizer toker(line, " \t");
std::vector<std::string> split = toker.ToVector();
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/xtp-1.6.2/src/libxtp/dftengine/dftengine.cc
new/xtp-1.6.4/src/libxtp/dftengine/dftengine.cc
--- old/xtp-1.6.2/src/libxtp/dftengine/dftengine.cc 2020-08-22
15:31:18.000000000 +0200
+++ new/xtp-1.6.4/src/libxtp/dftengine/dftengine.cc 2021-01-12
19:26:43.000000000 +0100
@@ -23,6 +23,7 @@
#include "votca/xtp/qmmolecule.h"
#include <boost/filesystem.hpp>
#include <boost/format.hpp>
+#include <iomanip>
#include <vector>
#include <votca/tools/constants.h>
#include <votca/tools/elements.h>
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/xtp-1.6.2/src/libxtp/polarregion.cc
new/xtp-1.6.4/src/libxtp/polarregion.cc
--- old/xtp-1.6.2/src/libxtp/polarregion.cc 2020-08-22 15:31:18.000000000
+0200
+++ new/xtp-1.6.4/src/libxtp/polarregion.cc 2021-01-12 19:26:43.000000000
+0100
@@ -18,6 +18,7 @@
*/
#include "votca/xtp/eeinteractor.h"
+#include <iomanip>
#include <numeric>
#include <votca/xtp/dipoledipoleinteraction.h>
#include <votca/xtp/polarregion.h>
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/xtp-1.6.2/src/libxtp/qmpackage.cc
new/xtp-1.6.4/src/libxtp/qmpackage.cc
--- old/xtp-1.6.2/src/libxtp/qmpackage.cc 2020-08-22 15:31:18.000000000
+0200
+++ new/xtp-1.6.4/src/libxtp/qmpackage.cc 2021-01-12 19:26:43.000000000
+0100
@@ -1,5 +1,5 @@
/*
- * Copyright 2009-2019 The VOTCA Development Team
+ * Copyright 2009-2020 The VOTCA Development Team
* (http://www.votca.org)
*
* Licensed under the Apache License, Version 2.0 (the "License")
@@ -19,6 +19,7 @@
#include "votca/xtp/qmpackage.h"
#include <boost/algorithm/string.hpp>
+#include <votca/tools/getline.h>
#include <votca/xtp/ecpaobasis.h>
#include <votca/xtp/orbitals.h>
@@ -145,7 +146,7 @@
std::vector<std::string> QMPackage::GetLineAndSplit(
std::ifstream& input_file, const std::string separators) const {
std::string line;
- getline(input_file, line);
+ tools::getline(input_file, line);
boost::trim(line);
tools::Tokenizer tok(line, separators);
return tok.ToVector();
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/xtp-1.6.2/src/libxtp/qmpackages/gaussian.cc
new/xtp-1.6.4/src/libxtp/qmpackages/gaussian.cc
--- old/xtp-1.6.2/src/libxtp/qmpackages/gaussian.cc 2020-08-22
15:31:18.000000000 +0200
+++ new/xtp-1.6.4/src/libxtp/qmpackages/gaussian.cc 2021-01-12
19:26:43.000000000 +0100
@@ -1,5 +1,5 @@
/*
- * Copyright 2009-2019 The VOTCA Development Team
+ * Copyright 2009-2020 The VOTCA Development Team
* (http://www.votca.org)
*
* Licensed under the Apache License, Version 2.0 (the "License")
@@ -24,6 +24,7 @@
#include <iomanip>
#include <stdio.h>
#include <votca/tools/constants.h>
+#include <votca/tools/getline.h>
#include <votca/xtp/ecpaobasis.h>
#include <votca/xtp/orbitals.h>
@@ -63,9 +64,9 @@
std::string::size_type iop_pos;
// check if the guess keyword is present, if yes, append the guess later
if (_write_guess) {
- iop_pos = _options.find("cards");
- if (iop_pos != std::string::npos) {
- _options = _options + " cards ";
+ iop_pos = _options.find("guess=cards");
+ if (iop_pos == std::string::npos) {
+ _options = _options + " guess=cards ";
}
}
@@ -539,13 +540,13 @@
}
// number of coefficients per line is in the first line of the file (5D15.8)
- getline(input_file, line);
+ tools::getline(input_file, line);
std::vector<std::string> strs;
boost::algorithm::split(strs, line, boost::is_any_of("(D)"));
while (input_file) {
- getline(input_file, line);
+ tools::getline(input_file, line);
// if a line has an equality sign, must be energy
std::string::size_type energy_pos = line.find("=");
@@ -645,7 +646,7 @@
} while (ch != '\n' && (Index)input_file.tellg() != -1);
std::string line;
- getline(input_file, line);
+ tools::getline(input_file, line);
input_file.close();
std::string::size_type success = line.find("Normal termination of Gaussian");
@@ -678,7 +679,7 @@
std::vector<std::string> archive;
while (input_file) {
- getline(input_file, line);
+ tools::getline(input_file, line);
boost::trim(line);
GetArchive(archive, line, input_file);
@@ -686,8 +687,8 @@
if (charge_pos != std::string::npos) {
has_charges = true;
XTP_LOG(Log::info, *_pLog) << "Getting charges" << flush;
- getline(input_file, line);
- getline(input_file, line);
+ tools::getline(input_file, line);
+ tools::getline(input_file, line);
std::vector<std::string> row = GetLineAndSplit(input_file, "\t ");
Index nfields = Index(row.size());
@@ -732,20 +733,20 @@
Eigen::Matrix3d pol = Eigen::Matrix3d::Zero();
while (input_file) {
- getline(input_file, line);
+ tools::getline(input_file, line);
boost::trim(line);
std::string::size_type pol_pos =
line.find("Dipole polarizability, Alpha (input orientation)");
if (pol_pos != std::string::npos) {
XTP_LOG(Log::error, *_pLog) << "Getting polarizability" << flush;
- getline(input_file, line);
- getline(input_file, line);
- getline(input_file, line);
- getline(input_file, line);
- getline(input_file, line);
+ tools::getline(input_file, line);
+ tools::getline(input_file, line);
+ tools::getline(input_file, line);
+ tools::getline(input_file, line);
+ tools::getline(input_file, line);
for (Index i = 0; i < 6; i++) {
- getline(input_file, line);
+ tools::getline(input_file, line);
tools::Tokenizer tok2(line, " ");
std::vector<std::string> values = tok2.ToVector();
if (values.size() != 4) {
@@ -776,7 +777,7 @@
boost::trim(line);
std::string sum = line;
while (line.size() != 0) {
- getline(input_file, line);
+ tools::getline(input_file, line);
boost::trim(line);
sum += line;
}
@@ -876,7 +877,7 @@
while (input_file) {
- getline(input_file, line);
+ tools::getline(input_file, line);
boost::trim(line);
/* Check for ScaHFX = factor of HF exchange included in functional */
@@ -943,7 +944,7 @@
occupied_levels += Index(energies.size());
energies.clear();
}
- getline(input_file, line);
+ tools::getline(input_file, line);
eigenvalues_pos = line.find("Alpha");
boost::trim(line);
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/xtp-1.6.2/src/libxtp/qmpackages/nwchem.cc
new/xtp-1.6.4/src/libxtp/qmpackages/nwchem.cc
--- old/xtp-1.6.2/src/libxtp/qmpackages/nwchem.cc 2020-08-22
15:31:18.000000000 +0200
+++ new/xtp-1.6.4/src/libxtp/qmpackages/nwchem.cc 2021-01-12
19:26:43.000000000 +0100
@@ -1,5 +1,5 @@
/*
- * Copyright 2009-2019 The VOTCA Development Team
+ * Copyright 2009-2020 The VOTCA Development Team
* (http://www.votca.org)
*
* Licensed under the Apache License, Version 2.0 (the "License")
@@ -21,7 +21,9 @@
#include <boost/algorithm/string.hpp>
#include <boost/filesystem.hpp>
#include <boost/format.hpp>
+#include <iomanip>
#include <votca/tools/filesystem.h>
+#include <votca/tools/getline.h>
#include <votca/xtp/ecpaobasis.h>
#include <votca/xtp/orbitals.h>
@@ -418,7 +420,7 @@
// the first 12 lines are garbage info
for (Index i = 0; i < 12; i++) {
- getline(input_file, line);
+ tools::getline(input_file, line);
}
// next line has basis set size
input_file >> basis_size;
@@ -526,7 +528,7 @@
ifstream input_file((_run_dir + "/" + _log_file_name));
bool has_charges = false;
while (input_file) {
- getline(input_file, line);
+ tools::getline(input_file, line);
boost::trim(line);
std::string::size_type charge_pos = line.find("ESP");
@@ -534,8 +536,8 @@
XTP_LOG(Log::error, *_pLog) << "Getting charges" << flush;
has_charges = true;
// two empty lines
- getline(input_file, line);
- getline(input_file, line);
+ tools::getline(input_file, line);
+ tools::getline(input_file, line);
// now starts the data in format
// _id type x y z q
@@ -576,14 +578,14 @@
Eigen::Matrix3d pol = Eigen::Matrix3d::Zero();
while (input_file) {
- getline(input_file, line);
+ tools::getline(input_file, line);
boost::trim(line);
std::string::size_type pol_pos =
line.find("DFT Linear Response polarizability / au");
if (pol_pos != std::string::npos) {
XTP_LOG(Log::error, *_pLog) << "Getting polarizability" << flush;
- getline(input_file, line);
+ tools::getline(input_file, line);
tools::Tokenizer tok(line, " ");
std::vector<std::string> line_split = tok.ToVector();
double frequency = std::stod(line_split[2]);
@@ -592,11 +594,11 @@
<< "Warning: Polarizability was calculated for frequency "
<< frequency << " normally f=0 for static polarizability" << flush;
}
- getline(input_file, line);
- getline(input_file, line);
- getline(input_file, line);
+ tools::getline(input_file, line);
+ tools::getline(input_file, line);
+ tools::getline(input_file, line);
for (Index i = 0; i < 3; i++) {
- getline(input_file, line);
+ tools::getline(input_file, line);
tools::Tokenizer tok2(line, " ");
std::vector<std::string> values = tok2.ToVector();
if (values.size() != 4) {
@@ -655,7 +657,7 @@
} while (ch != '\n' || (Index)input_file.tellg() == -1);
std::string line;
- getline(input_file, line); // Read the current line
+ tools::getline(input_file, line); // Read the current line
total_energy_pos = line.find("Total DFT energy");
diis_pos = line.find("diis");
// whatever is found first, determines the completeness of the file
@@ -705,7 +707,7 @@
// Start parsing the file line by line
ifstream input_file(log_file_name_full);
while (input_file) {
- getline(input_file, line);
+ tools::getline(input_file, line);
boost::trim(line);
/*
* basis set size (is only required for overlap matrix reading, rest is
@@ -743,9 +745,9 @@
//_has_coordinates = true;
bool has_QMAtoms = orbitals.hasQMAtoms();
// three garbage lines
- getline(input_file, line);
- getline(input_file, line);
- getline(input_file, line);
+ tools::getline(input_file, line);
+ tools::getline(input_file, line);
+ tools::getline(input_file, line);
// now starts the data in format
// _id type Qnuc x y z
std::vector<std::string> row = GetLineAndSplit(input_file, "\t ");
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/xtp-1.6.2/src/libxtp/qmpackages/orca.cc
new/xtp-1.6.4/src/libxtp/qmpackages/orca.cc
--- old/xtp-1.6.2/src/libxtp/qmpackages/orca.cc 2020-08-22 15:31:18.000000000
+0200
+++ new/xtp-1.6.4/src/libxtp/qmpackages/orca.cc 2021-01-12 19:26:43.000000000
+0100
@@ -1,5 +1,5 @@
/*
- * Copyright 2009-2019 The VOTCA Development Team
+ * Copyright 2009-2020 The VOTCA Development Team
* (http://www.votca.org)
*
* Licensed under the Apache License, Version 2.0 (the "License")
@@ -24,6 +24,7 @@
#include <iomanip>
#include <stdio.h>
#include <votca/tools/elements.h>
+#include <votca/tools/getline.h>
#include <votca/xtp/ecpaobasis.h>
#include <votca/xtp/orbitals.h>
@@ -402,7 +403,7 @@
std::ifstream input_file(log_file_name_full);
while (input_file) {
- getline(input_file, line);
+ tools::getline(input_file, line);
boost::trim(line);
GetCoordinates(result, line, input_file);
@@ -410,7 +411,7 @@
if (charge_pos != std::string::npos) {
XTP_LOG(Log::error, *_pLog) << "Getting charges" << flush;
- getline(input_file, line);
+ tools::getline(input_file, line);
std::vector<std::string> row = GetLineAndSplit(input_file, "\t ");
Index nfields = Index(row.size());
bool hasAtoms = result.size() > 0;
@@ -447,15 +448,15 @@
Eigen::Matrix3d pol = Eigen::Matrix3d::Zero();
while (input_file) {
- getline(input_file, line);
+ tools::getline(input_file, line);
boost::trim(line);
std::string::size_type pol_pos = line.find("THE POLARIZABILITY TENSOR");
if (pol_pos != std::string::npos) {
XTP_LOG(Log::error, *_pLog) << "Getting polarizability" << flush;
- getline(input_file, line);
- getline(input_file, line);
- getline(input_file, line);
+ tools::getline(input_file, line);
+ tools::getline(input_file, line);
+ tools::getline(input_file, line);
if (line.find("The raw cartesian tensor (atomic units)") ==
std::string::npos) {
@@ -464,7 +465,7 @@
}
for (Index i = 0; i < 3; i++) {
- getline(input_file, line);
+ tools::getline(input_file, line);
tools::Tokenizer tok2(line, " ");
std::vector<std::string> values = tok2.ToVector();
if (values.size() != 3) {
@@ -523,7 +524,7 @@
QMMolecule& mol = orbitals.QMAtoms();
while (input_file) {
- getline(input_file, line);
+ tools::getline(input_file, line);
boost::trim(line);
GetCoordinates(mol, line, input_file);
@@ -568,9 +569,9 @@
if (OE_pos != std::string::npos) {
number_of_electrons = 0;
- getline(input_file, line);
- getline(input_file, line);
- getline(input_file, line);
+ tools::getline(input_file, line);
+ tools::getline(input_file, line);
+ tools::getline(input_file, line);
if (line.find("E(Eh)") == std::string::npos) {
XTP_LOG(Log::error, *_pLog)
<< "Warning: Orbital Energies not found in log file" << flush;
@@ -658,7 +659,7 @@
XTP_LOG(Log::error, *_pLog) << "Getting the coordinates" << flush;
bool has_QMAtoms = mol.size() > 0;
// three garbage lines
- getline(input_file, line);
+ tools::getline(input_file, line);
// now starts the data in format
// _id type Qnuc x y z
vector<string> row = GetLineAndSplit(input_file, "\t ");
@@ -695,7 +696,7 @@
std::string line;
while (input_file) {
- getline(input_file, line);
+ tools::getline(input_file, line);
boost::trim(line);
std::string::size_type error = line.find("FATAL ERROR ENCOUNTERED");
if (error != std::string::npos) {
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/xtp-1.6.2/src/libxtp/tools/apdft.cc
new/xtp-1.6.4/src/libxtp/tools/apdft.cc
--- old/xtp-1.6.2/src/libxtp/tools/apdft.cc 2020-08-22 15:31:18.000000000
+0200
+++ new/xtp-1.6.4/src/libxtp/tools/apdft.cc 2021-01-12 19:26:43.000000000
+0100
@@ -16,6 +16,7 @@
*/
#include "apdft.h"
+#include <iomanip>
#include <votca/xtp/density_integration.h>
#include <votca/xtp/orbitals.h>
#include <votca/xtp/vxc_grid.h>
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/xtp-1.6.2/src/libxtp/tools/gencube.cc
new/xtp-1.6.4/src/libxtp/tools/gencube.cc
--- old/xtp-1.6.2/src/libxtp/tools/gencube.cc 2020-08-22 15:31:18.000000000
+0200
+++ new/xtp-1.6.4/src/libxtp/tools/gencube.cc 2021-01-12 19:26:43.000000000
+0100
@@ -1,5 +1,5 @@
/*
- * Copyright 2009-2019 The VOTCA Development Team
+ * Copyright 2009-2020 The VOTCA Development Team
* (http://www.votca.org)
*
* Licensed under the Apache License, Version 2.0 (the "License")
@@ -23,6 +23,7 @@
#include <stdio.h>
#include <votca/tools/constants.h>
#include <votca/tools/elements.h>
+#include <votca/tools/getline.h>
#include <votca/xtp/aobasis.h>
#include <votca/xtp/cubefile_writer.h>
#include <votca/xtp/orbitals.h>
@@ -92,12 +93,12 @@
std::ofstream out(_output_file);
// first two lines of header are garbage
- getline(in1, s);
+ tools::getline(in1, s);
out << s << "\n";
- getline(in1, s);
+ tools::getline(in1, s);
out << s << " substraction\n";
- getline(in2, s);
- getline(in2, s);
+ tools::getline(in2, s);
+ tools::getline(in2, s);
// read rest from header
Index natoms;
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/xtp-1.6.2/src/tests/test_cubefile_writer.cc
new/xtp-1.6.4/src/tests/test_cubefile_writer.cc
--- old/xtp-1.6.2/src/tests/test_cubefile_writer.cc 2020-08-22
15:31:18.000000000 +0200
+++ new/xtp-1.6.4/src/tests/test_cubefile_writer.cc 2021-01-12
19:26:43.000000000 +0100
@@ -1,5 +1,5 @@
/*
- * Copyright 2009-2019 The VOTCA Development Team (http://www.votca.org)
+ * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org)
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
@@ -17,6 +17,7 @@
#define BOOST_TEST_MODULE cubefilewriter_test
#include <boost/test/unit_test.hpp>
+#include <votca/tools/getline.h>
#include <votca/tools/tokenizer.h>
#include <votca/xtp/cubefile_writer.h>
@@ -31,16 +32,16 @@
std::string result = "";
std::string s;
- getline(in1, s);
- getline(in1, s);
- getline(in1, s);
+ votca::tools::getline(in1, s);
+ votca::tools::getline(in1, s);
+ votca::tools::getline(in1, s);
std::vector<double> cube_values;
do {
votca::tools::Tokenizer tok(s, " ");
std::vector<double> values;
tok.ConvertToVector<double>(values);
cube_values.insert(cube_values.end(), values.begin(), values.end());
- } while (getline(in1, s));
+ } while (votca::tools::getline(in1, s));
return Eigen::Map<Eigen::VectorXd>(cube_values.data(), cube_values.size());
}
