Codebase list votca-xtp / a89b4b8
Update upstream source from tag 'upstream/1.6.4' Update to upstream version '1.6.4' with Debian dir 629a020139ca57aa6414c94a5d657793f8060af4 Nicholas Breen 3 years ago
12 changed file(s) with 130 addition(s) and 22 deletion(s). Raw diff Collapse all Expand all
+48
-0
.gitignore less more
0 *~
1 Makefile
2
3 libvotca*.a
4 libvotca*.so
5 libvotca*.so.*
6
7 share/doc/html
8 share/doc/Doxyfile
9
10 include/votca/xtp/votca_config.h
11 src/libxtp/gitversion.h
12 include/votca/xtp/votca_config.h
13
14 src/tools/xtp_dump
15 src/tools/xtp_parallel
16 src/tools/xtp_map
17 src/tools/xtp_run
18 src/tools/xtp_tools
19 src/tools/xtp_overlap
20 src/tools/xtp_kmc_run
21 src/dipro/*.mod
22 src/dipro/*.x
23 src/tools/*.man
24
25 scripts/xtp_dipro.out
26 scripts/xtp_dipro
27 scripts/xtp_update
28 scripts/xtp_update.out
29 scripts/xtp_testsuite
30 scripts/xtp_testsuite.out
31 scripts/xtp_update_exciton
32 scripts/xtp_update_exciton.out
33 scripts/xtp_basisset
34 scripts/xtp_basisset.out
35 scripts/xtp_makeauxbasis
36 scripts/xtp_makeauxbasis.out
37
38 netbeans
39 .dep.inc
40 */nbproject/private
41
42 CMakeFiles
43 cmake_install.cmake
44 CMakeCache.txt
45 install_manifest.txt
46
47 /build
+4
-0
CHANGELOG.md less more
00 For more detailed information about the changes see the history of the
11 [repository](https://github.com/votca/xtp/commits/master).
2
3 ## Version 1.6.4 (released 12.01.21)
4 * fix build on openSUSE (#622)
5 * Refactored logger (#625)
26
37 ## Version 1.6.3 (released 09.12.20)
48 * switch to ghcr.io for CI (#555)
+1
-1
CMakeLists.txt less more
11 project(votca-xtp)
22
33
4 set(PROJECT_VERSION "1.6.3")
4 set(PROJECT_VERSION "1.6.4")
55 set(PROJECT_CONTACT "bugs@votca.org")
66 string(REGEX REPLACE "^[1-9]+\\.([1-9]+).*$" "\\1" SOVERSION "${PROJECT_VERSION}")
77 if (NOT ${SOVERSION} MATCHES "[1-9]+")
+12
-20
include/votca/xtp/logger.h less more
4141 /*
4242 * Custom buffer to store messages
4343 */
44 class LogBuffer : public std::stringbuf {
44 class LogBuffer final : public std::stringbuf {
4545
4646 public:
4747 LogBuffer() : std::stringbuf() { _LogLevel = Log::current_level; }
104104 bool _writePreface = true;
105105
106106 protected:
107 int sync() override {
107 int sync() {
108108
109109 std::ostringstream _message;
110110
164164 }
165165
166166 public:
167 Logger() : std::ostream(new LogBuffer()), _ReportLevel(Log::current_level) {
167 Logger() : std::ostream(&_buffer), _ReportLevel(Log::current_level) {
168168 setMultithreading(_maverick);
169169 }
170170 Logger(Log::Level ReportLevel)
171 : std::ostream(new LogBuffer()), _ReportLevel(ReportLevel) {
171 : std::ostream(&_buffer), _ReportLevel(ReportLevel) {
172172 setMultithreading(_maverick);
173173 }
174174
175 ~Logger() final {
176 delete rdbuf();
177 rdbuf(nullptr);
178 }
179
180175 Logger &operator()(Log::Level LogLevel) {
181 dynamic_cast<LogBuffer *>(rdbuf())->setLogLevel(LogLevel);
176 _buffer.setLogLevel(LogLevel);
182177 return *this;
183178 }
184179
185180 void setReportLevel(Log::Level ReportLevel) { _ReportLevel = ReportLevel; }
186181 void setMultithreading(bool maverick) {
187182 _maverick = maverick;
188 dynamic_cast<LogBuffer *>(rdbuf())->setMultithreading(_maverick);
183 _buffer.setMultithreading(_maverick);
189184 }
190185 bool isMaverick() const { return _maverick; }
191186
192187 Log::Level getReportLevel() const { return _ReportLevel; }
193188
194189 void setPreface(Log::Level level, const std::string &preface) {
195 dynamic_cast<LogBuffer *>(rdbuf())->setPreface(level, preface);
190 _buffer.setPreface(level, preface);
196191 }
197192
198193 void setCommonPreface(const std::string &preface) {
202197 setPreface(Log::warning, preface);
203198 }
204199
205 void EnablePreface() { dynamic_cast<LogBuffer *>(rdbuf())->EnablePreface(); }
206
207 void DisablePreface() {
208 dynamic_cast<LogBuffer *>(rdbuf())->DisablePreface();
209 }
200 void EnablePreface() { _buffer.EnablePreface(); }
201
202 void DisablePreface() { _buffer.DisablePreface(); }
210203
211204 private:
205 LogBuffer _buffer;
212206 // at what level of detail output messages
213207 Log::Level _ReportLevel = Log::error;
214208
215209 // if true, only a single processor job is executed
216210 bool _maverick = false;
217211
218 std::string Messages() {
219 return dynamic_cast<LogBuffer *>(rdbuf())->Messages();
220 }
212 std::string Messages() { return _buffer.Messages(); }
221213 };
222214
223215 /**
+1
-0
src/libxtp/dftengine/dftengine.cc less more
2222 #include "votca/xtp/qmmolecule.h"
2323 #include <boost/filesystem.hpp>
2424 #include <boost/format.hpp>
25 #include <iomanip>
2526 #include <vector>
2627 #include <votca/tools/constants.h>
2728 #include <votca/tools/elements.h>
+1
-0
src/libxtp/polarregion.cc less more
1717 */
1818
1919 #include "votca/xtp/eeinteractor.h"
20 #include <iomanip>
2021 #include <numeric>
2122 #include <votca/xtp/dipoledipoleinteraction.h>
2223 #include <votca/xtp/polarregion.h>
+1
-0
src/libxtp/qmpackages/nwchem.cc less more
2020 #include <boost/algorithm/string.hpp>
2121 #include <boost/filesystem.hpp>
2222 #include <boost/format.hpp>
23 #include <iomanip>
2324 #include <votca/tools/filesystem.h>
2425 #include <votca/tools/getline.h>
2526 #include <votca/xtp/ecpaobasis.h>
+1
-0
src/libxtp/tools/apdft.cc less more
1515 */
1616
1717 #include "apdft.h"
18 #include <iomanip>
1819 #include <votca/xtp/density_integration.h>
1920 #include <votca/xtp/orbitals.h>
2021 #include <votca/xtp/vxc_grid.h>
+1
-1
tutorials/CMakeLists.txt less more
11
22 project(xtp-tutorials)
33
4 set(PROJECT_VERSION "1.6.3")
4 set(PROJECT_VERSION "1.6.4")
55
66 set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/CMakeModules)
77 include(GNUInstallDirs)
+20
-0
tutorials/GROMACS/Methane/QC_FILES/g09/anion_geo/polar/molpol.xml~ less more
0 <options>
1 <molpol help="Molecular polarizability calculator (and optimizer)" label="tool:molpol">
2 <mpsfiles>
3 <input help="mps input file">CH4_i.mps</input>
4 <output help="mps output file">CH4_i.mps</output>
5 <polar help="xml file with infos on polarizability tensor">output.xml</polar>
6 </mpsfiles>
7 <induction>
8 <expdamp help="Thole sharpness parameter">0.39000</expdamp>
9 <wSOR help="mixing factor for convergence">0.35000</wSOR>
10 <maxiter help="maximum number of iterations">1024</maxiter>
11 <tolerance help="rel. tolerance for induced moments">0.00001</tolerance>
12 </induction>
13 <target>
14 <optimize help="if 'true', refine atomic polarizabilities to match molecular polarizable volume specified in target.molpol">true</optimize>
15 <molpol help="target polarizability tensor in format xx xy xz yy yz zz (this should be in the eigen-frame, hence xy = xz = yz = 0), if optimize=true the associated polarizable volume will be matched iteratively and the resulting set of polar sites written to mpsfiles.output">2.3191 0.0 0.0 2.3199 0.0 2.3204</molpol>
16 <tolerance help="relative tolerance when optimizing the polarizable volume">0.00001</tolerance>
17 </target>
18 </molpol>
19 </options>
+20
-0
tutorials/GROMACS/Methane/QC_FILES/g09/cation_geo/polar/molpol.xml~ less more
0 <options>
1 <molpol help="Molecular polarizability calculator (and optimizer)" label="tool:molpol">
2 <mpsfiles>
3 <input help="mps input file">CH4_h.mps</input>
4 <output help="mps output file">CH4_h.mps</output>
5 <polar help="xml file with infos on polarizability tensor">output.xml</polar>
6 </mpsfiles>
7 <induction>
8 <expdamp help="Thole sharpness parameter">0.39000</expdamp>
9 <wSOR help="mixing factor for convergence">0.35000</wSOR>
10 <maxiter help="maximum number of iterations">1024</maxiter>
11 <tolerance help="rel. tolerance for induced moments">0.00001</tolerance>
12 </induction>
13 <target>
14 <optimize help="if 'true', refine atomic polarizabilities to match molecular polarizable volume specified in target.molpol">true</optimize>
15 <molpol help="target polarizability tensor in format xx xy xz yy yz zz (this should be in the eigen-frame, hence xy = xz = yz = 0), if optimize=true the associated polarizable volume will be matched iteratively and the resulting set of polar sites written to mpsfiles.output">1.4451 0.0 0.0 2.0267 0.0 2.0267</molpol>
16 <tolerance help="relative tolerance when optimizing the polarizable volume">0.00001</tolerance>
17 </target>
18 </molpol>
19 </options>
+20
-0
tutorials/GROMACS/Methane/QC_FILES/g09/neutral_geo/polar/molpol.xml~ less more
0 <options>
1 <molpol help="Molecular polarizability calculator (and optimizer)" label="tool:molpol">
2 <mpsfiles>
3 <input help="mps input file">CH4_n.mps</input>
4 <output help="mps output file">CH4_n.mps</output>
5 <polar help="xml file with infos on polarizability tensor">output.xml</polar>
6 </mpsfiles>
7 <induction>
8 <expdamp help="Thole sharpness parameter">0.39000</expdamp>
9 <wSOR help="mixing factor for convergence">0.35000</wSOR>
10 <maxiter help="maximum number of iterations">1024</maxiter>
11 <tolerance help="rel. tolerance for induced moments">0.00001</tolerance>
12 </induction>
13 <target>
14 <optimize help="if 'true', refine atomic polarizabilities to match molecular polarizable volume specified in target.molpol">true</optimize>
15 <molpol help="target polarizability tensor in format xx xy xz yy yz zz (this should be in the eigen-frame, hence xy = xz = yz = 0), if optimize=true the associated polarizable volume will be matched iteratively and the resulting set of polar sites written to mpsfiles.output">2.3191 0.0 0.0 2.3199 0.0 2.3204</molpol>
16 <tolerance help="relative tolerance when optimizing the polarizable volume">0.00001</tolerance>
17 </target>
18 </molpol>
19 </options>