Package list votca-xtp / 7238a38
Updates to new upstream version 1.6 Nicholas Breen 1 year, 7 months ago
17 changed file(s) with 530 addition(s) and 106 deletion(s). Raw diff Collapse all Expand all
0 votca-xtp (1.5-1) unstable; urgency=medium
0 votca-xtp (1.6-1) unstable; urgency=medium
11
22 * Initial release. (Closes: #921202)
33
4 -- Nicholas Breen <nbreen@debian.org> Tue, 05 Feb 2019 18:03:36 -0800
4 -- Nicholas Breen <nbreen@debian.org> Sun, 19 Apr 2020 13:13:55 -0700
55 Build-Depends: cmake,
66 debhelper (>= 12),
77 dh-python,
8 libboost-chrono-dev,
89 libboost-filesystem-dev,
910 libboost-program-options-dev,
1011 libboost-serialization-dev,
1314 libboost-timer-dev,
1415 libceres-dev,
1516 libeigen3-dev,
17 libfftw3-dev,
1618 libhdf5-dev,
1719 libsqlite3-dev,
18 libvotca-csg-dev (>= 1.5),
19 libvotca-csg-dev (<< 1.6~),
20 libvotca-tools-dev (>= 1.5),
21 libvotca-tools-dev (<< 1.6~),
20 libvotca-csg-dev (>= 1.6),
21 libvotca-csg-dev (<< 1.7~),
22 libvotca-tools-dev (>= 1.6),
23 libvotca-tools-dev (<< 1.7~),
2224 libxc-dev,
2325 pkg-config,
24 python
25 Standards-Version: 4.3.0
26 python3,
27 votca-csg (>= 1.6)
28 Standards-Version: 4.5.0
2629 Rules-Requires-Root: no
2730 Homepage: http://www.votca.org/
2831 Vcs-Browser: https://salsa.debian.org/debichem-team/votca-xtp
3235 Section: libdevel
3336 Architecture: any
3437 Multi-Arch: same
35 Depends: libvotca-xtp5 (= ${binary:Version}), ${misc:Depends}
38 Depends: libvotca-xtp6 (= ${binary:Version}), ${misc:Depends}
3639 Description: VOTCA's exciton transport library, development kit
3740 VOTCA is a software package which focuses on the analysis of molecular
3841 dynamics data, the development of systematic coarse-graining techniques as
4245 libvotca-xtp is VOTCA's exciton transport simulation library. This package
4346 contains header files and pkg-config files for programs using VOTCA.
4447
45 Package: libvotca-xtp5
48 Package: libvotca-xtp6
4649 Section: libs
4750 Architecture: any
4851 Multi-Arch: same
5760
5861 Package: votca-xtp
5962 Architecture: any
60 Depends: ${misc:Depends}, ${shlibs:Depends}, ${python:Depends}
63 Depends: ${misc:Depends}, ${shlibs:Depends}, ${python3:Depends}
64 Suggests: libvotca-xtp-tutorials
6165 Description: VOTCA's exciton transport engine
6266 VOTCA is a software package which focuses on the analysis of molecular
6367 dynamics data, the development of systematic coarse-graining techniques as
6569 disordered semiconductors.
6670 .
6771 xtp is Votca's exciton transport simulation engine.
72
73 Package: votca-xtp-tutorials
74 Architecture: all
75 Depends: bash (>= 4), ${misc:Depends}
76 Recommends: votca-xtp, python3:any
77 Description: VOTCA's coarse-graining tutorials
78 VOTCA is a software package which focuses on the analysis of molecular
79 dynamics data, the development of systematic coarse-graining techniques as
80 well as methods used for simulating microscopic charge transport in
81 disordered semiconductors.
82 .
83 This package contains architecture-independent tutorials for votca-xtp.
84
22 Source: https://github.com/votca/xtp/releases
33
44 Files: *
5 Copyright: 2018,2019 The VOTCA Development Team
5 Copyright: 2009-2020 The VOTCA Development Team
66 License: Apache-2.0
77 Licensed under the Apache License, Version 2.0 (the "License");
88 you may not use this file except in compliance with the License.
1919 On Debian systems, the complete text of the Apache License 2.0 can
2020 be found in "/usr/share/common-licenses/Apache-2.0"
2121
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335 Files: share/basis_sets/*
336 Copyright: 2020 The Molecular Sciences Software Institute, Virginia Tech
337 1994-2020 Pacific Northwest National Laboratory, Batelle Memorial Institute
338 License: BSD-3-Clause
339 Redistribution and use in source and binary forms, with or without
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365 POSSIBILITY OF SUCH DAMAGE.
366
22367 Files: debian/*
23 Copyright: 2019 Debichem team <debichem-devel@lists.alioth.debian.org>
368 Copyright: 2019,2020 Debichem team <debichem-devel@lists.alioth.debian.org>
24369 License: GPL-2+
25370 This package is free software; you can redistribute it and/or modify
26371 it under the terms of the GNU General Public License as published by
00 usr/lib/*/libvotca_xtp.so
1 usr/lib/*/pkgconfig/*
1 #usr/lib/*/pkgconfig/*
22 usr/include/*
33 #usr/share/votca/template
44 #usr/share/man/man7/*
+0
-1
debian/libvotca-xtp5.install less more
0 usr/lib/*/libvotca_xtp.so.*
0 usr/lib/*/libvotca_xtp.so.*
+0
-27
debian/man/xtp_update_exciton.1 less more
0 .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.8.
1 .TH XTP_UPDATE_EXCITON "1" "February 2019" "xtp_update_exciton 1.5" "User Commands"
2 .SH NAME
3 xtp_update_exciton \- Updates the state file for singlets and triplets + optional arguments
4 .SH DESCRIPTION
5 ==================================================
6 .br
7 ======== VOTCA (http://www.votca.org) ========
8 .br
9 ==================================================
10 .PP
11 THE VOTCA::XTP STATE\-FILE UPDATER FOR EXCITON EXTENSION
12 .PP
13 please submit bugs to bugs@votca.org
14 .br
15 xtp_update_exciton, version 1.5
16 .PP
17 Updates the CTP state file to additionally use singlets and triplets +
18 .SS "optional arguments:"
19 .TP
20 \fB\-h\fR, \fB\-\-help\fR
21 show this help message and exit
22 .TP
23 \fB\-f\fR SQLFILE, \fB\-\-file\fR SQLFILE
24 State file to update.
25 .SH "SEE ALSO"
26 http://www.votca.org/
0 .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.13.
1 .TH XTP_UPDATE_MAPFILE "1" "April 2020" "xtp_update_mapfile 1.6" "User Commands"
2 .SH NAME
3 xtp_update_mapfile \- Updates the CTP mapping file to VOTCA XTP
4 .SH DESCRIPTION
5 ==================================================
6 ======== VOTCA (http://www.votca.org) ========
7 ==================================================
8 .PP
9 THE VOTCA::XTP MAPPING FILE UPDATER
10 .PP
11 please submit bugs to bugs@votca.org
12 xtp_update_mapfile, version 1.6
13 .PP
14 Updates the CTP mapping file to VOTCA XTP
15 .SS "optional arguments:"
16 .TP
17 \fB\-h\fR, \fB\-\-help\fR
18 show this help message and exit
19 .TP
20 \fB\-sin\fR S_INPUT, \fB\-\-S_input\fR S_INPUT
21 Mapping file to update.
22 .TP
23 \fB\-sout\fR S_OUTPUT, \fB\-\-S_output\fR S_OUTPUT
24 Filename of new Mapping file.
25 .SH "SEE ALSO"
26 Tutorials for VOCTA-XTP are contained in the
27 .B votca-xtp-tutorials
28 package.
0 Quick python2 -> python3 conversion for a pair of tutorial scripts, until
1 the next upstream release.
2 Index: votca/votca-xtp/tutorials/GROMACS/KMC_Methane/change_energy.py
3 ===================================================================
4 --- votca-xtp/tutorials/GROMACS/KMC_Methane/change_energy.py
5 +++ votca-xtp/tutorials/GROMACS/KMC_Methane/change_energy.py
6 @@ -1,4 +1,4 @@
7 -#!/usr/bin/python
8 +#!/usr/bin/python3
9
10 import lxml.etree as lxml
11 import argparse as ap
12 @@ -17,4 +17,4 @@ for entry in root.iter('job'):
13 estat=region.find("E_static").text
14 output.find("E_tot").text=estat
15
16 -print(lxml.tostring(root, pretty_print=True))
17 +print((lxml.tostring(root, pretty_print=True)))
18 Index: votca/votca-xtp/tutorials/LAMMPS/KMC_Thiophene/plotting_scripts/xtp_kmc_makemovie_traj.py
19 ===================================================================
20 --- votca-xtp/tutorials/LAMMPS/KMC_Thiophene/plotting_scripts/xtp_kmc_makemovie_traj.py
21 +++ votca-xtp/tutorials/LAMMPS/KMC_Thiophene/plotting_scripts/xtp_kmc_makemovie_traj.py
22 @@ -1,4 +1,4 @@
23 -#!/usr/bin/env python
24 +#!/usr/bin/env python3
25 import matplotlib as mpl
26 from mpl_toolkits.mplot3d import Axes3D
27 from mpl_toolkits.mplot3d import proj3d
28 @@ -23,7 +23,7 @@ class carrier(object):
29 def __init__(self):
30 carrier.numberofobjects+=1
31 self.id=carrier.numberofobjects
32 - print("Charge {} has been added".format(self.id))
33 + print(("Charge {} has been added".format(self.id)))
34 self.t=[]
35 self.x=[]
36 self.y=[]
37 @@ -54,8 +54,8 @@ class carrier(object):
38 self.color=color
39
40 def info(self):
41 - print("Carrier No. ",self.id)
42 - print(self.array())
43 + print(("Carrier No. ",self.id))
44 + print((self.array()))
45
46
47 class carriercollection(object):
48 @@ -92,7 +92,7 @@ class carriercollection(object):
49 self.xinterval=1.2*np.array([np.min(boxsizes[:,0]),np.max(boxsizes[:,1])])
50 self.yinterval=1.2*np.array([np.min(boxsizes[:,2]),np.max(boxsizes[:,3])])
51 self.zinterval=1.2*np.array([np.min(boxsizes[:,4]),np.max(boxsizes[:,5])])
52 - print(self.xinterval,self.yinterval,self.zinterval)
53 + print((self.xinterval,self.yinterval,self.zinterval))
54 def mergeonto(self,other):
55 self.listofcarriers=self.listofcarriers+other.listofcarriers
56
57 @@ -107,14 +107,14 @@ class carriercollection(object):
58
59 def readinfile(self, infile):
60 with open (infile, "rb") as csvfile:
61 - print("Opening file {}".format(infile))
62 + print(("Opening file {}".format(infile)))
63 reader = csv.reader(csvfile, dialect="excel-tab")
64 for row in reader:
65 if reader.line_num>self.steps and self.steps!=False:
66 break
67 if "time" in row[0]:
68 if "charges" in ''.join(row):
69 - print(''.join(row))
70 + print((''.join(row)))
71 m=re.search('\( ([0-9].?) charges \)',''.join(row))
72 noofcharges=int(m.group(1))
73 else:
74 @@ -128,7 +128,7 @@ class carriercollection(object):
75 for carrier in self.listofcarriers:
76 carrier.array()
77
78 - print("Found {} charges in file.".format(noofcharges))
79 + print(("Found {} charges in file.".format(noofcharges)))
80
81
82 def plottimestep(self,time,step):
83 @@ -162,13 +162,13 @@ class carriercollection(object):
84
85 if os.path.isdir(self.foldername+str(i)) and (os.path.isdir(self.foldername+str(i-1)) or (os.path.isdir(self.foldername) and i==1)):
86 os.rename(self.foldername+str(i),self.foldername+str(i+1))
87 - print("backing up folder {} to {}".format(self.foldername+str(i),self.foldername+str(i+1)))
88 + print(("backing up folder {} to {}".format(self.foldername+str(i),self.foldername+str(i+1))))
89 if os.path.isdir(self.foldername) and i==0:
90 os.rename(self.foldername,self.foldername+str(i+1))
91 - print("backing up folder {} to {}".format(self.foldername,self.foldername+str(i+1)))
92 + print(("backing up folder {} to {}".format(self.foldername,self.foldername+str(i+1))))
93 if i==0:
94 os.mkdir(self.foldername)
95 - print("creating folder {}".format(self.foldername))
96 + print(("creating folder {}".format(self.foldername)))
97 elif i>0:
98 self.createfolder(i-1)
99 else:
100 @@ -182,9 +182,9 @@ class carriercollection(object):
101 os.chdir(self.foldername)
102 tmin=self.tmin()
103 print(tmin)
104 - steps=range(int(length*framerate)+1)
105 + steps=list(range(int(length*framerate)+1))
106 for step in steps:
107 - print("evaluating frame {} of {}.".format(step,length*framerate))
108 + print(("evaluating frame {} of {}.".format(step,length*framerate)))
109 time=step*tmin/(length*framerate)
110 self.plottimestep(time,step)
111 command='ffmpeg -i frame_%04d.png {}'.format(filename)
0 python3-tutorial-scripts.patch
1212 override_dh_auto_test:
1313 -dh_auto_test
1414
15 override_dh_auto_install:
16 dh_auto_install
17 cp -r tutorials debian/tmp/usr/share/votca/tutorials-xtp
18 find debian/tmp/usr/share/votca/tutorials-xtp \( -name .gitignore -o -name .gitlab-ci.yml -o -name .travis.yml \) -exec rm {} \;
19 find debian/tmp/usr/share/votca/tutorials-xtp -name system.com -exec chmod a-x {} \;
20 -rm -rf debian/tmp/usr/share/votca/tutorials-xtp/CMakeModules debian/tmp/usr/share/votca/tutorials-xtp/CMakeLists.txt
21
1522 override_dh_installman:
1623 dh_installman --sourcedir=$(CURDIR)/debian/man
1724
1825 %:
19 dh $@ --with python2
26 dh $@ --with python3
2027
0 usr/share/votca/tutorials-xtp
0 usr/share/votca/*
10 usr/bin/*
21 usr/share/man/man1/*
3
2 usr/share/votca/xtp/*
00 xtp_basisset.1
11 xtp_makeauxbasis.1
2 xtp_update_exciton.1
2 xtp_update_mapfile.1
+0
-20
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>
+0
-20
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>
+0
-20
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>