-
Notifications
You must be signed in to change notification settings - Fork 3
/
README
282 lines (257 loc) · 10.7 KB
/
README
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
The distribution contains 20 directories, 220 files. The list of
directories and files is given at the end of this file (following the
starred line)
===========================================================================
B R I E F C O N T E N T S D E S C R I P T I O N
===========================================================================
README: (This file)
LICENSE: The GNU-GPLv3 license copy.
README.md (instructions for git users)
scr/* This directory contains the source code files. For the general user
the important files are:
src/Makefile: This file is the main makefile to be used by the
gnu make program in order to build the programs of the suite.
src/checkdependencies: small script for testing the intallation of
auxiliary programs, required to render plots and images
of the data computed by DensToolKit's programs.
tex/dtkmanual/*: This directory contains the latex-source of the dtk-manual,
including the needed figures to compile it.
For the user, important files are:
tex/dtkmanual/LICENSE: The GNU-FDLv1.3 license copy.
tex/dtkmanual/dtk-manual.pdf : The actual manual of DensToolKit.
wavefiles/* : Some wavefunction files used for testing the installation of DTK.
===========================================================================
I N S T A L L A T I O N
===========================================================================
1. Single cpu build: We assume that the source code is located at
'/top/dir'
Usually, typing on the terminal the following commands, should suffice.
$cd src
$make
$sudo make install
1.1 Testing the build:
After a succesfull compilation, if you want to test the programs, you may run
$make runtest
This will create a series of dat, tsv, cube, gnp, pdf and png files located at
'/top/dir/outputs'
2. Multi-cpu build: Change the line "SETDTKNPROC=1" in /top/dir/src/Makefile"
to be "SETDTKNPROC=N", where N is the number of processors you
want to use. Follow the same instructions as for the single
cpu build.
====================================================================================
R U N N I N G T H E P R O G R A M S
====================================================================================
For examples of how to run the programs, and a more detailed installation guide,
please refer to the file '/top/dir/tex/dtkmanual/dtk-manual.pdf', on Chapter "Programs".
After a successful installation, the binaries should be accessible from the command line.
Typing
$dtk**** -h
displays the help menu of the program. Here *** stands for any of the programs contained
in the suite. In linux systems, typing "dtk" followed by two tabs shows a list of the programs.
The general syntax of the programs is
$dtk**** wavefunctionname.wf? [option [arguments] ] ... [option [arguments] ]
wf? means that the input files can be saved to wfn or wfx format. The options are
activated by a dash and a letter. After one option, the user may be requested to
input more arguments. See the help menu of each program for a detailed syntax, and
also to the dtk-manual.
====================================================================================
L I S T O F F I L E S
====================================================================================
***********************************************************************
├── LICENSE
├── README
├── README.md
├── src
│ ├── DESIGNTODOS
│ ├── INFODEVELOP
│ ├── Makefile
│ ├── TODO
│ ├── bump_version.sh
│ ├── checkdependencies
│ ├── common
│ │ ├── atomcolschcust.h
│ │ ├── atomcolschjmol.cpp
│ │ ├── atomcolschjmol.h
│ │ ├── atomradiicust.cpp
│ │ ├── atomradiicust.h
│ │ ├── bondnetwork.cpp
│ │ ├── bondnetwork.h
│ │ ├── critptnetwork.cpp
│ │ ├── critptnetwork.h
│ │ ├── cudawavefunctionclass.cu
│ │ ├── cudawavefunctionclass.cuh
│ │ ├── custfld-wfnclass.cpp
│ │ ├── demat1critptnetwork.cpp
│ │ ├── demat1critptnetwork.h
│ │ ├── eig2-4.cpp
│ │ ├── eig2-4.h
│ │ ├── figname.h
│ │ ├── fldtypesdef.h
│ │ ├── iofuncts-cpx.cpp
│ │ ├── iofuncts-cpx.h
│ │ ├── iofuncts-wfn.cpp
│ │ ├── iofuncts-wfn.h
│ │ ├── iofuncts-wfx.cpp
│ │ ├── iofuncts-wfx.h
│ │ ├── solcubetools.cpp
│ │ ├── solcubetools.h
│ │ ├── solcudatools.cu
│ │ ├── solcudatools.cuh
│ │ ├── solfileutils.cpp
│ │ ├── solfileutils.h
│ │ ├── solgnuplottools.cpp
│ │ ├── solgnuplottools.h
│ │ ├── solmath.cpp
│ │ ├── solmath.h
│ │ ├── solmemhand.cpp
│ │ ├── solmemhand.h
│ │ ├── solpovtools.cpp
│ │ ├── solpovtools.h
│ │ ├── solscrutils.cpp
│ │ ├── solscrutils.h
│ │ ├── solstringtools.cpp
│ │ ├── solstringtools.h
│ │ ├── wavefunctionclass.cpp
│ │ ├── wavefunctionclass.h
│ │ ├── wfgrid1d.cpp
│ │ ├── wfgrid1d.h
│ │ ├── wfgrid2d.cpp
│ │ ├── wfgrid2d.h
│ │ ├── wfgrid3d.cpp
│ │ └── wfgrid3d.h
│ ├── devdoc
│ │ └── Doxyfile
│ ├── dtkbpdens
│ │ ├── ChangeLog
│ │ ├── Makefile
│ │ ├── crtflnms.cpp
│ │ ├── crtflnms.h
│ │ ├── dtkbpdens.cpp
│ │ ├── optflags.cpp
│ │ ├── optflags.h
│ │ └── soldefines.h
│ ├── dtkcube
│ │ ├── ChangeLog
│ │ ├── Makefile
│ │ ├── crtflnms.cpp
│ │ ├── crtflnms.h
│ │ ├── dtkcube.cpp
│ │ ├── optflags.cpp
│ │ ├── optflags.h
│ │ └── soldefines.h
│ ├── dtkdemat1
│ │ ├── ChangeLog
│ │ ├── Makefile
│ │ ├── crtflnms.cpp
│ │ ├── crtflnms.h
│ │ ├── dtkdemat1.cpp
│ │ ├── optflags.cpp
│ │ ├── optflags.h
│ │ ├── soldefines.h
│ │ └── tips4gnuplot.txt
│ ├── dtkfindcp
│ │ ├── ChangeLog
│ │ ├── Makefile
│ │ ├── crtflnms.cpp
│ │ ├── crtflnms.h
│ │ ├── custfmtmathfuncts.cpp
│ │ ├── custfmtmathfuncts.h
│ │ ├── dtkfindcp.cpp
│ │ ├── optflags.cpp
│ │ ├── optflags.h
│ │ └── soldefines.h
│ ├── dtkline
│ │ ├── ChangeLog
│ │ ├── Makefile
│ │ ├── crtflnms.cpp
│ │ ├── crtflnms.h
│ │ ├── dtkline.cpp
│ │ ├── optflags.cpp
│ │ ├── optflags.h
│ │ └── soldefines.h
│ ├── dtkmomd
│ │ ├── ChangeLog
│ │ ├── Makefile
│ │ ├── crtflnms.cpp
│ │ ├── crtflnms.h
│ │ ├── dtkmomd.cpp
│ │ ├── optflags.cpp
│ │ ├── optflags.h
│ │ └── soldefines.h
│ ├── dtkplane
│ │ ├── ChangeLog
│ │ ├── Makefile
│ │ ├── crtflnms.cpp
│ │ ├── crtflnms.h
│ │ ├── dtkplane.cpp
│ │ ├── optflags.cpp
│ │ ├── optflags.h
│ │ └── soldefines.h
│ ├── dtkpoint
│ │ ├── ChangeLog
│ │ ├── Makefile
│ │ ├── crtflnms.cpp
│ │ ├── crtflnms.h
│ │ ├── dtkpoint.cpp
│ │ ├── optflags.cpp
│ │ ├── optflags.h
│ │ └── soldefines.h
│ ├── dtkqdmol
│ │ ├── ChangeLog
│ │ ├── Makefile
│ │ ├── crtflnms.cpp
│ │ ├── crtflnms.h
│ │ ├── dtkqdmol.cpp
│ │ ├── optflags.cpp
│ │ ├── optflags.h
│ │ └── soldefines.h
│ ├── preprelease
│ └── scripts
│ ├── dtkeps2pdf
│ └── dtkpov2png
├── tex
│ └── dtkmanual
│ ├── LICENSE
│ ├── availablefields.tex
│ ├── custfld-wfnclass.cpp
│ ├── cyclopCPs.pdf
│ ├── cyclopELFLine.pdf
│ ├── cyclopLOLPlane.pdf
│ ├── cyclopLap.pdf
│ ├── cyclopQDMolLine.pdf
│ ├── cyclopQDMolPlane.pdf
│ ├── cyclopropaneBPDM1-C1-C2-1D1.pdf
│ ├── cyclopropaneBPDM1-C1-C2-1D2.pdf
│ ├── cyclopropaneBPDM1-C1-C2-2D.pdf
│ ├── cyclopropaneBPDM1-C1-C2-3D.pdf
│ ├── cyclopropaneBPSLMagGradLOL-C1-C2.pdf
│ ├── cyclopropaneMomDens-PxPy.pdf
│ ├── cyclopropaneMomDens-PyPz.pdf
│ ├── dtk-manual.pdf
│ ├── dtk-manual.tex
│ ├── dtkbibliography.bib
│ ├── dtkqdmolusex.pdf
│ ├── fdl-1.3.tex
│ ├── helpmenus
│ │ └── makefile
│ ├── hmdtkbpdens.tex
│ ├── hmdtkcube.tex
│ ├── hmdtkdemat1.tex
│ ├── hmdtkeps2pdf.tex
│ ├── hmdtkfindcp.tex
│ ├── hmdtkline.tex
│ ├── hmdtkmomd.tex
│ ├── hmdtkplane.tex
│ ├── hmdtkpoint.tex
│ ├── hmdtkpov2png.tex
│ ├── hmdtkqdmol.tex
│ ├── impnewfld.tex
│ ├── introduction.tex
│ ├── programsscripts.tex
│ └── topology.tex
└── wavefiles
├── benzene.wfn
├── ch4.wfx
├── cubano_sto3g.wfx
├── cyclopropane.wfx
└── ethanol.wfn