README

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 -j 4
   $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: 
   Add the variable SETDTKNPROC during the compilation step:
      $cd src
      $make -j4 SETDTKNPROC=4
      $sudo make install
   The line 'make -j4 SETDTKNPROC=4' will compile DTK using parallelized functions
   (OpenMP), and will use 4 cores. Change '4' by the number of cores you
   consider adequate. However, we recommend a maximum of 4 if you are
   installing DTK on an Intel-CPU server, and of 2 if you are using
   M1 Pro Apple processors.

====================================================================================
              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
|-- notes
|   |-- WFNFormatSpecs.txt
|   |-- diatomicquadrules
|   |   |-- diatomicquadrules.tex
|   |   `-- images
|   |       |-- numIntegDiatCore.tex
|   |       `-- numIntegDiatValence.tex
|   `-- gammprojection
|       |-- gammaprojection.tex
|       `-- plots
|           |-- CurveParam00.dia
|           `-- CurveParam01.tex
|-- src
|   |-- CHANGES
|   |-- CONTRIBUTORS
|   |-- DESIGNTODOS
|   |-- INFODEVELOP
|   |-- README
|   |-- TODO
|   |-- VERSION
|   |-- bump_version.sh
|   |-- checkdependencies
|   |-- common
|   |   |-- atom.cpp
|   |   |-- atom.h
|   |   |-- atomcolschcust.h
|   |   |-- atomcolschjmol.cpp
|   |   |-- atomcolschjmol.h
|   |   |-- atomradiicust.cpp
|   |   |-- atomradiicust.h
|   |   |-- basegausslegendre.cpp
|   |   |-- basegausslegendre.h
|   |   |-- basesphtdesign.cpp
|   |   |-- basesphtdesign.h
|   |   |-- bondnetwork.cpp
|   |   |-- bondnetwork.h
|   |   |-- circledots3d.cpp
|   |   |-- circledots3d.h
|   |   |-- citations.h
|   |   |-- colorutils.cpp
|   |   |-- colorutils.h
|   |   |-- commonhelpers.cpp
|   |   |-- commonhelpers.h
|   |   |-- configLclSysDefs.sh
|   |   |-- critptnetwork.cpp
|   |   |-- critptnetwork.h
|   |   |-- custfld-wfnclass.cxx
|   |   |-- demat1critptnetworkbp.cpp
|   |   |-- demat1critptnetworkbp.h
|   |   |-- demat1critptnetworksl.cpp
|   |   |-- demat1critptnetworksl.h
|   |   |-- dtkscalarfunction3d.cpp
|   |   |-- dtkscalarfunction3d.h
|   |   |-- dtkscalarfunction6d.cpp
|   |   |-- dtkscalarfunction6d.h
|   |   |-- eig6.cpp
|   |   |-- eig6.h
|   |   |-- eigendecompositionjama.cpp
|   |   |-- eigendecompositionjama.h
|   |   |-- figname.cpp
|   |   |-- figname.h
|   |   |-- fileutils.cpp
|   |   |-- fileutils.h
|   |   |-- fldtypesdef.h
|   |   |-- function3d.cpp
|   |   |-- function3d.h
|   |   |-- gaussiancube.cpp
|   |   |-- gaussiancube.h
|   |   |-- gausswavefunction.cpp
|   |   |-- gausswavefunction.h
|   |   |-- globaldefs.h
|   |   |-- gnuplottools.cpp
|   |   |-- gnuplottools.h
|   |   |-- inputmolecule_cub.cpp
|   |   |-- inputmolecule_cub.h
|   |   |-- inputmolecule_xyz.cpp
|   |   |-- inputmolecule_xyz.h
|   |   |-- integrateoverbondpath.cpp
|   |   |-- integrateoverbondpath.h
|   |   |-- integrator3d.cpp
|   |   |-- integrator3d.h
|   |   |-- integrator3d_diatomics.cpp
|   |   |-- integrator3d_diatomics.h
|   |   |-- integrator3d_legsphtd.cpp
|   |   |-- integrator3d_legsphtd.h
|   |   |-- integrator3d_miser.cpp
|   |   |-- integrator3d_miser.h
|   |   |-- integrator3d_vegas.cpp
|   |   |-- integrator3d_vegas.h
|   |   |-- interpolators.cpp
|   |   |-- interpolators.h
|   |   |-- iofuncts-cpx.cpp
|   |   |-- iofuncts-cpx.h
|   |   |-- iofuncts-wfn.cpp
|   |   |-- iofuncts-wfn.h
|   |   |-- iofuncts-wfx.cpp
|   |   |-- iofuncts-wfx.h
|   |   |-- isosurface.cpp
|   |   |-- isosurface.h
|   |   |-- makefile
|   |   |-- makefile.hpc
|   |   |-- matrixvectoroperations3d.cpp
|   |   |-- matrixvectoroperations3d.h
|   |   |-- meshgrid.cpp
|   |   |-- meshgrid.h
|   |   |-- molecule.cpp
|   |   |-- molecule.h
|   |   |-- mymath.cpp
|   |   |-- mymath.h
|   |   |-- mymemory.cpp
|   |   |-- mymemory.h
|   |   |-- myrandom.cpp
|   |   |-- myrandom.h
|   |   |-- mytimer.cpp
|   |   |-- mytimer.h
|   |   |-- palette.cpp
|   |   |-- palette.h
|   |   |-- polygonize_marchingcubes.cpp
|   |   |-- polygonize_marchingcubes.h
|   |   |-- povraytools.cpp
|   |   |-- povraytools.h
|   |   |-- screenutils.cpp
|   |   |-- screenutils.h
|   |   |-- solcubetools.cpp
|   |   |-- solcubetools.h
|   |   |-- spline.cpp
|   |   |-- spline.h
|   |   |-- stringtools.cpp
|   |   |-- stringtools.h
|   |   |-- symmetricsurfacegrid.cpp
|   |   |-- symmetricsurfacegrid.h
|   |   |-- unitconversion.h
|   |   |-- vmdtools.cpp
|   |   |-- vmdtools.h
|   |   |-- wfgrid1d.cpp
|   |   |-- wfgrid1d.h
|   |   |-- wfgrid2d.cpp
|   |   |-- wfgrid2d.h
|   |   |-- wfgrid3d.cpp
|   |   `-- wfgrid3d.h
|   |-- devdoc
|   |   |-- Doxyfile
|   |   `-- Doxyfile.bkp
|   |-- dtkbpdens
|   |   |-- ChangeLog
|   |   |-- crtflnms.cpp
|   |   |-- crtflnms.h
|   |   |-- dtkbpdens.cc
|   |   |-- helpersplot.cpp
|   |   |-- helpersplot.h
|   |   |-- localdefs.h
|   |   |-- makefile
|   |   |-- makefile.hpc
|   |   |-- optflags.cpp
|   |   `-- optflags.h
|   |-- dtkcharcicp
|   |   |-- ChangeLog
|   |   |-- crtflnms.cpp
|   |   |-- crtflnms.h
|   |   |-- custfmtmathfuncts.cpp
|   |   |-- custfmtmathfuncts.h
|   |   |-- dtkcharcicp.cc
|   |   |-- localdefs.h
|   |   |-- makefile
|   |   |-- makefile.hpc
|   |   |-- optflags.cpp
|   |   `-- optflags.h
|   |-- dtkcube
|   |   |-- ChangeLog
|   |   |-- crtflnms.cpp
|   |   |-- crtflnms.h
|   |   |-- dtkcube.cc
|   |   |-- localdefs.h
|   |   |-- makefile
|   |   |-- makefile.hpc
|   |   |-- optflags.cpp
|   |   `-- optflags.h
|   |-- dtkdrawer
|   |   |-- 13DMXa.xyz
|   |   |-- 13DMXb.xyz
|   |   |-- 13DMXc.xyz
|   |   |-- 13DMXd.xyz
|   |   |-- 37DMXa.xyz
|   |   |-- 37DMXb.xyz
|   |   |-- 37DMXc.xyz
|   |   |-- 37DMXd.xyz
|   |   |-- ChangeLog
|   |   |-- crtflnms.cpp
|   |   |-- crtflnms.h
|   |   |-- dtkdrawer.cc
|   |   |-- helpersdrawer.cpp
|   |   |-- helpersdrawer.h
|   |   |-- localdefs.h
|   |   |-- makefile
|   |   |-- makefile.hpc
|   |   |-- optflags.cpp
|   |   |-- optflags.h
|   |   `-- renderTestFigs.sh
|   |-- dtkfindcp
|   |   |-- ChangeLog
|   |   |-- README
|   |   |-- crtflnms.cpp
|   |   |-- crtflnms.h
|   |   |-- custfmtmathfuncts.cpp
|   |   |-- custfmtmathfuncts.h
|   |   |-- dtkfindcp.cc
|   |   |-- localdefs.h
|   |   |-- makefile
|   |   |-- makefile.hpc
|   |   |-- optflags.cpp
|   |   `-- optflags.h
|   |-- dtkintegobondpath
|   |   |-- ChangeLog
|   |   |-- crtflnms.cpp
|   |   |-- crtflnms.h
|   |   |-- dtkintegobondpath.cc
|   |   |-- localdefs.h
|   |   |-- makefile
|   |   |-- makefile.hpc
|   |   |-- optflags.cpp
|   |   `-- optflags.h
|   |-- dtkintegrate
|   |   |-- crtflnms.cpp
|   |   |-- crtflnms.h
|   |   |-- dtkintegrate.cc
|   |   |-- helpersintegrate.cpp
|   |   |-- helpersintegrate.h
|   |   |-- localdefs.h
|   |   |-- makefile
|   |   |-- makefile.hpc
|   |   |-- optflags.cpp
|   |   `-- optflags.h
|   |-- dtkline
|   |   |-- ChangeLog
|   |   |-- crtflnms.cpp
|   |   |-- crtflnms.h
|   |   |-- dtkline.cc
|   |   |-- localdefs.h
|   |   |-- makefile
|   |   |-- makefile.hpc
|   |   |-- optflags.cpp
|   |   `-- optflags.h
|   |-- dtkmapfieldonisosurf
|   |   |-- crtflnms.cpp
|   |   |-- crtflnms.h
|   |   |-- dtkmapfieldonisosurf.cc
|   |   |-- helpersmapfieldonisosurf.cpp
|   |   |-- helpersmapfieldonisosurf.h
|   |   |-- localdefs.h
|   |   |-- makefile
|   |   |-- makefile.hpc
|   |   |-- optflags.cpp
|   |   `-- optflags.h
|   |-- dtkmomd
|   |   |-- ChangeLog
|   |   |-- crtflnms.cpp
|   |   |-- crtflnms.h
|   |   |-- dtkmomd.cc
|   |   |-- helpersplot.cpp
|   |   |-- helpersplot.h
|   |   |-- localdefs.h
|   |   |-- makefile
|   |   |-- makefile.hpc
|   |   |-- optflags.cpp
|   |   `-- optflags.h
|   |-- dtkplane
|   |   |-- ChangeLog
|   |   |-- crtflnms.cpp
|   |   |-- crtflnms.h
|   |   |-- dtkplane.cc
|   |   |-- helpersplot.cpp
|   |   |-- helpersplot.h
|   |   |-- localdefs.h
|   |   |-- makefile
|   |   |-- makefile.hpc
|   |   |-- optflags.cpp
|   |   `-- optflags.h
|   |-- dtkpoint
|   |   |-- ChangeLog
|   |   |-- crtflnms.cpp
|   |   |-- crtflnms.h
|   |   |-- dtkpoint.cc
|   |   |-- localdefs.h
|   |   |-- makefile
|   |   |-- makefile.hpc
|   |   |-- optflags.cpp
|   |   `-- optflags.h
|   |-- dtkproject6dto2d
|   |   |-- ChangeLog
|   |   |-- crtflnms.cpp
|   |   |-- crtflnms.h
|   |   |-- dtkproject6dto2d.cc
|   |   |-- helperplots.cpp
|   |   |-- helperplots.h
|   |   |-- localdefs.h
|   |   |-- makefile
|   |   |-- makefile.hpc
|   |   |-- optflags.cpp
|   |   |-- optflags.h
|   |   `-- tips4gnuplot.txt
|   |-- dtkpropcpsoniso
|   |   |-- ChangeLog
|   |   |-- crtflnms.cpp
|   |   |-- crtflnms.h
|   |   |-- dtkpropcpsoniso.cc
|   |   |-- helperspropcpsoniso.cpp
|   |   |-- helperspropcpsoniso.h
|   |   |-- localdefs.h
|   |   |-- makefile
|   |   |-- makefile.hpc
|   |   |-- optflags.cpp
|   |   `-- optflags.h
|   |-- dtkqdmol
|   |   |-- ChangeLog
|   |   |-- crtflnms.cpp
|   |   |-- crtflnms.h
|   |   |-- dtkqdmol.cc
|   |   |-- localdefs.h
|   |   |-- makefile
|   |   |-- makefile.hpc
|   |   |-- optflags.cpp
|   |   `-- optflags.h
|   |-- dtkview
|   |   |-- CMakeLists.txt
|   |   |-- DensToolKit.pro
|   |   |-- DensToolKitViewer.icns
|   |   |-- README.md
|   |   |-- TODO
|   |   |-- denstoolkitviewer.qrc
|   |   |-- dtkglbondnetwork.cpp
|   |   |-- dtkglbondnetwork.h
|   |   |-- dtkglcriticalpointnetwork.cpp
|   |   |-- dtkglcriticalpointnetwork.h
|   |   |-- dtkglutils.cpp
|   |   |-- dtkglutils.h
|   |   |-- dtkglwidget.cpp
|   |   |-- dtkglwidget.h
|   |   |-- dtkmainwindow.cpp
|   |   |-- dtkmainwindow.h
|   |   |-- dtkmainwindow.ui
|   |   |-- images
|   |   |   |-- drawatoms.png
|   |   |   |-- drawcplbls.png
|   |   |   |-- drawlinks.png
|   |   |   |-- dtk128x128.png
|   |   |   |-- dtk256x256.png
|   |   |   |-- dtk32x32.png
|   |   |   |-- open.png
|   |   |   |-- save.png
|   |   |   |-- showatlbls.png
|   |   |   |-- square.png
|   |   |   |-- toggletransp.png
|   |   |   |-- viewbgps.png
|   |   |   |-- viewcgps.png
|   |   |   `-- viewrgps.png
|   |   |-- localdefs.h
|   |   `-- main.cpp
|   |-- makefile
|   |-- makefile.hpc
|   |-- preprelease
|   |-- scripts
|   |   |-- dtkGetSumBCPRho
|   |   |-- dtkchgcurrversion
|   |   |-- dtkchgsuiteversion
|   |   |-- dtkeps2pdf
|   |   |-- dtkgetnciplot
|   |   `-- dtkpov2png
|   |-- test
|   |   |-- 42.wfx
|   |   |-- XeF2.wfx
|   |   |-- ch4.wfx
|   |   |-- localdefs.h
|   |   |-- makefile
|   |   |-- runParallelProfv2.0.sh
|   |   |-- test_derivsdm1.cc
|   |   |-- test_dtkscalarfunction.cc
|   |   |-- test_dtkscalarfunction6d.cc
|   |   |-- test_gausswavefunction.cc
|   |   |-- test_hessdm1.cc
|   |   |-- test_molecule.cc
|   |   |-- test_momgamma.cc
|   |   |-- test_rho2cs.cc
|   |   `-- test_rho2os.cc
|   `-- timeprofilev2.0
|       |-- 42.wfx
|       |-- README
|       |-- helpers.cpp
|       |-- helpers.h
|       |-- localdefs.h
|       |-- makefile
|       |-- optflags.cpp
|       |-- optflags.h
|       |-- optionflagsbase.cpp
|       |-- optionflagsbase.h
|       |-- timeprofile.cc
|       |-- timeprofileMacOSX.dat
|       `-- timeprofileXeon.dat
|-- tex
|   `-- dtkmanual
|       |-- LICENSE
|       |-- NCISvsRho-Cutoff.pdf
|       |-- NCISvsRho.pdf
|       |-- NCIvmd-Cutoff.pdf
|       |-- NCIvmd.pdf
|       |-- availablefields.tex
|       |-- ccl2hMEPCPsOnRhoCap.pdf
|       |-- ccl2hMEPCPsOnRhoCapTransp.pdf
|       |-- ccl2hMEPCPsOnRhoIso.pdf
|       |-- cubaneCPs.pdf
|       |-- custfld-wfnclass.cpp
|       |-- custfld-wfnclass.cxx
|       |-- 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.tex
|       |-- dtkbibliography.bib
|       |-- dtkqdmolusex.pdf
|       |-- dtkview01.pdf
|       |-- dtkview02.pdf
|       |-- dtkview03trim.pdf
|       |-- fdl-1.3.tex
|       |-- h2oh2oNCI.pdf
|       |-- h2oh2oNCISvsRho.pdf
|       |-- helpmenus
|       |   `-- makefile
|       |-- hmdtkbpdens.tex
|       |-- hmdtkcharcicp.tex
|       |-- hmdtkcube.tex
|       |-- hmdtkdrawer.tex
|       |-- hmdtkeps2pdf.tex
|       |-- hmdtkfindcp.tex
|       |-- hmdtkgetnciplot.tex
|       |-- hmdtkintegrate.tex
|       |-- hmdtkline.tex
|       |-- hmdtkmapfieldonisosurf.tex
|       |-- hmdtkmomd.tex
|       |-- hmdtkplane.tex
|       |-- hmdtkpoint.tex
|       |-- hmdtkpov2png.tex
|       |-- hmdtkproject6dto2d.tex
|       |-- hmdtkpropcpsoniso.tex
|       |-- hmdtkqdmol.tex
|       |-- impnewfld.tex
|       |-- introduction.tex
|       |-- programsscripts.tex
|       `-- topology.tex
`-- wffiles
    |-- 4-Methylbenzoic_acid.wfn
    |-- benzene.wfn
    |-- benzyldiethylamine.wfx
    |-- ch4.wfx
    |-- cubano_sto3g.wfx
    |-- cyclopropane.wfx
    |-- ethanol.wfn
    |-- h2oh2o.wfx
    |-- maprotiline.wfx
    `-- mescaline.wfx