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Freemol
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README.md

README.md

Stories in Ready

freemol

freemol 2003

Copyright notice/Licences: Please read this

Please note that some code lines might be a copy of other sources, usually free source code, as this project started many years ago.

Minuit in particular: I started it from an original F77 (free from the 90s) code and translated into F90. I contacted CERN (current minuit copyright holder) for a confirmation but I could not get a clear answer. I think it is obvious as it is a really old code which was free on the net many years ago.

There is also some free code from CCL (Computational Chemistry List), it is mentioned as comment in the code.

If code, packages or else might not fit with this "main" repository licence they are present in the folder "others/". Please read each package or code licence. If a package/code is there, then the redistribution is granted but under the given package licence which you should read.

Why so complicated?

There is a different solution: Get the required packages from other/external sources.

But I want to create a "self-consistend" package which will run without external dependencies. For these reasons:

- It might need to compile for systems without a network connection.
- If an hardware system (for example) is not supported by the main distribution we can create patches which apply only to the given distribution.
- Security: It is better to: download, check, compile, run, check, put in "others/", check, compile, run, check then a simple download from the net.
- Then the obvious: I promote fortran as the most portable source code. I need all code in a unique package.

Warning: For example blas and lapack are definitly more optimised if you use your system ones.

Also linetools described in the Libraries has this top line:

!H----------------------------------------------------------------------
!H      Some Routine are adapted from FREEREAD package taken from CCL.
!H      CCL: Computational Chemistry List http://www.ccl.org/
!H      A statment from Jan Labanowski:
!H      This software was taken from anon. ftp on rani.chem.yale.edu
!H      It is a set of routines which allow format free input in FORTRAN
!H
!H      Jan Labanowski
!H      jkl@osc.edu
!H----------------------------------------------------------------------

All the rest should be considered within the latest GPL.

News

Added a branch to add travis CI services, to test. We have indeed travisCI working for the compilation step: the code compiles.

Build Status

Intro

The framework is at ./Freemol

For a quick example, You would add a program just by making a directory

mkdir programs/mycode

and adding .F90 files in there. There a makemake utility in place. You might need to add a Makelocal file like this:

USEDLIBS = -L$(FMLIBDIR) -lmodules -lmoduledata -lutils -lincludes \
           -lfmlapack -lfmblas

You would read the command line like this:

use pcmdline
!
! We read the command line for I/O file names
!--------------------------------------------
call pcmd_iargc(nargs)
allocate(cargs(nargs),STAT=irc)
!
! Get the current arguments
call pcmd_getarg(nargs,cargs)
!
! Check if there is -i or -o for input or output
call pcmd_getio(nargs,cargs,finput,foutput)
!
! Open the input
irc = baseio_open(iunin,finput,stat='OLD')
!
! Check a complex flag: -p noshift,onestep
irc = pcmd_checkarg(nargs,cargs,'-p',params)
irc = index(params,'noshift')
if(irc.gt.0) then
   demo_noshift = .true.
endif
!
irc = pcmd_checkarg(nargs,cargs,'-p',params)
irc = index(params,'onestep')
if(irc.gt.0) then
   demo_onestep = .true.
end if

Or an INI file or molden file section like this:

! We need the molecule section
!-----------------------------
rewind(iunin)
irc = osec_set(iunin,'molecule',params)
if(irc.lt.0) then
   call message(MESERRO,'[demo_rdinput] No molecule section.')
   return
end if
!
call message_comment(iunbin,'Got molecule section. With Parameters:')
call message_comment(iunbin,adjustl(params))
!
call message(MESLOG,"[demo_rdinput] molecule_init called.")
irc=molecule_init()
if(irc.lt.0) then
   call message(MESERRO,'[demo_rdinput] Cannot Initialize the molecule.')
   return
end if
!
call molecule_read(iunin,params)
call molecule_print(iunbin)

Framework

controlled configure and autoconfigure

automatic makefile creation

controlled help comment extraction

section for manuals

Programs

adfrom

A code to work with ADF (Amsterdam Density Functional)

ch4sym2cart

Convert coordinates from symmetric to Cartesian for CH4 (Methane) alike molecules

CSMG

Compute the CSM "Continuous Symmetry Measure" of weighted point objects using Gaussian functions. See this paper for details:

https://fabiomariotti.files.wordpress.com/2013/07/csm_paper.pdf

And eventually this short blog:

https://blog.techottis.ch/2016/04/01/continuous-symmetry-measure-an-old-work/

This is an example of input

# from symmetry_mod file
[molecule] nrec=3 format=nscxyz 
o  1 8 1.000000 2.000000 3.000000
h  2 1 2.000000 2.000000 3.000000
h  3 1 1.000000 3.000000 3.000000
[x-csmg-cgauss] 
1 2.883843 1.591247
2 3.838395 7.701635
3 3.838395 7.701635
[x-csmg-symop] 
 E    1.0000  0.0000  0.0000    0.0  0.0000  0.0000  0.0000  F 
 C2_2   0.707107 0.707107 0.000000 180.000000  0.0000  0.0000  0.0000  F 
 S1   -0.707107 0.707107 0.000000 180.0000  0.0000  0.0000  0.0000  I 
 S2   0.000000 0.000000 1.000000 180.0000  0.0000  0.0000  0.0000  I 

Dependencies

See Libraries

#
USEDLIBS = -L$(FMLIBDIR) -lmodules -lmoduledata -lutils -lincludes \
           -lfmlapack -lfmblas
#

fit1Dpol

Fit about anything in 1 dimension. Anything might mean you need to add your functions, but it has a nice polynomial setup. It has nice features to work with multi-columns ASCII files. You can script which data to fit with ranged commands like copy, add, sub, shift, scale etc..

Freemol

Just a placeholder at present

XY4Coord

Coordinates transformation

XY4PolySphere

Coordinates transformation, the polyspherical version

Libraries

These libraries and tools are used in the programs listed above. For a working example of their usage please check the programs. In order to link to these libraries or tools please check also the generated makefiles.

Includes

linetools: format free input

messages: a logging facility

pcmdline: to handle the command line

strtools: string manipulation routines

vartypes: standardize variables type within codes

chemconst: constants defined at different precision

Utils

mathtools: few simple and common matrix tools

qnumbers: a small tool for quantum numbers

Modules

baseio: a file manager

extio: extensions to baseio for easy file manipulation

osec, sections: a tool to work with sectioned files like molden format

minuit: a multidimensional minimization tool

Moduledata

molecules: a molden based structure and tools to store molecules data and read in "free" format

Tools

CSMD supporting tools

others

local blas and lapack

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