Ecosyste.ms: Awesome
An open API service indexing awesome lists of open source software.
https://github.com/nnairiitk/vreco_cpmd
CPMD Free Energy Surface Reconstruction
https://github.com/nnairiitk/vreco_cpmd
fortran fortran90 metadynamics
Last synced: 10 days ago
JSON representation
CPMD Free Energy Surface Reconstruction
- Host: GitHub
- URL: https://github.com/nnairiitk/vreco_cpmd
- Owner: NNairIITK
- License: gpl-3.0
- Created: 2017-05-24T03:42:32.000Z (over 7 years ago)
- Default Branch: master
- Last Pushed: 2018-05-14T14:32:33.000Z (over 6 years ago)
- Last Synced: 2024-07-30T18:27:55.461Z (4 months ago)
- Topics: fortran, fortran90, metadynamics
- Language: Roff
- Homepage: http://nnlabdoc.netlify.com/vreco_cpmd/introduction/
- Size: 8.32 MB
- Stars: 3
- Watchers: 2
- Forks: 1
- Open Issues: 1
-
Metadata Files:
- Readme: README
- Changelog: ChangeLog
- License: COPYING
Awesome Lists containing this project
README
# Vreco_CPMD
## Installation Instructions
This is the development version of the code and needs to be configured as follows:
```bash
$ aclocal
$ autoheader
$ autoconf
$ automake --add-missing
$ ./configure
$ make
```
Manual for Vreco_CPMD.f90 code version 10.3 (Nisanth N. Nair 08/07/08)
## General Description
This program is useful for reconstructing the free energy surface from a
metadynamics simulation using CPMD. There is no limitation on the number of
collective variables (CV) the program can handle. For runs with 1 (2) CVs, the
2D (3D) reconstructed free energy surfaces, can be viewed in GNUPLOT or
OpenDX. For a 3 CV case, it is possible to print the 4D free energy surface in
a cube file format (for e.g., then using VMD/OpenDX to visualize). See the
example directory for examples to plot and visualize the data.
Important to note that, F(s), the free energy in collective variable space, is
printed, where
F(s) = -- SUM_t V(t,s).
Here V is the biasing potential added at time t in the collective variable
space s.
## Compiling Vreco_CPMD.f90
Adjust the Makefile for your compiler, if needed, and type:
make
Note that this program is written in free format standard FORTRAN 95. It was
tested with and without optimization with Intel Fortran version 9.0, 9.1,
10.1, g95 v0.91, gfortran v4.1.2, PGI's pgf90 version 6.2-5 and 7.1-6, and IBM
XLF v9.1 showing reasonably good performance.
The code is also parallelized using OpenMP. You have to set the required
compiler flags for that to enable OpenMP directives. Some examples are in the
Makefile. Many OpenMP compilers will try to use all available cpus, which may
lead to suboptimal performance. This can be modified by setting the environment
variable OMP_NUM_THREADS. e.g., to use two threads do:
```bash
env OMP_NUM_THREADS=2 ./Vreco_CPMD.x < vreco.inp > vreco.out
```
The output will indicate, whether you have an OpenMP compiled version and how
many threads will be used. Please note that when using PRINT DYNAMIC OpenMP
performance is only good for large values of PRINT_FRQ.
## Using Vreco_CPMD.x
The program reads in the files 'colvar_mtd' and 'parvar_mtd' generated by CPMD
metadynamics runs to reconstruct the free energy surface. Gaussian centers and
scaling factors during the runs are taken from 'colvar_mtd' and Gaussian width
and heights are taken from 'parvar_mtd'. Copy or link those files to the
working directory (they will _not_ be overwritten) and run an input.
```bash
./Vreco_CPMD.x < vreco.inp
```
or
```bash
./Vreco_CPMD.x < vreco.inp > vreco.out
```
Some keywords are required to instruct the program on what to do. They are
read standard input file, best through I/O redirection; see below a list of
the individual input keywords and their function.
The final reconstructed potential will be written to 'V.final.out' and/or
'V.final.cube'; see below for details. If PRINT DYNAMIC is present in the
input file (see below) 'V.dynamic.out' contain the potentials reconstructed at
given intervals of metadynamics steps.
---------------------------------------------------------------------------------
### Input keywords for Vreco_CPMD.f90
---------------------------------------------------------------------------------
IMPORTANT: Input file should begin with the keyword NCV and end with END.
Required keywords:
NCV:
Number of CVs used in the simulations is read from the next line.
This has to be the first keyword.
GRIDS:
Grid on which the reconstruction has to be performed, is read from
the following NCV lines. Minimum value of the grid, the maximum
value of the grid and the grid-width are read for each set of CVs,
in the same order as in the CPMD input file. Units of CVs are same
as in colvar_mtd output (note: even if ANGSTROM keyword is present
distances are in Bohr units in colvar_mtd file). Consult CPMD manual
for details on units.
HILLS { [SPHERE] [TUBE [RCUT]] }:
Type of biasing potential used (same keywords as in CPMD input file)
If SPHERE is present spherical Gaussians are used in the CPMD run.
If TUBE is present tube-type Gaussians are used.
If RCUT is present together with TUBE , shifted Gaussians are used.
Gaussians are then trimmed after hill_width*RCUT_value. The RCUT_value
is read from the next line if RCUT is present.
IMPORTANT! no other biasing potentials types are implemented in this version!
END
This must be the last keyword and is _required_.
Optional keywords: the following keywords must appear before the "END" keyword.
[ PRINT { [DYNAMIC] [WALKER] }]:
If DYNAMIC is present the reconstructed potential is printed out
during every PRINT_FRQ metadynamics steps to the 'V.dynamic.out'
file. The printing frequency, PRINT_FRQ, is read from the next
line. Note: each column (after the grid value, if OUT GRID is used)
will be the potential during the metadynamics steps in increasing
order. Similarly, printing the walker position and the total
potential at each walker positions can be requested by the keyword
WALKER. the corresponding output file is 'walker.out'. The
frequency of printing PRINT_FRQ is read from the next line. One can
use PRINT DYNAMIC and PRINT WALKER together, but also as separate
keywords.
[ OUT { [GRID] [NOGRID] } ] (OUT GRID is the default)
The reconstructed potential is printed out with the grid position
values (as first NCV columns) if OUT GRID is used. If OUT NOGRID is
present, the grid positions will not be printed.
[ UNITS { [KJ] [KC] [AU] }] (AU is default)
Units of energy used by the program for printing the free energies
or potential. KJ stands for kJ/mol, KC for kcal/mol and AU for
atomic units. IMPORTANT! This is only used for (all) output of this
program; CPMD units used in the colvar_mtd and parvar_mtd files are
properly taken care of by the program.
[ METASTEP ]
Number of metadynamics steps to reconstruction is read from the next
line. Default is to use all steps from colvar_mtd file.
[ CUBE [FULL] [CVMDCK] [COLVAR] [ONLY] ]
Print the reconstructed potential to a Gaussian-style cube format
file. Only allowed for cases having 3 CVs. FULL is the default;
the full final reconstructed free energy surface is written to
'V.final.cube'. If CVMDCK is also present, then the collective
coordinates along the trajectory present in the 'cvmdck_mtd' file is
read in, and the potential along this path is written to
'V.cvmdck.cube' If COLVAR is also present, then the free energy
values along the collective variable in the 'colvar_mtd' file is
written to 'V.colvar.cube'. If ONLY is present, 'V.final.out' will
not be written together with the above cube files.
---------------------------------------------------------------------------------
### Output files
---------------------------------------------------------------------------------
V.final.out
Reconstructed free energy surface F(s). Units of free energy is
according to the keyword UNITS (see above). IF OUT GRID is used, the
format of printing will be as follows for a 2 CV case:
grid_x0 grid_y0 F(x0,y0)
grid_x0 grid_y0+dy F(x0,y0+dy)
.......
grid_x0 grid_y0+(Ny-1)*dy F(x0,y0+(Ny-1)*dy)
-blank line-
grid_x0+dx grid_y0 F(x0+dx,y0)
grid_x0+dx grid_y0+dy F(x0+dx,y0+dy)
.......
If OUT NOGRID is used, then the first two columns will be absent;
everything else is the same.
V.dynamic.out
Reconstructed free energy surface F(s) during metadynamics run. It
is very useful to decide where to stop the runs for getting the
final free energy surface, and to observe the way the free energy
surface builds up during the dynamics. Units of free energy is
according to the keyword UNITS (see above). IF OUT GRID is used, the
format of printing will be as follows for a 2 CV case:
grid_x0 grid_y0 F(x0,y0,t) F(x0,y0,t+n*dt) F(x0,y0,t+2*n*dt) ....
grid_x0 grid_y0+dy F(x0,y0+dy,t) F(x0,y0+dy,t+n*dt) F(x0,y0+dy,t+2*n*dt) ....
.......
grid_x0 grid_y0+(Ny-1)*dy F(x0,y0+(Ny-1)*dy,t) F(x0,y0+(Ny-1)*dy,t+n*dt) F(x0,y0+(Ny-1)*dy,t+2*n*dt) ....
-blank line-
grid_x0+dx grid_y0 F(x0+dx,y0,t) F(x0+dx,y0,t+n*dt) F(x0+dx,y0,t+2*n*dt) ....
grid_x0+dx grid_y0+dy F(x0+dx,y0+dy,t) F(x0+dx,y0+dy,t+n*dt) F(x0+dx,y0+dy,t+2*n*dt) ....
.......
V.final.cube
Final reconstructed free energy surface in a Gaussian-style cube file.
V.colvar.cube
Free energy values along the trajectory of collective variables (read
from colvar_mtd file) in a Gaussian-style cube file
.
V.cvmdck.cube
Free energy values along the trajectory of collective coordinates (not
collective variables) as in the cvmdck_mtd file from CPMD, in the
Gaussian cube file format.
walker.out
position of the walker (Gaussian centers) and the total potential at
this point (read in from 'enevar_mtd') will be written to 'walker.out',
in the same format as that of 'V.final.out'.
# Manual for mtd_restart_extract.f90 code (Nisanth N. Nair 26/06/08)
This code reads a 'MTD_RESTART' file and recreates the corresponding
'colvar_mtd' and 'parvar_mtd' files, which are required for reconstructing the
free energy surface. Useful, if the *_mtd files got corrupted, or to check
the biasing hills used in CPMD for actual calculations. Output is written to
the files 'colvar_mtd.reco' and 'parvar_mtd.reco'.
To compile:
```bash
make
```
To use:
```bash
./mtd_restart_extract.x
```
Reads in 'MTD_RESTART' from the working directory and writes out
colvar_mtd.reco and parvar_mtd.reco
## Bugs/Comments/Suggestions
Please report bugs to [email protected]
# Credits
autotools-skeleton (https://github.com/gizero/autotools-skeleton)