This is the development version of the code and needs to be configured as follows:
$ aclocal
$ autoheader
$ autoconf
$ automake --add-missing
$ ./configure
$ makeManual for Vreco_CPMD.f90 code version 10.3 (Nisanth N. Nair 08/07/08)
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.
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:
env OMP_NUM_THREADS=2 ./Vreco_CPMD.x < vreco.inp > vreco.outThe 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.
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.
./Vreco_CPMD.x < vreco.inp or
./Vreco_CPMD.x < vreco.inp > vreco.outSome 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.
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.
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'.
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:
makeTo use:
./mtd_restart_extract.xReads in 'MTD_RESTART' from the working directory and writes out colvar_mtd.reco and parvar_mtd.reco
Please report bugs to nisanth.nair@theochem.rub.de
autotools-skeleton (https://github.com/gizero/autotools-skeleton)