EFPMD is a molecular simulation program based on LIBEFP. It supports single point energy and gradient calculations, semi-numerical Hessian and normal mode analysis, geometry optimization, molecular dynamics simulations in microcanonical (NVE), canonical (NVT), and isobaric-isothermal (NPT) ensembles.
Simulations can be accelerated by running in parallel mode on multi-core CPUs.
To enable parallel computation set OMP_NUM_THREADS environment variable to
the desired number of parallel threads. For example on a 4-core machine you can
set the OMP_NUM_THREADS environment variable to four before starting the
program:
export OMP_NUM_THREADS=4
This will enable parallel computation using 4 threads and should give almost 4x speedup in all calculations.
If you have compiled libefp with MPI support you can also run parallel calculations across multiple nodes using standard mpirun command:
mpirun -np 8 efpmd input.in
Note that you can achieve better scalability by using OpenMP for parallelization within a single node and MPI for inter-node communication.
Additional examples of input files can be found in the tests directory in source code archive.
Lines beginning with the # symbol are ignored during input parsing.
run_type [sp|grad|hess|opt|md|gtest]
sp - single point energy calculation.
grad - energy gradient calculation.
hess - semi-numerical Hessian calculation and normal mode analysis.
opt - geometry optimization.
md - molecular dynamics simulation.
efield - compute and print electric field on all atoms.
gtest - compute and compare numerical and analytical gradients.
Default value: sp
coord [xyzabc|points|rotmat]
xyzabc - Coordinates of the center of mass and Euler angles.
points - Coordinates of three atoms for each fragment.
rotmat - Coordinates of the center of mass and rotation matrix.
Default value: xyzabc
See fragment input specification for more details.
terms [elec [pol [disp [xr]]]]
elec - Include electrostatics energy.
pol - Include polarization energy.
disp - Include dispersion energy.
xr - Include exchange repulsion energy.
Default value: elec pol disp xr
elec_damp [screen|overlap|off]
screen - Damping formula based on SCREEN group in the EFP potential.
overlap - Overlap-based damping formula. This damping correction is printed
as charge penetration energy.
off - No electrostatic damping.
Default value: screen
disp_damp [tt|overlap|off]
tt - Damping based on the formula by Tang and Toennies.
overlap - Overlap-based dispersion damping.
off - No dispersion damping.
Default value: overlap
pol_damp [tt|off]
tt - Tang and Toennies like damping formula.
off - No polarization damping.
Default value: tt
pol_driver [iterative|direct]
iterative - Iterative solution of system of linear equations for polarization
induced dipoles.
direct - Direct solution of system of linear equations for polarization
induced dipoles. This solver does not have convergence issues but is unsuitable
for large systems (more than 2000 polarizable points). The direct solver is not
parallelized.
Default value: iterative
enable_ff [true|false]
Default value: false
enable_multistep [true|false]
Default value: false
ff_geometry <path>
Default value: ff.xyz
ff_parameters <path>
Default value: fraglib/params/amber99.prm
single_params_file [true|false]
Default value: false
efp_params_file <path>
Default value: params.efp
enable_cutoff [true|false]
Default value: false
swf_cutoff <value>
Default value: 10.0
Unit: Angstrom
max_steps <number>
Default value: 100
This specifies maximum number of steps for both geometry optimization and molecular dynamics.
multistep_steps <number>
Default value: 1
Currently only exchange-repulsion EFP term is affected.
fraglib_path <path>
Default value: "$(prefix)/share/libefp" (data install directory)
The <path> parameter should not contain spaces or should be inside double
quotes otherwise.
userlib_path <path>
Default value: "." (current directory)
The <path> parameter should not contain spaces or should be in double quotes
otherwise.
enable_pbc [true|false]
Default value: false
Setting enable_pbc to true also sets enable_cutoff to true.
periodic_box <x> <y> <z>
Default value: 30.0 30.0 30.0
Unit: Angstrom
The smallest box dimension must be greater than 2 * swf_cutoff.
opt_tol <value>
Default value: 0.0001
Unit: Hartree/Bohr
Optimization will stop when maximum gradient component is less than opt_tol
and RMS gradient is less than one third of opt_tol.
See also num_step_dist and num_step_angle.
gtest_tol <value>
Default value: 1.0e-6
Unit: Hartree/Bohr
ref_energy <value>
Default value: 0.0
Unit: Hartree
hess_central [true|false]
Default value: false
If hess_central is true then the more accurate central differences will be
used for numerical Hessian calculation. Otherwise only forward differences will
be used. Note that central differences require twice as many gradient
calculations.
num_step_dist <value>
Default value: 0.001
Unit: Angstrom
num_step_angle <value>
Default value: 0.01
Unit: Radian
ensemble [nve|nvt|npt]
nve - Microcanonical ensemble.
nvt - Canonical ensemble with Nose-Hoover thermostat. For the description of
the algorithm see Phys. Rev. A 31, 1695 (1985).
npt - Isobaric-isothermal ensemble. This also sets enable_pbc to true.
For the description of the algorithm see Mol. Phys. 78, 533 (1993).
Default value: nve
time_step <value>
Unit: Femtosecond
Default value: 1.0
print_step <value>
Default value: 1
Number of steps between outputs of the system state.
velocitize [true|false]
Default value: false
If true then random initial velocities will be assigned to fragments using
Gaussian distribution. Velocity magnitudes are chosen so that initial
temperature of the system is approximately equal to the target simulation
temperature.
temperature <value>
Unit: Kelvin
Default value: 300.0
Target simulation temperature for NVT and NPT thermostats.
pressure <value>
Unit: Bar
Default value: 1.0
Target simulation pressure for NPT barostat. Note that whether or not pressure coupling is used, the pressure value will oscillate significantly. Fluctuations on the order of hundreds of bar are typical. This variation is entirely normal due to the fact that pressure is a macroscopic property and can only be measured properly as time average. The actual variations of instantaneous pressure depend on the size of the system and the values of barostat parameters.
thermostat_tau <value>
Unit: Femtosecond
Default value: 1000.0
Temperature relaxation time parameter of the Nose-Hoover thermostat.
barostat_tau <value>
Unit: Femtosecond
Default value: 10000.0
Pressure relaxation time parameter of the barostat.
One or more fragment <name> groups.
If <name> contains an _l suffix the parameters (.efp files) for this
fragment will be searched for in the fraglib_path directory. Otherwise the
directory specified by the userlib_path option will be used. The name of the
.efp file must be the same as the name of the fragment without an _l suffix
and must be all lowercase. For example for the fragment named H2O_L the
parameters must be in the fraglib_path directory in the file named h2o.efp.
For the fragment named NH3 the parameters must be in the userlib_path
directory in the file named nh3.efp.
Fragment position and orientation are specified on the next line(s).
fragment h2o
0.0 0.0 0.0 0.0 0.0 0.0
The numbers are coordinates of the center of mass of a fragment in Angstroms and three Euler rotation angels in Radians.
fragment h2o
0.0 0.0 0.0
1.0 0.0 0.0
0.0 1.0 0.0
The numbers are coordinates of three points belonging to a fragment in Angstroms.
fragment h2o
0.0 0.0 0.0
1.0 0.0 0.0
0.0 1.0 0.0
0.0 0.0 1.0
The numbers are coordinates of the center of mass of a fragment in Angstroms and a 3 x 3 rotation matrix.
Fragment velocities for MD simulations can be specified using velocity
keyword with the center of mass velocity and angular velocity in atomic units
specified on the next line.
Quadratic constraint on the fragment center of mass can be specified using
constraint keyword with the force constant k (in a.u.) and constraint
position xyz (in angstroms) specified on the next line.
Additionally to fragments a system can contain a set of point charges. They can be specified using the following format for each charge:
charge <q> <x> <y> <z>