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libff
libopt
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tools
README.md

README.md

EFPMD

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.

Input file format

Lines beginning with the # symbol are ignored during input parsing.

Generic parameters

Type of the simulation

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

Format of fragment input

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.

Energy terms for EFP computation

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

Electrostatic damping type

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

Dispersion damping type

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

Polarization damping type

pol_damp [tt|off]

tt - Tang and Toennies like damping formula.

off - No polarization damping.

Default value: tt

Polarization solver

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 molecular-mechanics force-field for flexible EFP links

enable_ff [true|false]

Default value: false

Geometry of the molecular-mechanics part

ff_geometry <path>

Default value: ff.xyz

Molecular-mechanics force-field parameters file

ff_parameters <path>

Default value: fraglib/params/amber99.prm

Use single EFP parameters file

single_params_file [true|false]

Default value: false

Single EFP parameters file path

efp_params_file <path>

Default value: params.efp

Enable cutoff for fragment/fragment interactions

enable_cutoff [true|false]

Default value: false

Cutoff distance for fragment/fragment interactions

swf_cutoff <value>

Default value: 10.0

Unit: Angstrom

Maximum number of steps to make

max_steps <number>

Default value: 100

This specifies maximum number of steps for both geometry optimization and molecular dynamics.

The path to the directory with fragment library

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.

The path to the directory with user-created fragments

userlib_path <path>

Default value: "." (current directory)

The <path> parameter should not contain spaces or should be in double quotes otherwise.

Periodic Boundary Conditions (PBC)

Enable/Disable PBC

enable_pbc [true|false]

Default value: false

Setting enable_pbc to true also sets enable_cutoff to true.

Periodic Box Size

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.

Geometry optimization related parameters

Optimization tolerance

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.

Gradient test related parameters

See also num_step_dist and num_step_angle.

Test tolerance

gtest_tol <value>

Default value: 1.0e-6

Unit: Hartree/Bohr

Reference energy value

ref_energy <value>

Default value: 0.0

Unit: Hartree

Hessian calculation related parameters

Hessian accuracy

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.

Numerical differentiation step length for distances

num_step_dist <value>

Default value: 0.001

Unit: Angstrom

Numerical differentiation step length for angles

num_step_angle <value>

Default value: 0.01

Unit: Radian

Molecular dynamics related parameters

Ensemble

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

time_step <value>

Unit: Femtosecond

Default value: 1.0

Print step

print_step <value>

Default value: 1

Number of steps between outputs of the system state.

Assign initial velocities

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.

Simulation temperature

temperature <value>

Unit: Kelvin

Default value: 300.0

Target simulation temperature for NVT and NPT thermostats.

Simulation pressure

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 parameter

thermostat_tau <value>

Unit: Femtosecond

Default value: 1000.0

Temperature relaxation time parameter of the Nose-Hoover thermostat.

Barostat parameter

barostat_tau <value>

Unit: Femtosecond

Default value: 10000.0

Pressure relaxation time parameter of the barostat.

Fragment input

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).

Format of input when coord is xyzabc
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.

Format of input when coord is points
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.

Format of input when coord is rotmat
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

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.

Fragment constraints

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.

Input of point charges

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>