ForceField Engine Options¶
Details of the ForceField engine can be set via its input block. Some option are specific to UFF and others to other force fields.
Common options¶
These options apply to any force field.
Type¶
There are a few predefined force field types, that, if used, require no other input.
Type [UFF | Amber95 | GAFF | Tripos5.2 | APPLE&P | UserDefined]
Type- Type
Multiple Choice
- Default value
UFF
- Options
[UFF, Amber95, GAFF, Tripos5.2, APPLE&P, UserDefined]
- Description
Type of force field to be used
Non-bonded screening¶
The long range interaction (dispersion and Coulomb) are the most expensive to evaluate. This gives you the option to screen the interaction more aggressively.
NonBondedCutoff float
NonBondedCutoff- Type
Float
- Default value
15.0
- Unit
Angstrom
- Description
Distance beyond which the non-bonded pair interactions (Coulomb and Van der Waals) will be ignored. The interactions are smoothly damped starting from 0.9*NonBondedCutoff. Has no effect on the Coulomb term for 3D-periodic systems, as Ewald summation is used.
It is usually a good idea to add some “skin” to the cutoff above when it’s used for computing a neighbor list for changing geometries (e.g. during molecular dynamics or geometry optimization). This way, the neighbor list will not need to be re-computed when atoms move a little. This may save some time because generating a neighbor list can be quite costly. The following option sets the thickness of the “skin”:
NeighborListSkin float
NeighborListSkin- Type
Float
- Default value
2.5
- Unit
Angstrom
- Description
Thickness of the buffer region added to the NonBondedCutoff when building a neighbor list.
Note
This option also affects the cutoff used when generating a neighbor list in the real-space part of the Ewald summation but then it is added to the cutoff radius is used there.
Feedback¶
If you want to know more about the details of the force field you should crank up the verbosity.
Verbosity [Silent | Normal | Verbose | VeryVerbose]
Verbosity- Type
Multiple Choice
- Default value
Silent
- Options
[Silent, Normal, Verbose, VeryVerbose]
- Description
Controls the verbosity of the engine.
Bonds usage¶
Bonds can be specified in the input, still you may not want to use those. Here are some options to control this.
BondsUsage [Input | None | Guess | Auto]
BondsUsage- Type
Multiple Choice
- Default value
Auto
- Options
[Input, None, Guess, Auto]
- Description
Controls what bonds are used by the engine. The choice auto means: guess in case there are no bonds. Guessing only happens at the first MD step, or first geometry optimization step.
Ewald summation¶
For periodic systems the Ewald summation is performed for the Coulomb interaction. It has a couple of options:
EwaldSummation
Alpha float
Enabled Yes/No
GridSpacing float
RealSpaceCutoff float
Tolerance float
End
EwaldSummation- Type
Block
- Description
Configures the details of the particle mesh Ewald (PME) summation of the Coulomb interaction.
Alpha- Type
Float
- Default value
-1.0
- Unit
1/Angstrom
- Description
This parameter shifts the workload from real space (smaller alpha) to reciprocal space (larger alpha). Using a larger [Alpha] without decreasing [GridSpacing] may increase the error in the reciprocal-space contribution. Set to zero to disable the reciprocal-space Ewald part. Negative value means the [Alpha] will be determined automatically from the [Tolerance] and [RealSpaceCutoff] values.
Enabled- Type
Bool
- Default value
Yes
- Description
Set to false to use real-space pair summation instead of the Ewald, which is the default and the only option for molecules, 1D and 2D periodic systems.
GridSpacing- Type
Float
- Default value
0.5
- Unit
Angstrom
- Description
Grid spacing in the particle mesh Ewald method. Smaller grid spacing will make the reciprocal energy calculation more accurate but slower. Using a larger [Alpha] value may require a smaller GridSpacing to be accurate.
RealSpaceCutoff- Type
Float
- Default value
0.0
- Unit
Angstrom
- Description
Set the cutoff value for the real-space summation. Zero means the internal defaults will be used depending on the [Alpha] (if Alpha=0 then the cutoff will be set to 50 Bohr, otherwise to 20 Bohr).
Tolerance- Type
Float
- Default value
1e-10
- Description
Value of the error function that should be used to determine the cutoff radius for real-space Ewald summation if [Alpha] is set on input. Alternatively, if the [RealSpaceCutoff] is set but [Alpha] is not then the [Tolerance] value affects the [Alpha]. Larger values will make the real-space summation faster but less accurate.
Disabling energy terms¶
By default all force field energy terms are calculated, however, you can disable each one of them individually.
EnergyTerms
Angle Yes/No
Coulomb Yes/No
Dispersion Yes/No
Inversion Yes/No
Stretch Yes/No
Torsion Yes/No
End
EnergyTerms- Type
Block
- Description
expert key, that allows you to disable specific energy terms.
Angle- Type
Bool
- Default value
Yes
- Description
Whether to use angle (bend) energy.
Coulomb- Type
Bool
- Default value
Yes
- Description
Whether to use coulomb energy.
Dispersion- Type
Bool
- Default value
Yes
- Description
Whether to use dispersion energy.
Inversion- Type
Bool
- Default value
Yes
- Description
Whether to use inversion energy.
Stretch- Type
Bool
- Default value
Yes
- Description
Whether to use stretch energy.
Torsion- Type
Bool
- Default value
Yes
- Description
Whether to use torsion energy.
Guessing or loading partial charges¶
The UFF forcefield has some very rudimentary partial charges guessing, only setting charges for atoms in water molecules. By default the partial charges in a force field calculation are zero. Essentially you will always need to specify atomic charges to make the results more realistic, either via the input or using one or the following options.
See also example LoadCharges, and ChargedMolecules.
GuessCharges¶
The simplest way is the use the GuessCharges key, that uses an engine that can calculate atomic charges. By default DFTB is used. DFTB is of course much more expensive than a forcefield, but if you run a MD calculation you can maybe afford a single DFTB calculation on the system.
GuessCharges Yes/No
GuessCharges- Type
Bool
- Default value
No
- Description
Use another engine to calculate/guess the charges to be used by the force field.
If you want to control the engine use the GuessChargesConfig key.
GuessChargesConfig
EngineType string
End
GuessChargesConfig- Type
Block
- Description
Guess charges to be used by the forcefield
EngineType- Type
String
- Default value
dftb
- Description
Engine that can calculate or guess charges
LoadCharges¶
You have more control over the charge guessing, by loading the charges of another calculation. This way you can set any engine specific detail, such as the basis set, or functional.
You can load charges form a previous calculation to be used as force field charges.
LoadCharges
File string
Section string
Variable string
End
LoadCharges- Type
Block
- Description
Load charges from a file to be used as forcefield charges
File- Type
String
- Description
Name of the (kf) file
Section- Type
String
- Default value
AMSResults
- Description
Section name of the kf file
Variable- Type
String
- Default value
Charges
- Description
variable name of the kf file
Amber force field options¶
These options are relevant for the Amber and GAFF force fields:
AllowMissingParameters Yes/No
AllowMissingParameters- Type
Bool
- Default value
No
- Description
When parameters are not found for bonds, angles, dihedrals, or inversions, the first entry in the database will be used.
CheckDuplicateRules Yes/No
CheckDuplicateRules- Type
Bool
- Default value
Yes
- Description
The database could contain duplicate entries. For torsions this is a feature, and the potentials will be added. For all other terms this is no allowed, and if detected the program stops. One should fix the database or set the checking to false. As always the last entry will be used.
ForceFieldFile string
ForceFieldFile- Type
String
- Default value
- GUI name
Force field library
- Description
Path to the force field parameter file
UFF options¶
The following options are only relevant for the UFF force field:
UFF
AtomTypesFile string
Database string
ElementsFile string
Library [UFF | UFF4MOF | UFF4MOF-II]
End
UFF- Type
Block
- Description
Option for the UFF force filed.
AtomTypesFile- Type
String
- Default value
mmatomtypes_db
- Description
Expert option: Select the file that defines how UFF determines the atom types
Database- Type
String
- Default value
general_db
- Description
Expert option: Select the file that defines the UFF parameters per atom type
ElementsFile- Type
String
- Default value
elements_db
- Description
Expert option: Select the file that defines the elements known to UFF
Library- Type
Multiple Choice
- Default value
UFF
- Options
[UFF, UFF4MOF, UFF4MOF-II]
- GUI name
Force field library
- Description
Selects the used parameter library.
APPLE&P force field options¶
The ForceFieldFile key is mandatory and it should contain path to the APPLE&P forcefield file. This file is usually tailored for each system specifically.
Additionally, the following options are relevant for the APPLE&P force field.
DipoleConvergenceThreshold float
DipoleConvergenceThreshold- Type
Float
- Default value
1e-06
- Unit
eBohr
- Description
Convergence criterion for induced point dipoles, in atomic units. When the length of every atomic delta_mu vector between two iterations becomes below the tolerance, the procedure is considered converged.
The repulsion/dispersion and Coulomb interaction between atoms connected by a bond or by a valence angle are excluded in APPLE&P. Those between atoms connected by a dihedral (the so called 1-4 neighbors) may be scaled down and the scaling factors can be changed using the following options:
APPLE&P
LongRangeCorrection Yes/No
MuMu14Scaling float
QMu14Scaling float
QQ14Scaling float
RD14Scaling float
End
APPLE&P- Type
Block
- Description
Options for the APPLE&P force field.
LongRangeCorrection- Type
Bool
- Default value
Yes
- GUI name
Add long-range correction
- Description
Add a long-range dispersion correction to the energy and pressure for 3D-periodic systems. This correction should be enabled only for a homogeneous liquid.
MuMu14Scaling- Type
Float
- Default value
1.0
- GUI name
Mu-Mu 3rd-neighbor scaling
- Description
Scaling factor for dipole-dipole interactions between atoms connected to 3rd order (via a dihedral).
QMu14Scaling- Type
Float
- Default value
0.2
- GUI name
Q-Mu 3rd-neighbor scaling
- Description
Scaling factor for charge-dipole interactions between atoms connected to 3rd order (via a dihedral).
QQ14Scaling- Type
Float
- Default value
1.0
- GUI name
Q-Q 3rd-neighbor scaling
- Description
Scaling factor for charge-charge interactions between atoms connected to 3rd order (via a dihedral).
RD14Scaling- Type
Float
- Default value
1.0
- GUI name
RD 3rd-neighbor scaling
- Description
Scaling factor for repulsion/dispersion interactions between atoms connected to 3rd order (via a dihedral).
Offloading calculations to LAMMPS¶
The ForceField engine can optionally offload the evaluation of energies and forces to LAMMPS to accelerate the calculation, possibly leveraging a GPU.
In this mode, the engine will still set up all force field parameters as usual, but instead of evaluating the potential directly in AMS, the engine converts the parameters into a a LAMMPS data file and then invokes LAMMPS as an external pipe worker.
As of AMS2023, this option is fully supported only for Type UFF.
Setting up LAMMPS¶
The interface between AMS and LAMMPS relies on the LAMMPS Python package which in turn requires LAMMPS to be built as a dynamic library. LAMMPS is not distributed together with the Amsterdam Modeling Suite and has to be installed separately from lammps.org. If you already have an installation of LAMMPS including its Python module, it might be possible to use it directly, but often the easiest solution is to compile LAMMPS from source.
Consult the LAMMPS documentation for a detailed description of the steps necessary to install the LAMMPS Python module and shared library. For example, the following commands can be used to build LAMMPS including the necessary packages:
# Start in the top-level lammps directory (which contains the cmake/, src/, and lib/ subdirectories, among others)
mkdir build
cd build
cmake ../cmake -DBUILD_LIB=yes -DBUILD_SHARED_LIBS=yes -DLAMMPS_EXCEPTIONS=yes -DBUILD_MPI=no -DBUILD_OMP=yes -DPKG_OPENMP=yes -DPKG_GPU=yes -DPKG_MOLECULE=yes -DPKG_EXTRA-MOLECULE=yes -DPKG_KSPACE=yes
cmake --build .
-DBUILD_SHARED_LIBS=yesis strictly required by the Python module-DLAMMPS_EXCEPTIONS=yesis necessary to allow AMS to display any error messages generated by LAMMPS. A LAMMPS library compiled without this option will still work, but any error in LAMMPS will make AMS print only a generic error message.-DBUILD_MPI=no -DBUILD_OMP=yes -DPKG_OPENMP=yesare strongly recommended to enable OpenMP parallelization of the CPU code of LAMMPS. AMS currently cannot use the MPI framework to parallelize LAMMPS and linking to a MPI-enabled library can cause issues.-DPKG_GPU=yesbuilds LAMMPS with GPU support. Both AMD and nVidia cards are able to accelerate the calculation of non-bonded interactions significantly.-DPKG_MOLECULE=yes -DPKG_EXTRA-MOLECULE=yes -DPKG_KSPACE=yesenable the potential terms required by UFF.
Before running AMS, it is necessary to set up appropriate environment variables to make sure the amspython interpreter can find the lammps Python module.
This can be done by any of the approaches outlined in the LAMMPS documentation.
However, it is necessary to use SCM_PYTHONPATH instead of PYTHONPATH and amspython instead of python3.
If you have followed the example above to build LAMMPS, the following commands should work for Bash and similar shells on Linux:
# Here /path/to/lammps is again the path to the top-level lammps directory
export SCM_PYTHONPATH=/path/to/lammps/python
export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/path/to/lammps/src
Afterwards, you can try running amspython -c 'import lammps; lammps.lammps()' to test if the environment is set up correctly.
This command should print the LAMMPS version it found.
Otherwise, an ImportError means the SCM_PYTHONPATH variable is probably not set correctly, and an error about liblammps.so suggests an incorrect LD_LIBRARY_PATH.
Input options¶
LAMMPSOffload
Enabled Yes/No
Input
UseGPU Yes/No
UseOpenMP Yes/No
WorkerCommand string
End
LAMMPSOffload- Type
Block
- Description
Offload the calculation to LAMMPS via AMSPipe.
Enabled- Type
Bool
- Default value
No
- Description
Enable offloading the force field evaluation to LAMMPS instead of handling it internally in AMS. This is currently only supported for Type=UFF.
Input- Type
Block
- Description
Commands to be passed to LAMMPS to set up the calculation. If this is left empty, AMS will generate a set of commands to set LAMMPS up according to the settings of the ForceField engine. Any LAMMPS commands entered in this input block will be used to set LAMMPS up instead of those generated by AMS. To merge the AMS-generated lines with your customizations, include lines like ‘AMS somelammpskeyword’ anywhere in this block. Any such line will be replaced by the AMS-generated line for ‘somelammpskeyword’. Any text after ‘somelammpskeyword’ will be appended to the generated line verbatim, which can be used to modify the generated command by additional options. A special line ‘AMS everything’ will be replaced by the entire block of AMS-generated commands, except those overridden anywhere in this input block (defined manually or inserted using ‘AMS somelammpskeyword’. Any customized Input block should probably include ‘AMS read_data’ near or at the end to load the AMS-generated data file defining the system.
UseGPU- Type
Bool
- Default value
No
- Description
Accelerate LAMMPS calculations using a GPU. Requires a LAMMPS library built with the GPU package.
UseOpenMP- Type
Bool
- Default value
No
- Description
Parallelize LAMMPS calculations using OpenMP threading. Requires a LAMMPS library built with the OMP package.
WorkerCommand- Type
String
- Default value
exec “$AMSBIN/amspython” “$AMSHOME/scripting/scm/external_engines/lmpworker.py”
- Description
The command to execute to run the external worker. The command is executed in a subdirectory of the results directory. The LAMMPS input commands will be passed to the worker on standard input.