Documentation - Revision history

Tigany Zarrouk: /* Special Features */

2026-03-22T14:36:26Z

Special Features

Tigany Zarrouk: /* Special Features */

2026-03-22T14:35:52Z

Special Features

Tigany Zarrouk at 14:34, 22 March 2026

2026-03-22T14:34:54Z

Tigany Zarrouk: /* Output files */

2026-03-22T14:21:31Z

Output files

Tigany Zarrouk: /* Calculation mode */

2026-03-22T14:18:50Z

Calculation mode

Tigany Zarrouk: /* Calculation mode */

2023-11-02T13:58:08Z

Calculation mode

Tigany Zarrouk: /* Calculation mode */

2023-11-02T13:44:53Z

Calculation mode

Miguel Caro: /* Input file (input) */

2023-02-21T13:05:30Z

Input file (input)

Miguel Caro: /* Atoms file (.xyz) /

2022-04-09T11:16:05Z

Atoms file (*.xyz)

Miguel Caro: /* Atoms file (.xyz) /

2022-04-09T11:15:16Z

Atoms file (*.xyz)

@@ Line 59: / Line 59: @@
 Local hirshfeld volumes can be predicted given an appropriate model, which can be used for including van der Waals interactions via a Tkatchenko-Scheffler formalism, or many-body dispersion.
-TurboGAP can also perform experimental observable predictions (pair-distribution functions, x-ray diffraction, neutron diffraction and x-ray photoelectron spectra - the latter via Gaussian Process Prediction of local core-electron binding energies).
+TurboGAP can also perform experimental observable predictions (pair-distribution functions, x-ray diffraction, neutron diffraction and x-ray photoelectron spectra - the latter via Gaussian Process Prediction of local core-electron binding energies). The keyword options can be found in [[Experimental Observable Options]].
 Structural inference of experimental data of all the above types can be invoked by Reverse Monte-Carlo (RMC) or Molecular Augmented Dynamics (MAD). This performs a multi-objective optimization of the interatomic potential energy and experimental agreement. Relevant options are found in [[Experimental Observable Options]] and [[Structural Inference Options]].

@@ Line 61: / Line 61: @@
 TurboGAP can also perform experimental observable predictions (pair-distribution functions, x-ray diffraction, neutron diffraction and x-ray photoelectron spectra - the latter via Gaussian Process Prediction of local core-electron binding energies).
-Structural inference of experimental data of all the above types can be invoked by Reverse Monte-Carlo (RMC) or Molecular Augmented Dynamics (MAD). This performs a multi-objective optimization of the interatomic potential energy and experimental agreement. Relevant options are found on [[Structural Inference Options]].
+Structural inference of experimental data of all the above types can be invoked by Reverse Monte-Carlo (RMC) or Molecular Augmented Dynamics (MAD). This performs a multi-objective optimization of the interatomic potential energy and experimental agreement. Relevant options are found in [[Experimental Observable Options]] and [[Structural Inference Options]].
 == Parallel support ==
 Parallel support in '''TurboGAP''' is provided specifically via MPI. To build the '''TurboGAP''' code with MPI support you need an MPI-enabled Fortran compiler. '''TurboGAP''' is routinely tested and works reliably with the <code>gfortran</code> MPI wrapper, usually called <code>mpif90</code>. It should also be possible to build '''TurboGAP''' with Intel's <code>mpifort</code>, but we do not usually test the code with it. Note that the BLAS/LAPACK libraries used by '''TurboGAP''' should be compiled with the same compiler suite used to build '''TurboGAP''', to ensure compatibility. Also note that OpenMP support can be available from BLAS/LAPACK. In that case, hybrid MPI/OpenMP '''TurboGAP''' execution can be achieved, although be mindful that OpenMP acceleration can only be exploited for energy and force evaluation, not descriptor construction. We recommend to run '''TurboGAP''' with exclusive MPI parallelization, and our tests showed MPI performance to be superior to hybrid MPI/OpenMP. Since system architecture and the details of the potential might affect said performance, run your own tests to evaluate whether you gain speed up from BLAS/LAPACK's threading support.

@@ Line 52: / Line 52: @@
 Besides standard output (basic messages, progress bar, etc.) that you get printed to stdout, '''TurboGAP''' produces one or two output files, depending on whether you are running a static calculation (<code>turbogap predict</code>) or molecular dynamics (<code>turbogap md</code>). Output file <code>[[trajectory_out.xyz]]</code> is always written out, and it contains atomic positions, predicted energy and forces, etc. Output file <code>[[thermo.log]]</code> is only written when doing MD, and it contains basic thermodynamic information (energy, temperature, pressure, etc.). One can control the frequency with which each file is written (for MD only) with <code>[[write_xyz]]</code> and <code>[[write_thermo]]</code>, respectively. For finer control over which properties are written and which are not, refer to [[writeouts]]. <code>turbogap mc</code> mode writes <code>mc_all.xyz</code>, which contains all accepted monte-carlo moves, <code>mc_current.xyz</code> which contains the last accepted monte-carlo move, for ease of restarting, and <code>mc.log</code> which contains information of the monte-carlo trials done during the simulation.
 == Parallel support ==
 Parallel support in '''TurboGAP''' is provided specifically via MPI. To build the '''TurboGAP''' code with MPI support you need an MPI-enabled Fortran compiler. '''TurboGAP''' is routinely tested and works reliably with the <code>gfortran</code> MPI wrapper, usually called <code>mpif90</code>. It should also be possible to build '''TurboGAP''' with Intel's <code>mpifort</code>, but we do not usually test the code with it. Note that the BLAS/LAPACK libraries used by '''TurboGAP''' should be compiled with the same compiler suite used to build '''TurboGAP''', to ensure compatibility. Also note that OpenMP support can be available from BLAS/LAPACK. In that case, hybrid MPI/OpenMP '''TurboGAP''' execution can be achieved, although be mindful that OpenMP acceleration can only be exploited for energy and force evaluation, not descriptor construction. We recommend to run '''TurboGAP''' with exclusive MPI parallelization, and our tests showed MPI performance to be superior to hybrid MPI/OpenMP. Since system architecture and the details of the potential might affect said performance, run your own tests to evaluate whether you gain speed up from BLAS/LAPACK's threading support.

@@ Line 51: / Line 51: @@
 === Output files ===
-Besides standard output (basic messages, progress bar, etc.) that you get printed to stdout, '''TurboGAP''' produces one or two output files, depending on whether you are running a static calculation (<code>turbogap predict</code>) or molecular dynamics (<code>turbogap md</code>). Output file <code>[[trajectory_out.xyz]]</code> is always written out, and it contains atomic positions, predicted energy and forces, etc. Output file <code>[[thermo.log]]</code> is only written when doing MD, and it contains basic thermodynamic information (energy, temperature, pressure, etc.). One can control the frequency with which each file is written (for MD only) with <code>[[write_xyz]]</code> and <code>[[write_thermo]]</code>, respectively. For finer control over which properties are written and which are not, refer to [[writeouts]].
+Besides standard output (basic messages, progress bar, etc.) that you get printed to stdout, '''TurboGAP''' produces one or two output files, depending on whether you are running a static calculation (<code>turbogap predict</code>) or molecular dynamics (<code>turbogap md</code>). Output file <code>[[trajectory_out.xyz]]</code> is always written out, and it contains atomic positions, predicted energy and forces, etc. Output file <code>[[thermo.log]]</code> is only written when doing MD, and it contains basic thermodynamic information (energy, temperature, pressure, etc.). One can control the frequency with which each file is written (for MD only) with <code>[[write_xyz]]</code> and <code>[[write_thermo]]</code>, respectively. For finer control over which properties are written and which are not, refer to [[writeouts]]. <code>turbogap mc</code> mode writes <code>mc_all.xyz</code>, which contains all accepted monte-carlo moves, <code>mc_current.xyz</code> which contains the last accepted monte-carlo move, for ease of restarting, and <code>mc.log</code> which contains information of the monte-carlo trials done during the simulation.
 == Parallel support ==
 Parallel support in '''TurboGAP''' is provided specifically via MPI. To build the '''TurboGAP''' code with MPI support you need an MPI-enabled Fortran compiler. '''TurboGAP''' is routinely tested and works reliably with the <code>gfortran</code> MPI wrapper, usually called <code>mpif90</code>. It should also be possible to build '''TurboGAP''' with Intel's <code>mpifort</code>, but we do not usually test the code with it. Note that the BLAS/LAPACK libraries used by '''TurboGAP''' should be compiled with the same compiler suite used to build '''TurboGAP''', to ensure compatibility. Also note that OpenMP support can be available from BLAS/LAPACK. In that case, hybrid MPI/OpenMP '''TurboGAP''' execution can be achieved, although be mindful that OpenMP acceleration can only be exploited for energy and force evaluation, not descriptor construction. We recommend to run '''TurboGAP''' with exclusive MPI parallelization, and our tests showed MPI performance to be superior to hybrid MPI/OpenMP. Since system architecture and the details of the potential might affect said performance, run your own tests to evaluate whether you gain speed up from BLAS/LAPACK's threading support.

@@ Line 3: / Line 3: @@
 == Calculation mode ==
-There are two basic modes for running a '''TurboGAP''' calculation, <code>turbogap predict</code> and <code>turbogap md</code>. They are invoked by simply typing <code>turbogap predict</code> or <code>turbogap md</code> in the command line or a bash script (e.g., to run MD in parallel on 8 CPU cores: <code>mpirun -np 8 turbogap md</code>). Both execution modes require an <code>input</code> file with '''TurboGAP''' options, a <code>gap_files</code> directory with the GAP potential to be used in the calculation, and an XYZ file in ASE's extended XYZ format with atomic positions, lattice vectors and chemical species information (for MD, also atomic velocities are needed).
+There are three basic modes for running a '''TurboGAP''' calculation, <code>turbogap predict</code>, <code>turbogap md</code> and <code>turbogap mc</code>. They are invoked by simply typing <code>turbogap predict</code>, <code>turbogap md</code> or <code>turbogap mc</code> in the command line or a bash script (e.g., to run MD in parallel on 8 CPU cores: <code>mpirun -np 8 turbogap md</code>). All execution modes require an <code>input</code> file with '''TurboGAP''' options, a <code>gap_files</code> directory with the GAP potential to be used in the calculation, and an XYZ file in ASE's extended XYZ format with atomic positions, lattice vectors and chemical species information (for MD, also atomic velocities are needed).
 === turbogap predict ===

← Older revision		Revision as of 13:58, 2 November 2023
Line 12:		Line 12:

	<code>turbogap md</code> performs [[molecular dynamics]] (default) or [[energy minimization]] according to the [[MD options\|options]] specified in the <code>input</code> file. Currently only Velocity-Verlet MD and gradient descent energy minimization are supported. We expect to add support for Monte Carlo and other simulation protocols in the near future. To choose between different methods to propagate the atomic positions, take a look at the <code>[[optimize]]</code> keyword. If there are more than one atomic structures in the XYZ file, <code>turbogap md</code> will use the first one as starting point. Note how this differs from the behavior of <code>turbogap predict</code>, where single-point calculations are performed for ''all'' the structures in the XYZ file.		<code>turbogap md</code> performs [[molecular dynamics]] (default) or [[energy minimization]] according to the [[MD options\|options]] specified in the <code>input</code> file. Currently only Velocity-Verlet MD and gradient descent energy minimization are supported. We expect to add support for Monte Carlo and other simulation protocols in the near future. To choose between different methods to propagate the atomic positions, take a look at the <code>[[optimize]]</code> keyword. If there are more than one atomic structures in the XYZ file, <code>turbogap md</code> will use the first one as starting point. Note how this differs from the behavior of <code>turbogap predict</code>, where single-point calculations are performed for ''all'' the structures in the XYZ file.
−

	=== turbogap mc ===		=== turbogap mc ===

← Older revision		Revision as of 13:44, 2 November 2023
Line 12:		Line 12:

	<code>turbogap md</code> performs [[molecular dynamics]] (default) or [[energy minimization]] according to the [[MD options\|options]] specified in the <code>input</code> file. Currently only Velocity-Verlet MD and gradient descent energy minimization are supported. We expect to add support for Monte Carlo and other simulation protocols in the near future. To choose between different methods to propagate the atomic positions, take a look at the <code>[[optimize]]</code> keyword. If there are more than one atomic structures in the XYZ file, <code>turbogap md</code> will use the first one as starting point. Note how this differs from the behavior of <code>turbogap predict</code>, where single-point calculations are performed for ''all'' the structures in the XYZ file.		<code>turbogap md</code> performs [[molecular dynamics]] (default) or [[energy minimization]] according to the [[MD options\|options]] specified in the <code>input</code> file. Currently only Velocity-Verlet MD and gradient descent energy minimization are supported. We expect to add support for Monte Carlo and other simulation protocols in the near future. To choose between different methods to propagate the atomic positions, take a look at the <code>[[optimize]]</code> keyword. If there are more than one atomic structures in the XYZ file, <code>turbogap md</code> will use the first one as starting point. Note how this differs from the behavior of <code>turbogap predict</code>, where single-point calculations are performed for ''all'' the structures in the XYZ file.
		+
		+
		+	=== turbogap mc ===
		+	<code>turbogap mc</code> performs (Grand-Canonical) [[Monte-Carlo]] simulations. These can be (NVT), (NPT), (mu VT) or (mu PT). Hybrid MC (using molecular dynamics to produce a trial move) can be performed as well as relaxation after specific trial moves. The user can specify a large number of move types. For reference on the specification see [[Monte-Carlo]]. The outputs are <code>mc.log</code> (the log file), <code>mc_all.xyz</code> all of the accepted MC steps, <code>mc_trial.xyz</code> which is an .xyz containing a trial move and <code>mc_current.xyz</code> which is the current accepted step. The .xyz files are written every <code>write_xyz=N</code> steps.

	== Files ==		== Files ==

@@ Line 24: / Line 24: @@
   [[n_species]] = 3
   [[species]] = H C O
-  [[masses]] = 1.01 12.01 16.00 ! this is optional for single point, mandatory for MD
+  [[masses]] = 1.01 12.01 16.00 ! this is optional for single point, for MD TurboGAP will try to get them from a database if not provided
   [[e0]] = 0. 0. 0. ! this is optional, to specify per-species energy offsets

@@ Line 40: / Line 40: @@
   Atom_name_nat posx posy posz (velx vely velz)
-where the velocity information is needed for MD ('''TurboGAP''' will generate random velocities if not provided). The positions must be in units of Angstrom, the velocities in Angstrom/fs and the masses in amu. '''TurboGAP''' XYZ reading adheres strictly to extXYZ format, with "species" (S:1), "pos" (R:3), "vel" (R:3) and "fix_atom" (S:3, with values F or T allowed), "mass" (R:1) read from the Properties attribute. "positions", "velocities", "fix_atoms" and "masses" are used as synonyms for "pos", "vel", "fix_atom" and "mass", respectively.
+where the velocity information is needed for MD ('''TurboGAP''' will generate random velocities if not provided). The positions must be in units of Angstrom, the velocities in Angstrom/fs and the masses in amu. '''TurboGAP''' XYZ reading adheres strictly to extXYZ format, with "species" (S:1), "pos" (R:3), "vel" (R:3), "fix_atom" (S:3, with values F or T allowed) and "mass" (R:1) read from the Properties attribute. "positions", "velocities", "fix_atoms" and "masses" are used as synonyms for "pos", "vel", "fix_atom" and "mass", respectively.
 === Potential directory (gap_files/) ===

Documentation - Revision history

Tigany Zarrouk: /* Special Features */

Tigany Zarrouk: /* Special Features */

Tigany Zarrouk at 14:34, 22 March 2026

Tigany Zarrouk: /* Output files */

Tigany Zarrouk: /* Calculation mode */

Tigany Zarrouk: /* Calculation mode */

Tigany Zarrouk: /* Calculation mode */

Miguel Caro: /* Input file (input) */

Miguel Caro: /* Atoms file (*.xyz) */

Miguel Caro: /* Atoms file (*.xyz) */

Miguel Caro: /* Atoms file (.xyz) /

Miguel Caro: /* Atoms file (.xyz) /