Socorro requires a set of input files, with the exact number depending on the type of calculation being performed, and a unix directory system. The input file names and the directories where the input files are located can be customized by editing /socorro/src/path_mod.f90. The only exception is the control file, which must be located in the run directory. The names of the output files can likewise be customized by editing /socorro/src/path_mod.f90, however their locations can only be the run directory. Descriptions of the various input and output files are given below using the default directories and names set in path_mod.f90.
Input files
- argvf
- Parameters used to specify and control a run. The parameters are denoted with the tags described further below.
- data/crystal
- Lattice vectors, atom types, and atom positions. The format is:
<identifier_string><lattice constant><lattice vector 1><lattice vector 2><lattice vector 3><atom coordinate type><number of atoms><atom tag> <position>….<atom tag> <position>
- <identifier string>
- Arbitrary text string namingthe simulation.
- <lattice constant>
- Arbitrary scale factor for lattice vectors.
- <lattive vector>
- Lattice vector coordinates, (v1, v2 v3), in either cartesian or lattice coordinates.
- <atom coordinate type>
- Either lattice or cartesian denoting the format for the atom positions, <position>.
- <number_of_atoms>
- Total number of atoms
- <atom tag>
- This is used to construct the filename containing the pseudopotential for the species which are stored in the data directory as discussed below.
- <position>>
- Position of atom, (p1, p2 p3), in either cartesian or lattice coordinates.
- data/NCP.<atom tag>
- Data for the <atom tag> norm-conserving pseudopotential.
- data/PAW.<atom tag>
- Data for the <atom tag> projector augmented wave pseudopotential.
- data/kpoints (optional)
- Sampling points in the Brillouin zone. Use this for specifying specific k-points. See k-point tags for automatic K-point generation. The file format is:
<number of k-points><k-point format><k-point vector> <degeneracy>…<k-point vector> <degeneracy>
- <number of k-points
- Integer number of k-points in the list.
- <k-point format>
- Either lattice or cartesian denoting the format for the k-point vectors.
- <k-point vector>
- K-point vector triple, (k1, k2, k3)
- <degeneracy>
- Degeneracy for k-point.
- data/initial_velocity (optional)
- Initial velocities for an MD run. The format is:
<velocity components for atom 1><velocity components for atom 2>…
- <velocity components for atom n>
- Atom’s initial velocity in cartesian coordinates.
- data/lgroup
- (optional):Lattice point-group operations. The format is:
<number of point operators> <number of translations per point operation><space><3×3 matrix denoting a point-group operator in lattice representation>…
- data/restartf (optional)
- Restart file.
- data/stopf (optional)
- File containing command to halt a running program. This can be added at any time and is checked between iterations. The file has a single command which is one of the following:
stop - Program to halt gracefully at next iteration.abort - Causes a program to halt as soon as possible.
Output files
- errorf_xxx
- Error and warning messages for process xxx.
- diaryf
- Diary of the run.
- new_crystal
- New crystal file after an update of the atom positions.
- new velocity
- New atom velocities after an MD update.
- new_kpoints (optional)
- Brillouin zone sampling points generated using the Monkhorst-Pack scheme.
- new_lgroup (optional)
- Lattice point-group operations.
- new_pgroup (optional)
- Point-group operations of the space group.
- new sgroup (optional)
- Space-group operations.
- new_restartf (optional)
- Restart file.
- md_trajectory
- Atom positions during an MD run.
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