pychemia.code package

Modules to manipulate input and output for several atomistic simulation codes. Currently there are implementations for ABINIT, DFTB+, Fireball, an internal LennardJones ‘calculator’, Octopus and VASP.

Subpackages

Submodules

pychemia.code.codes module

class pychemia.code.codes.Codes[source]

Bases: object

finalize()[source]
get_outputs()[source]
initialize(structure, workdir=None, kpoints=None, binary=None)[source]
run(use_mpi=False, omp_max_threads=0, mpi_num_procs=1)[source]

Execute the binary and return a reference to the subprocess created

Parameters:
  • use_mpi – If mpirun will be called to execute the binary
  • omp_max_threads – Number of OpenMP threads to be created by default the environment variable OMP_NUM_THREADS is not changed
  • mpi_num_procs – Number of MPI processes
Returns:
set_inputs()[source]

pychemia.code.relaxator module

class pychemia.code.relaxator.Relaxator(target_forces)[source]

Bases: object

get_final_geometry()[source]
get_forces_stress_energy()[source]
get_max_force_stress()[source]
relaxation_status()[source]
run()[source]

pychemia.code.tasks module

class pychemia.code.tasks.Task(structure, task_params=None, workdir='.', binary=None)[source]

Bases: object

load()[source]
plot()[source]
report()[source]
report_end(html, file_format)[source]
run()[source]
save(filename=None)[source]
status()[source]