pwtools.parse.CpmdMDOutputFile

class pwtools.parse.CpmdMDOutputFile(*args, **kwds)[source]

Bases: TrajectoryFileParser, CpmdSCFOutputFile

Parse CPMD MD output.

Works with BO-MD and CP-MD, fixed and variable cell. Some attrs may be None or have different shapes (2d va 3d arrays) depending on what type of MD is parsed and what info/files are available.

Notes for the comments below:

{A,B,C} = A or B or C
(A) = A is optional
(A (B)) = A is optional, but only if present, B is optional

Extra files which will be parsed and MUST be present:

GEOMETRY.scale
GEOMETRY
TRAJECTORY
ENERGIES

Extra files which will be parsed and MAY be present depending on the type of MD:

(FTRAJECTORY)
(CELL)
(STRESS)

Notes

The input should look like that:

&CPMD
    MOLECULAR DYNAMICS {BO,CP}
    (PARRINELLO-RAHMAN (NPT))
    PRINT ON FORCES COORDINATES
    TRAJECTORY XYZ FORCES
    STRESS TENSOR
        <step>
    ...
&END

&SYSTEM
    SCALE
    ...
&END

Tested with CPMD 3.15.1, the following extra files are always written:

GEOMETRY.scale
GEOMETRY
TRAJECTORY
ENERGIES

In the listing below, we show which extra files are written (+) or not (-) if the input follows the example above.

Also, the order of columns in the ENERGIES file depends on what type of MD we are running. In case of BO-MD it depends on the kind of wavefunction optimizer, too! This is most unpleasant. Currently we rely on the fact that each tested case has a different number of columns, but this is very hackish b/c it is not guaranteed to be unique! Maybe, we should let the user set self.energies_order or a keywords mdtype={‘cp-npt’, ‘bo’, etc} instead of subclassed for each case.

This is what we tested so far (cpmd 3.15.1). For BO-MD + ODIIS, some columns are always 0.0, but all are there (e.g. EKINC is there but 0.0 b/c not defined for BO, only CP). For BO-MD, we list the wf optimizer (xxx for CP b/c there is none):

MOLECULAR DYNAMICS BO
    +FTRAJECTORY
    -CELL
    -STRESS         # why!?
  ODISS
    NFI EKINC TEMPP EKS ECLASSIC EHAM DIS TCPU
  LANCZOS DIAGONALIZATION
    NFI TEMPP EKS ECLASSIC DIS TCPU

MOLECULAR DYNAMICS CP
    +FTRAJECTORY
    -CELL
    +STRESS
  xxx
    NFI EKINC TEMPP EKS ECLASSIC EHAM DIS TCPU

MOLECULAR DYNAMICS BO
PARRINELLO-RAHMAN
    not implemented !

MOLECULAR DYNAMICS CP
PARRINELLO-RAHMAN
    -FTRAJECTORY    # why!?
    +CELL
    +STRESS
  xxx
    NFI EKINC EKINH TEMPP EKS ECLASSIC EHAM DIS TCPU

MOLECULAR DYNAMICS BO
PARRINELLO-RAHMAN NPT
    -FTRAJECTORY    # why!?
    +CELL
    +STRESS
  ODIIS
    NFI EKINC EKINH TEMPP EKS ECLASSIC EHAM DIS TCPU

MOLECULAR DYNAMICS CP
PARRINELLO-RAHMAN NPT
    -FTRAJECTORY    # why!?
    +CELL
    +STRESS
  xxx
    NFI EKINC EKINH TEMPP EKS ECLASSIC EHAM DIS TCPU
__init__(*args, **kwds)[source]
Parameters:

filename (file to parse) –

Methods

apply_units()

Like _apply_units_raw(), make sure that units are only applied once.

assert_attr(attr)

Raise AssertionError if self.<attr> is not set (is_set_attr() returns False.

assert_attr_lst(attr_lst)

assert_set_attr(attr)

Same as assert_attr(), but run try_set_attr() first.

assert_set_attr_lst(attr_lst)

check_set_attr(attr)

Run try_set_attr() and return the result of is_set_attr(), i.e. True or False.

check_set_attr_lst(attr_lst)

dump(dump_filename[, mkdir])

Write object to binary file using pickle.

get_cell()

2d cell [Bohr]

get_cont([auto_calc])

Populate and return a Container object.

get_coords()

get_coords_frac()

get_econst()

[Ha]

get_ekin()

get_ekin_cell()

get_ekin_elec()

get_ekinc()

get_ekinh()

get_etot()

[Ha]

get_forces()

Cartesian forces [Ha/Bohr].

get_natoms()

Number of atoms.

get_nkpoints()

get_nstep_scf()

get_return_attr(attr_name)

Call try_set_attr() are return self.<attr_name> if set.

get_scf_converged()

get_stress()

Stress tensor from STRESS file if available [kbar]

get_struct(**kwds)

get_symbols()

get_temperature()

[K]

get_temperature_cell()

[K]

get_timestep()

Timestep [thart].

get_traj(**kwds)

get_velocity()

init_attr_lst([attr_lst])

Set each self.<attr> in attr_lst to None.

is_set_attr(attr)

Check if self has the attribute self.<attr> and if it is _not_ None.

is_set_attr_lst(attr_lst)

load(dump_filename)

Load pickled object.

parse()

raw_return(attr_name)

Call try_set_attr(_<attr_name>_raw) and return it if set, else None.

raw_slice_get(attr_name, sl, axis)

Shortcut method:

set_all([attr_lst])

Call getter for each attr name in attr_lst.

set_attr_lst(attr_lst)

Set self.attr_lst and init each attr to None.

try_set_attr(attr)

If self.<attr> does not exist or is None, then invoke an appropirately named getter as if this command would be executed.

try_set_attr_lst(attr_lst)

update_units(units)

Update self.units dict from units.

Attributes

default_units

timeaxis