Crystal

(contributed by Patrick Melix)

More information about CRYSTAL can be found on its official website.

PLAMS offers a simple CRYSTAL interface which does not offer access to all possible input types of CRYSTAL just most. CRYSTAL14 was used by the developer, but as far as the developer can tell the new input features from CRYSTAL17 can be achieved with this interface. Older CRYSTAL versions are more restrictive with the input, so they have not been tested. The relevant classes are CrystalJob and Results.

Preparing a calculation

Preparing an instance of CrystalJob follows the general principles for SingleJob. Information adjusting the input file is stored in the myjob.settings.input branch. The geometry of your system can be supplied via the class Molecule and will be parsed into a fort.34 file using the EXTERNAL keyword (only if you have ASE installed). It can also be supplied to the myjob.settings.input branch by using the function mol2CrystalConf to create a CRYSTAL-type input of your structure inside the input file (set myjob.settings.ignore_molecule = True). Consult the manual for further information on the different input options of CRYSTAL.

Input

Settings must contain at least (case insensitive):

  • one geometry key (‘CRYSTAL’,’SLAB’,’POLYMER’,’HELIX’,’MOLECULE’,’EXTERNAL’,’DLVINPUT’), if the Molecule parser of CrystalJob is used the ‘EXTERNAL’ keyword is added automatically. For using mol2CrystalConf, see below).

  • one basis key (‘BASISSET’)

  • one option_key (‘options’ and anything else)

The ordering inside the geometry-, basis- and option-block can be controlled:

settings.input.basisset._h = 'top line'
settings.input.basisset._1 = 'first line'
settings.input.basisset._2 = 'second line'

and so on. Note that you can also pass lists to the ordered version. Every item will end up in one line.

To make input nicer, the ‘options’ key will never be printed, since the input does not allow an opening statement for this block. This way you can use:

settings.input.options.bla = 'bla'
settings.input.options.test = ''
settings.input.options._h = 'FIRST'

without the ‘options’ being printed, but the section will still be closed with an ‘END’.

Runscript

The command crystal should point to the crystal binary or a runscript (so make sure it is in your $PATH), that the input can be piped to. Modify CrystalJob._command if necessary. PLAMS will not clean up the mess of files that crystal produces. If you want that, your runscript should do it for you. Standard output is written to $JN.out.

Molecule parsing

The Molecule parser of CrystalJob makes use of the EXTERNAL keyword by writing the Molecule instance to the file fort.34. This is done using the write_crystal method from ASE.

If you do not have ASE installed you cannot use this feature. In this case use the function mol2CrystalConf to create a list to pass to myjob.settings.input.<geomKey>. Remember to set myjob.settings.ignore_molecule = True if you are doing this.

Results extraction

There is no special results extraction yet, use the standard methods from the Results class.

Example

mol = Molecule('test.xyz')
common = Settings()
geom = ['0 0 0',
'194',
'2.456 6.696',
'2',
'6 0.0     0.0     0.25',
'6 0.333333  0.666667  0.75',
'SLAB',
'0 0 1',
'1 1',
'OPTGEOM',
'FULLOPTG',
'ENDGEOM']

common.input.basisset = 'STO-3G'
common.input.options.shrink = '9 18'
common.input.options.scfdir = ''
common.input.options._h = 'RHF'
common.input.options.dft.exchange = 'PBE'
common.input.options.dft.correlat = 'PBE'
common.input.options.maxcycle = 250
common.input.options.fmixing = 90
#common.input.options.test = True

common.input.crystal = geom
common.ignore_molecule = True

#alternative 1
#common.input.crystal = mol2CrystalConf(mol)
#common.ignore_molecule = True

#alternative 2
#just pass the molecule to CrystalJob if you have ASE

job = CrystalJob(name='crystaltest', settings=common, molecule=mol)
jobres = job.run()

API

class CrystalJob(name='plamsjob', settings=None, depend=None)[source]

A class representing a single computational job with CRYSTAL <https://www.crystal.unito.it/> Use Crystal version >= 14, lower versions have an even stricter and more complicated input.

get_input()[source]

Transform all contents of input branch of settings into string.

get_runscript()[source]

Run Crystal.

check()[source]

Look for the normal termination signal in output. Note, that does not mean your calculation was successful!

mol2CrystalConf(molecule)[source]

Call this function to create a CRYSTAL-type input of your structure:

Returns a given Molecule object as a geomkey and a list of strings that can be used to create a Settings instance for Crystal.

>>> print(crystalMol2Conf(mol))
'GEOMKEY', ['0 0 0', '1', 'lattice', 'nAtoms', 'ElementNumber1 X1 Y1 Z1','ElementNumber2 X2 Y2 Z2', ...]

  • IFLAG,IFHR and IFSO are returned as 0,0,0 by default with Symmetry group P1 (number 1). This should allow most calculations to run. The user needs to change them if he wants to take advantage of symmetry.

  • The geometry key is guessed from the number of lattice vectors. For special stuff change it by hand.

  • The number of lattice vectors in the given molecule should correspond to the dimensionality of the system. Do not fill them with zeros or unit vectors, this will result in a 3D-Periodic system with wrong fractional coordinates. So stick with the standard PLAMS way of doing things.