Program displacement

Namelist input ↑

inpFile, refFile ↑

(type: character string , default: '-' , mandatory: yes )
Name of the structure file used as input (strained) and reference. If inpFile='-' or refFile="-", the structure is read from keyboard. The file formats are defined by refXyz | refCfg | refGin | refSiesta | refNDM | refLammps | refPoscar and by inpXyz | inpCfg | inpGin | inpSiesta | inpNDM | inpLammps | inpPoscar Reference structure file is needed only if one wants to compute the total displacement or its gradient, or the total or plastic strain.

See also: inpXyz, inpCfg, inpGin, inpSiesta, inpNDM, inpLammps, inpPoscar , refXyz, refCfg, refGin, refSiesta, refNDM, refLammps, refPoscar


inpXyz, inpCfg, inpGin, inpSiesta, inpNDM, inpLammps, inpPoscar ↑

(type: logical , default: .false. , mandatory: one should be set to .true. )
If inpXyz=.true. the input structure file is given in xyz format.

See also: Structure file formats , inpFile, refFile


refXyz, refCfg, refGin, refSiesta, refNDM, refLammps, refPoscar ↑

(type: logical , default: .false. , mandatory: one should be set to .true. )
If refXyz=.true. the reference structure file is given in xyz format.

See also: Structure file formats , inpFile, refFile


imm ↑

(type: integer , default: 0 , mandatory: no )
Maximal number of atom in the structure. imm needs to be defined if the input structure is duplicated to dimension the arrays. Otherwise, the actual number of atoms, read from input structure file, is used.

See also: duplicate


duplicate ↑

(type: logical , default: .false. , mandatory: no )
If duplicate=.true., the crystal is duplicated, both the input and reference structures. lat(1:3) is the number of times the crystal should be duplicated in each direction given by the vectors at(1:3,i) read in the structure file. If lat(i) is negative, then the opposite of the vector at(1:3,i) is used. The maximal number of atoms in the duplicated structure needs to be set with imm and the periodicity vectors have to be defined. When the structure is also rotated, the duplication is done first and then the rotation. The periodicity vectors used for duplication are thus those before rotation. For small simulation boxes, it may be necessary to duplicate the structure to find all neighbours of the atoms, when neighbours are needed (to extract Nye tensors or calculate strain for instance)

See also: imm , lat


lat ↑

(type: integer, dim(3) , default: 1 , mandatory: no )
Number of replicas in each direction when duplicating the structure files.

See also: duplicate


rotate ↑

(type: logical , default: .false. , mandatory: no )
If rotate=.true., the crystal is rotated using rotation matrix defined in rot(1:3,1:3) Both the input and reference structures are rotated.

See also: rot


rot ↑

(type: real, dim(3,3) , default: identity matrix , mandatory: no )
Rotation matrix used when rotate=.true.

See also: rotate


translate ↑

(type: logical , default: .false. , mandatory: no )
If translate=.true., the crystal is translated with the vector uTranslate(1:3) Both the input and reference structures are translated.

See also: uTranslate


uTranslate ↑

(type: real, dim(3) , default: 0. , mandatory: no )
Translation vector used when translate=.true. If alat is defined, uTranslate(1:3) is multiplied by alat.

See also: translate , alat


clipAtom ↑

(type: logical , default: .false. , mandatory: no )
If clipAtom=.true., periodic boundary conditions are applied to atom coordinates to bring them back in the primitive unit cell. The periodicity vectors have to be defined. The transformation is applied both to the input and the reference structures.


clipDisplacement ↑

(type: logical , default: .false. , mandatory: no )
If clipDisplacement=.true., periodic boundary conditions are applied to atom displacements. The periodicity vectors have to be defined.


alat ↑

(type: real , default: 1. , mandatory: no )
Length used to scale all distances in the present input file. For program displacement, it affects the quantities rNeigh and uTranslate(1:3).


fixGravity ↑

(type: logical , default: .false. , mandatory: no )
If fixGravity=.true., a solid displacement is added to atom positions in the input structure to keep fixed the gravity center compared to the reference structure. The same solid displacement is added to the calculated atom displacements. As a consequence, the displacement average is null.


patternFile ↑

(type: character string , default: empty , mandatory: no )
Name of the file where are stored the crystallographic patterns defining the atom reference neighbourhoods. This is necessary to calculate elastic or plastic strains, Nye tensors or Burgers density. This file can then be generated with programs patternInit or patternDetect.

See also: patternAngleThreshold , patternSelectionMethod


patternAngleThreshold ↑

(type: real , default: 10. , mandatory: no )
Threshold angle for pairing neighbour vectors when associating each atom with a reference crystallographic pattern. Two bonds, in the atom neighbourhood of the input structure and in the reference crystallographic pattern, match if the angle difference between the two corresponding directions is smaller than this threshold.

See also: patternFile , patternSelectionMethod


patternSelectionMethod ↑

(type: integer , default: 3 , mandatory: no )
Method used to associate a reference crystallographic pattern to each atom by comparing the atomic bonds of the corresponding neighbourhoods patternSelectionMethod = 1 : Select pattern which maximises the number of matches look to the NORM OF THE DISPLACEMENT if 2 patterns are equivalent = 2 : Select pattern which maximises the number of matches look to the norm of the ELASTIC GRADIENT if 2 patterns are equivalent = 3 : Select pattern which minimizes the number of unmatched bonds look to the NORM OF THE DISPLACEMENT if 2 patterns are equivalent = 4 : Select pattern which minimizes the number of unmatched bonds look to the norm of the ELASTIC GRADIENT if 2 patterns are equivalent

See also: patternFile , patternAngleThreshold


rNeigh ↑

(type: real , default: -1. , mandatory: yes )
Distance cutoff defining the sphere where atom neighbours have to be looked for. If alat is defined, rNeigh is multiplied by alat.

See also: alat


max_nNeigh ↑

(type: integer , default: 16 , mandatory: no )
Maximal number of neighbours allowed for each atom.


bNye ↑

(type: real, dim(3) , default: 0. , mandatory: no )
Direction of the Burgers vector when projecting the Nye tensor to define dislocation density.

See also: lNye


lNye ↑

(type: real, dim(3) , default: 0. , mandatory: no )
Direction of the dislocation lines when projecting the Nye tensor to define dislocation density.

See also: bNye


outFile ↑

(type: character string , default: '-' , mandatory: no )
Name of the structure file where to save the input or the reference structure, depending of the value of variable 'initial', which auxiliary properties set for each atom (displacement, strain, dislocation density, ...) If outFile="-", the output file is printed on screen. The file format is defined by outXyz | outCfg | outOnlyAtoms

See also: outXyz, outCfg, outOnlyAtoms, outLammps, outPoscar , initial , out_alat


outXyz, outCfg, outOnlyAtoms, outLammps, outPoscar ↑

(type: logical , default: .false. , mandatory: no )
Format of the structure file used for output. If all variables are set to .false. (default), the output structure is not written.

See also: outFile


outVitek ↑

(type: logical , default: .false. , mandatory: no )
Write output files needed to plot Vitek differential displacement map with gnuplot. The program assumed screw dislocation orientated along z, for different crystal structures (bcc, fcc, hcp), as defined by variable VitekCrystalType. The lattice parameter needs to be known. It is defined with the variable out_alat The program assumes periodic boundary conditions, which means that the periodicity vectors need to be defined both for reference and input structures.

See also: VitekCrystalType , scriptVitekFileScrew , outVitekFileScrew , pointVitekFile , scriptVitekFileEdge , outVitekFileEdge , lVitekPerioXY , out_alat


VitekCrystalType ↑

(type: character string , default: 'bcc' , mandatory: no )
Define crystal type for differential displacement map. possible values: - 'bcc': 1/2[111] screw dislocation in bcc crystal - 'fcc': 1/2[110] screw dislocation in fcc crystal - 'hcp': 1/3[11-20] screw dislocation in hcp crystal The dislocation line should be along z axis

See also: outVitek


scriptVitekFileScrew ↑

(type: character string , default: 'vitek.gnu' , mandatory: no )
Name of the file where to write the gnuplot script to be used to draw the screw component of Vitek differential displacement map.

See also: outVitek , outVitekFileScrew , pointVitekFile , scriptVitekFileEdge , outVitekFileEdge


outVitekFileScrew ↑

(type: character string , default: 'vitek.res' , mandatory: no )
Name of the file where the screw component of Vitek differential displacement map is defined (definition of arrows).

See also: outVitek , scriptVitekFileScrew , pointVitekFile , scriptVitekFileEdge , outVitekFileEdge


pointVitekFile ↑

(type: character string , default: 'vitek.points' , mandatory: no )
Name of the file where the atom positions are defined for Vitek differential displacement maps (screw and edge components).

See also: outVitek , scriptVitekFileScrew , outVitekFileScrew , scriptVitekFileEdge , outVitekFileEdge


scriptVitekFileEdge ↑

(type: character string , default: 'vitek_edge.gnu' , mandatory: no )
Name of the file where to write the gnuplot script to be used to draw the edge component of Vitek differential displacement map.

See also: outVitek , scriptVitekFileScrew , outVitekFileScrew , pointVitekFile , outVitekFileEdge


outVitekFileEdge ↑

(type: character string , default: 'vitek_edge.res' , mandatory: no )
Name of the file where the edge component of Vitek differential displacement map is defined (definition of arrows).

See also: outVitek , scriptVitekFileScrew , outVitekFileScrew , pointVitekFile , scriptVitekFileEdge


lVitekPerioXY ↑

(type: logical , default: .FALSE. , mandatory: no )
When true, consider also periodic images of atoms in the plane XY perpendicular to the dislocation line when drawing differential displacement maps. It can be used to see differential displacements at the border of the simulation box.

See also: outVitek


out_alat ↑

(type: real , default: 1. , mandatory: no )
When the output structure is written with xyz or cfg file format, atomic positions and periodicity vectors can be scaled by a lattice parameter given in out_alat. This variable is also used to define the lattice parameter necessary to draw Vitek differential displacement maps.

See also: outFile , outVitek , Structure file formats


initial ↑

(type: logical , default: .false. , mandatory: no )
If initial=.true. (.false.), the coordinates of the input (reference) structure are used on output.


out_displacement ↑

(type: logical , default: .true. , mandatory: no )
If out_displacement=.true., the displacement defined on each atom is printed in output structure file.


out_gradDisplacement ↑

(type: logical , default: .false. , mandatory: no )
If out_gradDisplacement=.true., the gradient of the displacement defined on each atom is printed in output structure file. The gradient is obtained from atom displacements by finite differences. rNeigh needs to have been set to define atom neighbourhood used for finite differences.


out_strain ↑

(type: logical , default: .false. , mandatory: no )
If out_strain=.true., the total strain defined on each atom is printed in output structure file. The total strain is obtained from the gradient of the total displacement using Green-Lagrange (default) or Euler-Lagrange definition.

See also: out_gradDisplacement , EulerLagrange


EulerLagrange ↑

(type: logical , default: .false. , mandatory: no )
If EulerLagrange=.true., the Euler Lagrange definition is used to obtain strain from displacement gradient. If EulerLagrange=.false., the Green Lagrange definition is used.

See also: out_strain , out_elasticStrain


out_gradElasticDisplacement ↑

(type: logical , default: .false. , mandatory: no )
If out_gradElasticDisplacement=.true., the gradient of the elastic displacement defined on each atom is printed in output structure file. The gradient is obtained from atom displacements by finite differences, using only the elastic contribution to the displacement. Reference crystallographic patterns, read in file defined by patternFile, are used to calculate this elastic contribution. rNeigh needs to have been set to define atom neighbourhood used for finite differences.


out_elasticStrain ↑

(type: logical , default: .false. , mandatory: no )
If out_elasticStrain=.true., the elastic strain defined on each atom is printed in output structure file. The elastic strain is obtained from the gradient of the elastic displacement using Green-Lagrange (default) or Euler-Lagrange definition.

See also: out_gradDisplacement , EulerLagrange


out_plasticStrain ↑

(type: logical , default: .false. , mandatory: no )
If out_plasticStrain=.true., the plastic strain defined on each atom is printed in output structure file. The plastic strain is obtained from the difference between the total and the elastic strains.

See also: out_strain , out_elasticStrain


out_nye ↑

(type: logical , default: .false. , mandatory: no )
If out_nye=.true., the Nye tensor defined on each atom is printed in output structure file. The Nye tensor is obtained from the plastic strain by finite differences.

See also: out_plasticStrain


out_BurgersDensity ↑

(type: logical , default: .false. , mandatory: no )
If out_burgersDensity=.true., the Burgers density defined on each atom is printed in output structure file. The Burgers density is obtained by projection of the Nye tensor using lNye and bNye for the directions of the dislocation lines and of the Burgers vector.

See also: out_nye , bNye , lNye


out_neighbours ↑

(type: logical , default: .false. , mandatory: no )
If out_neighbours=.true., the number of neighbours is saved in output structure file for each atom.

See also: outFile


out_pattern ↑

(type: logical , default: .false. , mandatory: no )
If out_pattern=.true., the output pattern is saved in output structure file for each atom.

See also: outFile


verbosity ↑

(type: integer , default: 4 , mandatory: no )
Integer values defining amount of information on output unit. verbosity=0: no output verbosity=4: normal output verbosity>=10: debugging


debug ↑

(type: logical , default: .false , mandatory: no )
For debug purpose.