forked from lijiext/lammps
import contributed code for computes coord/atom and orientorder/atom
This commit is contained in:
Axel Kohlmeyer
parent
c31f1e9f22
commit
95706ac846
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@ -10,22 +10,34 @@ compute coord/atom command :h3
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[Syntax:]
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compute ID group-ID coord/atom cutoff type1 type2 ... :pre
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compute ID group-ID coord/atom cstyle args ... :pre
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ID, group-ID are documented in "compute"_compute.html command
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coord/atom = style name of this compute command
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cutoff = distance within which to count coordination neighbors (distance units)
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typeN = atom type for Nth coordination count (see asterisk form below) :ul
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one cstyle must be appended :ul
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cstyle = {cutoff} or {orientorder}
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{cutoff} args = cutoff typeN
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cutoff = distance within which to count coordination neighbors (distance units)
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typeN = atom type for Nth coordination count (see asterisk form below) :pre
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{orientorder} args = orientorderID threshold
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orientorderID = ID of a previously defined orientorder/atom compute
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threshold = minimum value of the scalar product between two 'connected' atoms (see text for explanation) :pre
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[Examples:]
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compute 1 all coord/atom 2.0
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compute 1 all coord/atom 6.0 1 2
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compute 1 all coord/atom 6.0 2*4 5*8 * :pre
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compute 1 all coord/atom cutoff 2.0
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compute 1 all coord/atom cutoff 6.0 1 2
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compute 1 all coord/atom cutoff 6.0 2*4 5*8 *
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compute 1 all coord/atom orientorder 2 0.5 :pre
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[Description:]
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Define a computation that calculates one or more coordination numbers
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This compute performs generic calculations between neighboring atoms. So far,
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there are two cstyles implemented: {cutoff} and {orientorder}.
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The {cutoff} cstyle calculates one or more coordination numbers
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for each atom in a group.
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A coordination number is defined as the number of neighbor atoms with
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@ -49,6 +61,14 @@ from 1 to N. A leading asterisk means all types from 1 to n
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(inclusive). A middle asterisk means all types from m to n
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(inclusive).
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The {orientorder} cstyle calculates the number of 'connected' atoms j
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around each atom i. The atom j is connected to i if the scalar product
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({Ybar_lm(i)},{Ybar_lm(j)}) is larger than {threshold}. Thus, this cstyle
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will work only if a "compute orientorder/atom"_compute_orientorder_atom.html
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has been previously defined. This cstyle allows one to apply the
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ten Wolde's criterion to identify cristal-like atoms in a system
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(see "ten Wolde et al."_#tenWolde).
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The value of all coordination numbers will be 0.0 for atoms not in the
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specified compute group.
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@ -83,10 +103,19 @@ options.
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The per-atom vector or array values will be a number >= 0.0, as
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explained above.
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[Restrictions:] none
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[Restrictions:]
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The cstyle {orientorder} can only be used if a
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"compute orientorder/atom"_compute_orientorder_atom.html command
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was previously defined. Otherwise, an error message will be issued.
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[Related commands:]
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"compute cluster/atom"_compute_cluster_atom.html
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"compute orientorder/atom"_compute_orientorder_atom.html
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[Default:] none
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:line
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:link(tenWolde)
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[(tenWolde)] P. R. ten Wolde, M. J. Ruiz-Montero, D. Frenkel, J. Chem. Phys. 104, 9932 (1996).
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@ -15,17 +15,19 @@ compute ID group-ID orientorder/atom keyword values ... :pre
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ID, group-ID are documented in "compute"_compute.html command :ulb,l
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orientorder/atom = style name of this compute command :l
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one or more keyword/value pairs may be appended :l
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keyword = {cutoff} or {nnn} or {degrees}
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keyword = {cutoff} or {nnn} or {degrees} or {components}
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{cutoff} value = distance cutoff
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{nnn} value = number of nearest neighbors
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{degrees} values = nlvalues, l1, l2,... :pre
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{degrees} values = nlvalues, l1, l2,...
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{components} value = l :pre
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:ule
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[Examples:]
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compute 1 all orientorder/atom
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compute 1 all orientorder/atom degrees 5 4 6 8 10 12 nnn NULL cutoff 1.5 :pre
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compute 1 all orientorder/atom degrees 5 4 6 8 10 12 nnn NULL cutoff 1.5
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compute 1 all orientorder/atom degrees 4 6 components 6 nnn NULL cutoff 3.0 :pre
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[Description:]
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@ -71,6 +73,13 @@ The numerical values of all order parameters up to {Q}12
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for a range of commonly encountered high-symmetry structures are given
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in Table I of "Mickel et al."_#Mickel.
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The optional keyword {components} will output the components of
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the normalized complex vector {Ybar_lm} of degree {l}, which must be
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explicitly included in the keyword {degrees}. This option can be used
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in conjunction with "compute coord_atom"_compute_coord_atom.html to
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calculate the ten Wolde's criterion to identify crystal-like particles
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(see "ten Wolde et al."_#tenWolde96).
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The value of {Ql} is set to zero for atoms not in the
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specified compute group, as well as for atoms that have less than
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{nnn} neighbors within the distance cutoff.
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@ -98,6 +107,12 @@ the neighbor list.
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This compute calculates a per-atom array with {nlvalues} columns, giving the
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{Ql} values for each atom, which are real numbers on the range 0 <= {Ql} <= 1.
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If the keyword {components} is set, then the real and imaginary parts of each
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component of (normalized) {Ybar_lm} will be added to the output array in the
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following order:
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Re({Ybar_-m}) Im({Ybar_-m}) Re({Ybar_-m+1}) Im({Ybar_-m+1}) ... Re({Ybar_m}) Im({Ybar_m}).
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This way, the per-atom array will have a total of {nlvalues}+2*(2{l}+1) columns.
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These values can be accessed by any command that uses
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per-atom values from a compute as input. See "Section
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6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
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@ -117,5 +132,9 @@ The option defaults are {cutoff} = pair style cutoff, {nnn} = 12, {degrees} = 5
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:link(Steinhardt)
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[(Steinhardt)] P. Steinhardt, D. Nelson, and M. Ronchetti, Phys. Rev. B 28, 784 (1983).
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:link(Mickel)
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[(Mickel)] W. Mickel, S. C. Kapfer, G. E. Schroeder-Turkand, K. Mecke, J. Chem. Phys. 138, 044501 (2013).
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:link(tenWolde96)
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[(tenWolde)] P. R. ten Wolde, M. J. Ruiz-Montero, D. Frenkel, J. Chem. Phys. 104, 9932 (1996).
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@ -15,6 +15,7 @@
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#include <string.h>
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#include <stdlib.h>
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#include "compute_coord_atom.h"
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#include "compute_orientorder_atom.h"
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#include "atom.h"
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#include "update.h"
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#include "modify.h"
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@ -29,37 +30,72 @@
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using namespace LAMMPS_NS;
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#define INVOKED_PERATOM 8
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/* ---------------------------------------------------------------------- */
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ComputeCoordAtom::ComputeCoordAtom(LAMMPS *lmp, int narg, char **arg) :
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Compute(lmp, narg, arg),
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typelo(NULL), typehi(NULL), cvec(NULL), carray(NULL)
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cstyle(NULL), id_orientorder(NULL), typelo(NULL), typehi(NULL), cvec(NULL), carray(NULL)
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{
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if (narg < 4) error->all(FLERR,"Illegal compute coord/atom command");
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if (narg < 5) error->all(FLERR,"Illegal compute coord/atom command");
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double cutoff = force->numeric(FLERR,arg[3]);
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cutsq = cutoff*cutoff;
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int n = strlen(arg[3]) + 1;
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cstyle = new char[n];
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strcpy(cstyle,arg[3]);
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ncol = narg-4 + 1;
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int ntypes = atom->ntypes;
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typelo = new int[ncol];
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typehi = new int[ncol];
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if (strcmp(cstyle,"cutoff") == 0) {
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double cutoff = force->numeric(FLERR,arg[4]);
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cutsq = cutoff*cutoff;
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ncol = narg-5 + 1;
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int ntypes = atom->ntypes;
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typelo = new int[ncol];
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typehi = new int[ncol];
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if (narg == 5) {
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ncol = 1;
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typelo[0] = 1;
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typehi[0] = ntypes;
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} else {
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ncol = 0;
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int iarg = 5;
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while (iarg < narg) {
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force->bounds(FLERR,arg[iarg],ntypes,typelo[ncol],typehi[ncol]);
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if (typelo[ncol] > typehi[ncol])
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error->all(FLERR,"Illegal compute coord/atom command");
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ncol++;
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iarg++;
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}
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if (narg == 4) {
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ncol = 1;
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typelo[0] = 1;
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typehi[0] = ntypes;
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} else {
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ncol = 0;
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int iarg = 4;
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while (iarg < narg) {
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force->bounds(FLERR,arg[iarg],ntypes,typelo[ncol],typehi[ncol]);
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if (typelo[ncol] > typehi[ncol])
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error->all(FLERR,"Illegal compute coord/atom command");
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ncol++;
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iarg++;
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}
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}
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} else if (strcmp(cstyle,"orientorder") == 0) {
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if (narg != 6) error->all(FLERR,"Illegal compute coord/atom command");
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n = strlen(arg[4]) + 1;
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id_orientorder = new char[n];
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strcpy(id_orientorder,arg[4]);
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int iorientorder = modify->find_compute(id_orientorder);
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if (iorientorder < 0)
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error->all(FLERR,"Could not find compute coord/atom compute ID");
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if (strcmp(modify->compute[iorientorder]->style,"orientorder/atom") != 0)
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error->all(FLERR,"Compute coord/atom compute ID does not compute orientorder/atom");
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threshold = force->numeric(FLERR,arg[5]);
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if (threshold <= -1.0 || threshold >= 1.0)
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error->all(FLERR,"Compute coord/atom threshold value must lie between -1 and 1");
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ncol = 1;
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typelo = new int[ncol];
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typehi = new int[ncol];
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typelo[0] = 1;
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typehi[0] = atom->ntypes;
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} else error->all(FLERR,"Invalid cstyle in compute coord/atom");
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peratom_flag = 1;
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if (ncol == 1) size_peratom_cols = 0;
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@ -82,6 +118,17 @@ ComputeCoordAtom::~ComputeCoordAtom()
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void ComputeCoordAtom::init()
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{
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if (strcmp(cstyle,"orientorder") == 0) {
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int iorientorder = modify->find_compute(id_orientorder);
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c_orientorder = (ComputeOrientOrderAtom*)(modify->compute[iorientorder]);
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cutsq = c_orientorder->cutsq;
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l = c_orientorder->qlcomp;
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// communicate real and imaginary 2*l+1 components of the normalized vector
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comm_forward = 2*(2*l+1);
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if (c_orientorder->iqlcomp < 0)
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error->all(FLERR,"Compute coord/atom requires components option in compute orientorder/atom be defined");
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}
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if (force->pair == NULL)
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error->all(FLERR,"Compute coord/atom requires a pair style be defined");
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if (sqrt(cutsq) > force->pair->cutforce)
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@ -122,6 +169,9 @@ void ComputeCoordAtom::compute_peratom()
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invoked_peratom = update->ntimestep;
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// printf("Number of degrees %i components degree %i",nqlist,l);
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// printf("Particle \t %i \t Norm \t %g \n",0,norm[0][0]);
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// grow coordination array if necessary
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if (atom->nmax > nmax) {
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@ -138,6 +188,19 @@ void ComputeCoordAtom::compute_peratom()
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}
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}
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if (strcmp(cstyle,"orientorder") == 0) {
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if (!(c_orientorder->invoked_flag & INVOKED_PERATOM)) {
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c_orientorder->compute_peratom();
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c_orientorder->invoked_flag |= INVOKED_PERATOM;
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}
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nqlist = c_orientorder->nqlist;
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int ltmp = l;
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// l = c_orientorder->qlcomp;
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if (ltmp != l) error->all(FLERR,"Debug error, ltmp != l\n");
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normv = c_orientorder->array_atom;
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comm->forward_comm_compute(this);
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}
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// invoke full neighbor list (will copy or build if necessary)
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neighbor->build_one(list);
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@ -154,65 +217,131 @@ void ComputeCoordAtom::compute_peratom()
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int *type = atom->type;
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int *mask = atom->mask;
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if (ncol == 1) {
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for (ii = 0; ii < inum; ii++) {
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i = ilist[ii];
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if (mask[i] & groupbit) {
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xtmp = x[i][0];
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ytmp = x[i][1];
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ztmp = x[i][2];
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jlist = firstneigh[i];
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jnum = numneigh[i];
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if (strcmp(cstyle,"cutoff") == 0) {
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n = 0;
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for (jj = 0; jj < jnum; jj++) {
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j = jlist[jj];
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j &= NEIGHMASK;
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if (ncol == 1) {
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jtype = type[j];
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delx = xtmp - x[j][0];
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dely = ytmp - x[j][1];
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delz = ztmp - x[j][2];
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rsq = delx*delx + dely*dely + delz*delz;
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if (rsq < cutsq && jtype >= typelo[0] && jtype <= typehi[0]) n++;
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}
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for (ii = 0; ii < inum; ii++) {
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i = ilist[ii];
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if (mask[i] & groupbit) {
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xtmp = x[i][0];
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ytmp = x[i][1];
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ztmp = x[i][2];
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jlist = firstneigh[i];
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jnum = numneigh[i];
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cvec[i] = n;
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} else cvec[i] = 0.0;
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}
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n = 0;
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for (jj = 0; jj < jnum; jj++) {
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j = jlist[jj];
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j &= NEIGHMASK;
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} else {
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for (ii = 0; ii < inum; ii++) {
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i = ilist[ii];
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count = carray[i];
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for (m = 0; m < ncol; m++) count[m] = 0.0;
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jtype = type[j];
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delx = xtmp - x[j][0];
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dely = ytmp - x[j][1];
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delz = ztmp - x[j][2];
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rsq = delx*delx + dely*dely + delz*delz;
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if (rsq < cutsq && jtype >= typelo[0] && jtype <= typehi[0])
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n++;
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}
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if (mask[i] & groupbit) {
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xtmp = x[i][0];
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ytmp = x[i][1];
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ztmp = x[i][2];
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jlist = firstneigh[i];
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jnum = numneigh[i];
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cvec[i] = n;
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} else cvec[i] = 0.0;
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}
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} else {
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for (ii = 0; ii < inum; ii++) {
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i = ilist[ii];
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count = carray[i];
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for (m = 0; m < ncol; m++) count[m] = 0.0;
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if (mask[i] & groupbit) {
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xtmp = x[i][0];
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ytmp = x[i][1];
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ztmp = x[i][2];
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jlist = firstneigh[i];
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jnum = numneigh[i];
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for (jj = 0; jj < jnum; jj++) {
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j = jlist[jj];
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j &= NEIGHMASK;
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for (jj = 0; jj < jnum; jj++) {
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j = jlist[jj];
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j &= NEIGHMASK;
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jtype = type[j];
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delx = xtmp - x[j][0];
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dely = ytmp - x[j][1];
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delz = ztmp - x[j][2];
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rsq = delx*delx + dely*dely + delz*delz;
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if (rsq < cutsq) {
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for (m = 0; m < ncol; m++)
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if (jtype >= typelo[m] && jtype <= typehi[m])
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count[m] += 1.0;
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jtype = type[j];
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delx = xtmp - x[j][0];
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dely = ytmp - x[j][1];
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delz = ztmp - x[j][2];
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rsq = delx*delx + dely*dely + delz*delz;
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if (rsq < cutsq) {
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for (m = 0; m < ncol; m++)
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if (jtype >= typelo[m] && jtype <= typehi[m])
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count[m] += 1.0;
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}
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}
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}
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}
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}
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} else if (strcmp(cstyle,"orientorder") == 0) {
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for (ii = 0; ii < inum; ii++) {
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i = ilist[ii];
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if (mask[i] & groupbit) {
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xtmp = x[i][0];
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ytmp = x[i][1];
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ztmp = x[i][2];
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jlist = firstneigh[i];
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jnum = numneigh[i];
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n = 0;
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for (jj = 0; jj < jnum; jj++) {
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j = jlist[jj];
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j &= NEIGHMASK;
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delx = xtmp - x[j][0];
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dely = ytmp - x[j][1];
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delz = ztmp - x[j][2];
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rsq = delx*delx + dely*dely + delz*delz;
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if (rsq < cutsq) {
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double dot_product = 0.0;
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for (int m=0; m < 2*(2*l+1); m++) {
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dot_product += normv[i][nqlist+m]*normv[j][nqlist+m];
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}
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if (dot_product > threshold) n++;
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}
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}
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||||
cvec[i] = n;
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||||
} else cvec[i] = 0.0;
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||||
}
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||||
}
|
||||
}
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||||
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||||
/* ---------------------------------------------------------------------- */
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||||
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||||
int ComputeCoordAtom::pack_forward_comm(int n, int *list, double *buf,
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int pbc_flag, int *pbc)
|
||||
{
|
||||
int i,m=0,j;
|
||||
for (i = 0; i < n; ++i) {
|
||||
for (j = nqlist; j < nqlist + 2*(2*l+1); ++j) {
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||||
buf[m++] = normv[list[i]][j];
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||||
}
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||||
}
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||||
|
||||
return m;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void ComputeCoordAtom::unpack_forward_comm(int n, int first, double *buf)
|
||||
{
|
||||
int i,last,m=0,j;
|
||||
last = first + n;
|
||||
for (i = first; i < last; ++i) {
|
||||
for (j = nqlist; j < nqlist + 2*(2*l+1); ++j) {
|
||||
normv[i][j] = buf[m++];
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
|
|
|
|||
|
|
@ -31,6 +31,8 @@ class ComputeCoordAtom : public Compute {
|
|||
void init();
|
||||
void init_list(int, class NeighList *);
|
||||
void compute_peratom();
|
||||
int pack_forward_comm(int, int *, double *, int, int *);
|
||||
void unpack_forward_comm(int, int, double *);
|
||||
double memory_usage();
|
||||
|
||||
private:
|
||||
|
|
@ -41,6 +43,12 @@ class ComputeCoordAtom : public Compute {
|
|||
int *typelo,*typehi;
|
||||
double *cvec;
|
||||
double **carray;
|
||||
|
||||
class ComputeOrientOrderAtom *c_orientorder;
|
||||
char *cstyle,*id_orientorder;
|
||||
double threshold;
|
||||
double **normv;
|
||||
int nqlist,l;
|
||||
};
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -54,6 +54,7 @@ ComputeOrientOrderAtom::ComputeOrientOrderAtom(LAMMPS *lmp, int narg, char **arg
|
|||
|
||||
nnn = 12;
|
||||
cutsq = 0.0;
|
||||
qlcompflag = 0;
|
||||
|
||||
// specify which orders to request
|
||||
|
||||
|
|
@ -96,6 +97,20 @@ ComputeOrientOrderAtom::ComputeOrientOrderAtom(LAMMPS *lmp, int narg, char **arg
|
|||
if (qlist[iw] > qmax) qmax = qlist[iw];
|
||||
}
|
||||
iarg += nqlist;
|
||||
if (strcmp(arg[iarg],"components") == 0) {
|
||||
qlcompflag = 1;
|
||||
if (iarg+2 > narg) error->all(FLERR,"Illegal compute orientorder/atom command");
|
||||
qlcomp = force->numeric(FLERR,arg[iarg+1]);
|
||||
if (qlcomp <= 0) error->all(FLERR,"Illegal compute orientorder/atom command");
|
||||
iqlcomp = -1;
|
||||
for (int iw = 0; iw < nqlist; iw++)
|
||||
if (qlcomp == qlist[iw]) {
|
||||
iqlcomp = iw;
|
||||
break;
|
||||
}
|
||||
if (iqlcomp < 0) error->all(FLERR,"Illegal compute orientorder/atom command");
|
||||
iarg += 2;
|
||||
}
|
||||
} else if (strcmp(arg[iarg],"cutoff") == 0) {
|
||||
if (iarg+2 > narg) error->all(FLERR,"Illegal compute orientorder/atom command");
|
||||
double cutoff = force->numeric(FLERR,arg[iarg+1]);
|
||||
|
|
@ -105,7 +120,9 @@ ComputeOrientOrderAtom::ComputeOrientOrderAtom(LAMMPS *lmp, int narg, char **arg
|
|||
} else error->all(FLERR,"Illegal compute orientorder/atom command");
|
||||
}
|
||||
|
||||
ncol = nqlist;
|
||||
if (qlcompflag) ncol = nqlist + 2*(2*qlcomp+1);
|
||||
else ncol = nqlist;
|
||||
|
||||
peratom_flag = 1;
|
||||
size_peratom_cols = ncol;
|
||||
|
||||
|
|
@ -434,6 +451,7 @@ void ComputeOrientOrderAtom::calc_boop(double **rlist,
|
|||
}
|
||||
|
||||
double fac = sqrt(MY_4PI) / ncount;
|
||||
double normfac = 0.0;
|
||||
for (int iw = 0; iw < nqlist; iw++) {
|
||||
int n = qlist[iw];
|
||||
double qm_sum = 0.0;
|
||||
|
|
@ -443,6 +461,18 @@ void ComputeOrientOrderAtom::calc_boop(double **rlist,
|
|||
// qnm_r[iw][m]*qnm_r[iw][m] + qnm_i[iw][m]*qnm_i[iw][m]);
|
||||
}
|
||||
qn[iw] = fac * sqrt(qm_sum / (2*n+1));
|
||||
if (qlcompflag && iqlcomp == iw) normfac = 1.0/sqrt(qm_sum);
|
||||
|
||||
}
|
||||
|
||||
// output of the complex vector
|
||||
|
||||
if (qlcompflag) {
|
||||
int j = nqlist;
|
||||
for(int m = 0; m < 2*qlcomp+1; m++) {
|
||||
qn[j++] = qnm_r[iqlcomp][m] * normfac;
|
||||
qn[j++] = qnm_i[iqlcomp][m] * normfac;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -32,6 +32,10 @@ class ComputeOrientOrderAtom : public Compute {
|
|||
void init_list(int, class NeighList *);
|
||||
void compute_peratom();
|
||||
double memory_usage();
|
||||
double cutsq;
|
||||
int iqlcomp, qlcomp, qlcompflag;
|
||||
int *qlist;
|
||||
int nqlist;
|
||||
|
||||
private:
|
||||
int nmax,maxneigh,ncol,nnn;
|
||||
|
|
@ -39,11 +43,8 @@ class ComputeOrientOrderAtom : public Compute {
|
|||
double *distsq;
|
||||
int *nearest;
|
||||
double **rlist;
|
||||
int *qlist;
|
||||
int nqlist;
|
||||
int qmax;
|
||||
double **qnarray;
|
||||
double cutsq;
|
||||
double **qnm_r;
|
||||
double **qnm_i;
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue