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Revert "Added fix bond/create/angle code and docu"

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This reverts commit 16eab647d4.
This commit is contained in:
Oliver Henrich
2020-07-02 23:11:50 +01:00
parent f0a3256151
commit 40088f558c
6 changed files with 5 additions and 252 deletions
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1
doc/src/Commands_fix.rst
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@ -42,7 +42,6 @@ OPT.
* :doc:`bocs <fix_bocs>`
* :doc:`bond/break <fix_bond_break>`
* :doc:`bond/create <fix_bond_create>`
* :doc:`bond/create/angle <fix_bond_create>`
* :doc:`bond/react <fix_bond_react>`
* :doc:`bond/swap <fix_bond_swap>`
* :doc:`box/relax <fix_box_relax>`

28
doc/src/fix_bond_create.rst
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@ -2,8 +2,6 @@
fix bond/create command
=======================
fix bond/create/angle command
=============================
Syntax
""""""
@ -19,8 +17,8 @@ Syntax
* Rmin = 2 atoms separated by less than Rmin can bond (distance units)
* bondtype = type of created bonds
* zero or more keyword/value pairs may be appended to args
* keyword = *iparam* or *jparam* or *prob* or *atype* or *dtype* or *itype* or *aconstrain*
* keyword = *iparam* or *jparam* or *prob* or *atype* or *dtype* or *itype*
.. parsed-literal::
*iparam* values = maxbond, newtype
@ -38,9 +36,6 @@ Syntax
dihedraltype = type of created dihedrals
*itype* value = impropertype
impropertype = type of created impropers
*aconstrain* value = amin amax
amin = minimal angle at which new bonds can be created
amax = maximal angle at which new bonds can be created
Examples
""""""""
@ -50,7 +45,6 @@ Examples
fix 5 all bond/create 10 1 2 0.8 1
fix 5 all bond/create 1 3 3 0.8 1 prob 0.5 85784 iparam 2 3
fix 5 all bond/create 1 3 3 0.8 1 prob 0.5 85784 iparam 2 3 atype 1 dtype 2
fix 5 all bond/create/angle 10 1 2 1.122 1 aconstrain 120 180 prob 1 4928459 iparam 2 1 jparam 2 2
Description
"""""""""""
@ -116,16 +110,7 @@ actually created. The *fraction* setting must be a value between 0.0
and 1.0. A uniform random number between 0.0 and 1.0 is generated and
the eligible bond is only created if the random number < fraction.
The *aconstrain* keyword allows to specify a minimal and maximal angle
*amin* and *amax* between the two prospective bonding partners and a
third particle that is already bonded to one of the two partners.
Such a criterion can be important, for instance when new angle
potentials are simultaneously introduced after the formation of the
new bond. Without a restriction on the permissible angle, and for
stiffer angle potentials very large energies can arise and lead to
uncontrolled behavior.
Any bond that is created is assigned a bond type of *bondtype*.
Any bond that is created is assigned a bond type of *bondtype*
When a bond is created, data structures within LAMMPS that store bond
topology are updated to reflect the creation. If the bond is part of
@ -252,11 +237,8 @@ Restrictions
""""""""""""
This fix is part of the MC package. It is only enabled if LAMMPS was
built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
The *aconstrain* keyword is only available
when LAMMPS was built with the FixBondCreateAngle class.
built with that package. See the :doc:`Build package <Build_package>`
doc page for more info.
Related commands
""""""""""""""""

32
src/MC/fix_bond_create.cpp
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@ -79,11 +79,6 @@ FixBondCreate::FixBondCreate(LAMMPS *lmp, int narg, char **arg) :
int seed = 12345;
atype = dtype = itype = 0;
constrainflag = 0;
constrainpass = 0;
amin = 0;
amax = 180;
int iarg = 8;
while (iarg < narg) {
if (strcmp(arg[iarg],"iparam") == 0) {
@ -125,20 +120,6 @@ FixBondCreate::FixBondCreate(LAMMPS *lmp, int narg, char **arg) :
itype = force->inumeric(FLERR,arg[iarg+1]);
if (itype < 0) error->all(FLERR,"Illegal fix bond/create command");
iarg += 2;
} else if (strcmp(arg[iarg],"aconstrain") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal fix bond/create command");
amin = force->numeric(FLERR,arg[iarg+1]);
amax = force->inumeric(FLERR,arg[iarg+2]);
if (amin >= amax)
error->all(FLERR,"Illegal fix bond/create command");
if (amin < 0 || amin > 180)
error->all(FLERR,"Illegal fix bond/create command");
if (amax < 0 || amax > 180)
error->all(FLERR,"Illegal fix bond/create command");
amin = (3.14159265358979323846/180.0) * amin;
amax = (3.14159265358979323846/180.0) * amax;
constrainflag = 1;
iarg += 3;
} else error->all(FLERR,"Illegal fix bond/create command");
}
@ -453,11 +434,6 @@ void FixBondCreate::post_integrate()
rsq = delx*delx + dely*dely + delz*delz;
if (rsq >= cutsq) continue;
if (constrainflag) {
constrainpass = constrain(i,j,amin,amax);
if (!constrainpass) continue;
}
if (rsq < distsq[i]) {
partner[i] = tag[j];
distsq[i] = rsq;
@ -466,7 +442,6 @@ void FixBondCreate::post_integrate()
partner[j] = tag[i];
distsq[j] = rsq;
}
}
}
@ -1431,13 +1406,6 @@ double FixBondCreate::memory_usage()
/* ---------------------------------------------------------------------- */
int FixBondCreate::constrain(int i, int j, double amin, double amax)
{
return 1;
}
/* ---------------------------------------------------------------------- */
void FixBondCreate::print_bb()
{
for (int i = 0; i < atom->nlocal; i++) {

5
src/MC/fix_bond_create.h
View File

@ -52,12 +52,9 @@ class FixBondCreate : public Fix {
int btype,seed;
int imaxbond,jmaxbond;
int inewtype,jnewtype;
int constrainflag,constrainpass;
double amin,amax;
double cutsq,fraction;
int atype,dtype,itype;
int angleflag,dihedralflag,improperflag;
int overflow;
tagint lastcheck;
@ -87,8 +84,6 @@ class FixBondCreate : public Fix {
void create_impropers(int);
int dedup(int, int, tagint *);
virtual int constrain(int, int, double, double);
// DEBUG
void print_bb();

151
src/MC/fix_bond_create_angle.cpp
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@ -1,151 +0,0 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors:
Joao Gregorio, Oliver Henrich (University of Strathclyde, Glasgow, UK)
------------------------------------------------------------------------- */
#include "fix_bond_create_angle.h"
#include "atom.h"
#include <cmath>
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
FixBondCreateAngle::FixBondCreateAngle(LAMMPS *lmp, int narg, char **arg) :
FixBondCreate(lmp, narg, arg)
{
}
/* ---------------------------------------------------------------------- */
FixBondCreateAngle::~FixBondCreateAngle()
{
}
/* ---------------------------------------------------------------------- */
int FixBondCreateAngle::constrain(int i, int j, double amin, double amax)
{
double **x = atom->x;
tagint *tag = atom->tag;
tagint **bond_atom = atom->bond_atom;
int *num_bond = atom->num_bond;
int **nspecial = atom->nspecial;
tagint **special = atom->special;
int *mask = atom->mask;
int *type = atom->type;
double v1x = 0.0;
double v1y = 0.0;
double v1z = 0.0;
double v2x = 0.0;
double v2y = 0.0;
double v2z = 0.0;
int flag = 0;
// pass if both atoms have no neighbors: bond is always formed
if (nspecial[i][0] == 0 && nspecial[j][0] == 0){
flag = 1;
}
// pass if i has at least one neighbor and angle constraint is met
if (nspecial[i][0] != 0 && nspecial[j][0] == 0){
// calculate first vector between i and j
v1x = x[i][0] - x[j][0];
v1y = x[i][1] - x[j][1];
v1z = x[i][2] - x[j][2];
// calculate second vector between i and its first neighbor
v2x = x[i][0] - x[atom->map(special[i][0])][0];
v2y = x[i][1] - x[atom->map(special[i][0])][1];
v2z = x[i][2] - x[atom->map(special[i][0])][2];
// calculate angle between both vectors
angle1 = acos((v1x*v2x + v1y*v2y + v1z*v2z)/
(sqrt(v1x*v1x + v1y*v1y + v1z*v1z)*sqrt(v2x*v2x + v2y*v2y + v2z*v2z)));
// set flag if the angle constraint is met
if (amin <= angle1 && angle1 <= amax) {
flag = 1;
}
}
// pass if j has at least one neighbor and angle constraint is met
if (nspecial[j][0] != 0 && nspecial[i][0] == 0){
// calculate first vector between j and i
v1x = x[j][0] - x[i][0];
v1y = x[j][1] - x[i][1];
v1z = x[j][2] - x[i][2];
// calculate second vector between j and its first neighbor
v2x = x[j][0] - x[atom->map(special[j][0])][0];
v2y = x[j][1] - x[atom->map(special[j][0])][1];
v2z = x[j][2] - x[atom->map(special[j][0])][2];
// calculate angle between both vectors
angle1 = acos((v1x*v2x + v1y*v2y + v1z*v2z)/
(sqrt(v1x*v1x + v1y*v1y + v1z*v1z)*sqrt(v2x*v2x + v2y*v2y + v2z*v2z)));
// set flag if angle constraint is met
if (amin <= angle1 && angle1 <= amax) {
flag = 1;
}
}
// pass if both i and j have at least one neighbor and angle constraint is met
if (nspecial[i][0] != 0 && nspecial[j][0] != 0){
// Calculate 1st angle
// calculate first vector between i and j
v1x = x[i][0] - x[j][0];
v1y = x[i][1] - x[j][1];
v1z = x[i][2] - x[j][2];
// calculate second vector between i and its first neighbor
v2x = x[i][0] - x[atom->map(special[i][0])][0];
v2y = x[i][1] - x[atom->map(special[i][0])][1];
v2z = x[i][2] - x[atom->map(special[i][0])][2];
// calculate angle between both vectors
angle1 = acos((v1x*v2x + v1y*v2y + v1z*v2z)/
(sqrt(v1x*v1x + v1y*v1y + v1z*v1z)*sqrt(v2x*v2x + v2y*v2y + v2z*v2z)));
// Calculate 2nd angle
// calculate first vector between i and j
v1x = x[j][0] - x[i][0];
v1y = x[j][1] - x[i][1];
v1z = x[j][2] - x[i][2];
// calculate second vector between i and its first neighbor
v2x = x[j][0] - x[atom->map(special[j][0])][0];
v2y = x[j][1] - x[atom->map(special[j][0])][1];
v2z = x[j][2] - x[atom->map(special[j][0])][2];
// calculate angle between both vectors
angle2 = acos((v1x*v2x + v1y*v2y + v1z*v2z)/
(sqrt(v1x*v1x + v1y*v1y + v1z*v1z)*sqrt(v2x*v2x + v2y*v2y + v2z*v2z)));
// set flag if the angle constraint is met
if ((amin <= angle1 && angle1 <= amax) && (amin <= angle2 && angle2 <= amax)){
flag = 1;
}
}
return flag;
}

40
src/MC/fix_bond_create_angle.h
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@ -1,40 +0,0 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef FIX_CLASS
FixStyle(bond/create/angle,FixBondCreateAngle)
#else
#ifndef LMP_FIX_BOND_CREATE_ANGLE_H
#define LMP_FIX_BOND_CREATE_ANGLE_H
#include "fix_bond_create.h"
namespace LAMMPS_NS {
class FixBondCreateAngle : public FixBondCreate {
public:
FixBondCreateAngle(class LAMMPS *, int, char **);
~FixBondCreateAngle();
private:
double angle1,angle2,amin,amax;
int constrain(int,int,double,double);
};
}
#endif
#endif