Revert "Added fix bond/create/angle code and docu" (40088f55) · Commits · 郑智淋 / lammps

doc/src/Commands_fix.rst

+0 −1

Original line number	Diff line number	Diff line
		@@ -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>`

doc/src/fix_bond_create.rst

+5 −23

Original line number	Diff line number	Diff line
		@@ -2,8 +2,6 @@

		fix bond/create command
		=======================
		fix bond/create/angle command
		=============================

		Syntax
		""""""
		@@ -19,7 +17,7 @@ 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::

		@@ -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
		""""""""""""""""

src/MC/fix_bond_create.cpp

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Original line number	Diff line number	Diff line
		@@ -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 = delxdelx + delydely + 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++) {

src/MC/fix_bond_create.h

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Original line number	Diff line number	Diff line
		@@ -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();

src/MC/fix_bond_create_angle.cpp

deleted100644 → 0

+0 −151

Original line number	Diff line number	Diff line
		/* ----------------------------------------------------------------------
		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((v1xv2x + v1yv2y + v1z*v2z)/
		(sqrt(v1xv1x + v1yv1y + v1zv1z)sqrt(v2xv2x + v2yv2y + 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((v1xv2x + v1yv2y + v1z*v2z)/
		(sqrt(v1xv1x + v1yv1y + v1zv1z)sqrt(v2xv2x + v2yv2y + 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((v1xv2x + v1yv2y + v1z*v2z)/
		(sqrt(v1xv1x + v1yv1y + v1zv1z)sqrt(v2xv2x + v2yv2y + 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((v1xv2x + v1yv2y + v1z*v2z)/
		(sqrt(v1xv1x + v1yv1y + v1zv1z)sqrt(v2xv2x + v2yv2y + v2z*v2z)));
		// set flag if the angle constraint is met

		if ((amin <= angle1 && angle1 <= amax) && (amin <= angle2 && angle2 <= amax)){
		flag = 1;
		}

		}

		return flag;

		}

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