Implemented and verified oxRNA2 model (e6aa7910) · Commits · 郑智淋 / lammps

src/USER-CGDNA/bond_oxrna2_fene.cpp

0 → 100644

+49 −0

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		/* ----------------------------------------------------------------------
		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 author: Oliver Henrich (University of Strathclyde, Glasgow)
		------------------------------------------------------------------------- */

		#include <cmath>
		#include <cstdlib>
		#include "bond_oxrna2_fene.h"

		using namespace LAMMPS_NS;

		/* ---------------------------------------------------------------------- */

		BondOxrna2Fene::BondOxrna2Fene(LAMMPS *lmp) : BondOxdnaFene(lmp)
		{

		}

		/* ---------------------------------------------------------------------- */

		BondOxrna2Fene::~BondOxrna2Fene()
		{

		}

		/* ----------------------------------------------------------------------
		compute vector COM-sugar-phosphate backbone interaction site in oxRNA2
		------------------------------------------------------------------------- */
		void BondOxrna2Fene::compute_interaction_sites(double e1[3], double /e2/[3],
		double e3[3], double r[3])
		{
		double d_cs_x=-0.4, d_cs_z=+0.2;

		r[0] = d_cs_xe1[0] + d_cs_ze3[0];
		r[1] = d_cs_xe1[1] + d_cs_ze3[1];
		r[2] = d_cs_xe1[2] + d_cs_ze3[2];

		}

src/USER-CGDNA/bond_oxrna2_fene.h

0 → 100644

+65 −0

Original line number	Diff line number	Diff line
		/* -- 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 BOND_CLASS

		BondStyle(oxrna2/fene,BondOxrna2Fene)

		#else

		#ifndef LMP_BOND_OXRNA2_FENE_H
		#define LMP_BOND_OXRNA2_FENE_H

		#include "bond_oxdna_fene.h"

		namespace LAMMPS_NS {

		class BondOxrna2Fene : public BondOxdnaFene {
		public:
		BondOxrna2Fene(class LAMMPS *);
		virtual ~BondOxrna2Fene();
		virtual void compute_interaction_sites(double , double , double *,
		double *);
		};

		}

		#endif
		#endif

		/* ERROR/WARNING messages:

		W: FENE bond too long: %ld %d %d %g

		A FENE bond has stretched dangerously far. It's interaction strength
		will be truncated to attempt to prevent the bond from blowing up.

		E: Bad FENE bond

		Two atoms in a FENE bond have become so far apart that the bond cannot
		be computed.

		E: Incorrect args for bond coefficients

		Self-explanatory. Check the input script or data file.

		W: Use special bonds = 0,1,1 with bond style oxrna

		Most FENE models need this setting for the special_bonds command.

		W: FENE bond too long: %ld %g

		A FENE bond has stretched dangerously far. It's interaction strength
		will be truncated to attempt to prevent the bond from blowing up.

		*/

src/USER-CGDNA/pair_oxdna2_dh.cpp

+3 −3

Original line number	Diff line number	Diff line
		@@ -64,7 +64,7 @@ PairOxdna2Dh::~PairOxdna2Dh()
		compute vector COM-sugar-phosphate backbone interaction site in oxDNA2
		------------------------------------------------------------------------- */
		void PairOxdna2Dh::compute_interaction_sites(double e1[3],
		double e2[3], double r[3])
		double e2[3], double /e3/[3], double r[3])
		{
		double d_cs_x=-0.34, d_cs_y=+0.3408;

		@@ -125,7 +125,7 @@ void PairOxdna2Dh::compute(int eflag, int vflag)
		MathExtra::q_to_exyz(qa,ax,ay,az);

		// vector COM-backbone site a
		compute_interaction_sites(ax,ay,ra_cs);
		compute_interaction_sites(ax,ay,az,ra_cs);

		rtmp_s[0] = x[a][0] + ra_cs[0];
		rtmp_s[1] = x[a][1] + ra_cs[1];
		@@ -145,7 +145,7 @@ void PairOxdna2Dh::compute(int eflag, int vflag)
		MathExtra::q_to_exyz(qb,bx,by,bz);

		// vector COM-backbone site b
		compute_interaction_sites(bx,by,rb_cs);
		compute_interaction_sites(bx,by,bz,rb_cs);

		// vector backbone site b to a
		delr[0] = rtmp_s[0] - x[b][0] - rb_cs[0];

src/USER-CGDNA/pair_oxdna2_dh.h

+2 −1

Original line number	Diff line number	Diff line
		@@ -28,7 +28,8 @@ class PairOxdna2Dh : public Pair {
		public:
		PairOxdna2Dh(class LAMMPS *);
		virtual ~PairOxdna2Dh();
		virtual void compute_interaction_sites(double , double , double *);
		virtual void compute_interaction_sites(double , double , double *,
		double *);
		virtual void compute(int, int);
		void settings(int, char **);
		void coeff(int, char **);

src/USER-CGDNA/pair_oxdna_coaxstk.h

+1 −0

Original line number	Diff line number	Diff line
		@@ -14,6 +14,7 @@
		#ifdef PAIR_CLASS

		PairStyle(oxdna/coaxstk,PairOxdnaCoaxstk)
		PairStyle(oxrna2/coaxstk,PairOxdnaCoaxstk)

		#else

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