(d2d6d383) · Commits · 郑智淋 / lammps

src/RIGID/fix_rigid.cpp

+33 −15

Original line number	Diff line number	Diff line
		@@ -1652,6 +1652,15 @@ void FixRigid::setup_bodies_static()
		xcm[ibody][2] = all[ibody][2]/masstotal[ibody];
		}

		// set vcm, angmom = 0.0 in case infile is used
		// and doesn't overwrite all body's values
		// since setup_bodies_dynamic() will not be called

		for (ibody = 0; ibody < nbody; ibody++) {
		vcm[ibody][0] = vcm[ibody][1] = vcm[ibody][2] = 0.0;
		angmom[ibody][0] = angmom[ibody][1] = angmom[ibody][2] = 0.0;
		}

		// overwrite masstotal and center-of-mass with file values
		// inbody[i] = 0/1 if Ith rigid body is initialized by file

		@@ -1659,7 +1668,7 @@ void FixRigid::setup_bodies_static()
		if (infile) {
		memory->create(inbody,nbody,"rigid:inbody");
		for (ibody = 0; ibody < nbody; ibody++) inbody[ibody] = 0;
		readfile(0,masstotal,xcm,inbody);
		readfile(0,masstotal,xcm,vcm,angmom,inbody);
		}

		// set rigid body image flags to default values
		@@ -1769,7 +1778,7 @@ void FixRigid::setup_bodies_static()

		// overwrite Cartesian inertia tensor with file values

		if (infile) readfile(1,NULL,all,inbody);
		if (infile) readfile(1,NULL,all,NULL,NULL,inbody);

		// diagonalize inertia tensor for each body via Jacobi rotations
		// inertia = 3 eigenvalues = principal moments of inertia
		@@ -2100,14 +2109,17 @@ void FixRigid::setup_bodies_dynamic()

		/* ----------------------------------------------------------------------
		read per rigid body info from user-provided file
		which = 0 to read total mass and center-of-mass, store in vec and array
		which = 1 to read 6 moments of inertia, store in array
		which = 0 to read everthing except 6 moments of inertia
		which = 1 to read 6 moments of inertia
		flag inbody = 0 for bodies whose info is read from file
		nlines = # of lines of rigid body info
		one line = rigid-ID mass xcm ycm zcm ixx iyy izz ixy ixz iyz
		vxcm vycm vzcm lx ly lz
		------------------------------------------------------------------------- */

		void FixRigid::readfile(int which, double vec, double array, int inbody)
		void FixRigid::readfile(int which, double *vec,
		double array1, double array2, double **array3,
		int *inbody)
		{
		int j,nchunk,id,eofflag;
		int nlines;
		@@ -2158,7 +2170,7 @@ void FixRigid::readfile(int which, double vec, double array, int inbody)
		// tokenize the line into values
		// id = rigid body ID
		// use ID as-is for SINGLE, as mol-ID for MOLECULE, as-is for GROUP
		// for which = 0, store mass/com in vec/array
		// for which = 0, store all but inertia in vec and arrays
		// for which = 1, store inertia tensor array, invert 3,4,5 values to Voigt

		for (int i = 0; i < nchunk; i++) {
		@@ -2181,16 +2193,22 @@ void FixRigid::readfile(int which, double vec, double array, int inbody)

		if (which == 0) {
		vec[id] = atof(values[1]);
		array[id][0] = atof(values[2]);
		array[id][1] = atof(values[3]);
		array[id][2] = atof(values[4]);
		array1[id][0] = atof(values[2]);
		array1[id][1] = atof(values[3]);
		array1[id][2] = atof(values[4]);
		array2[id][0] = atof(values[11]);
		array2[id][1] = atof(values[12]);
		array2[id][2] = atof(values[13]);
		array3[id][0] = atof(values[14]);
		array3[id][1] = atof(values[15]);
		array3[id][2] = atof(values[16]);
		} else {
		array[id][0] = atof(values[5]);
		array[id][1] = atof(values[6]);
		array[id][2] = atof(values[7]);
		array[id][3] = atof(values[10]);
		array[id][4] = atof(values[9]);
		array[id][5] = atof(values[8]);
		array1[id][0] = atof(values[5]);
		array1[id][1] = atof(values[6]);
		array1[id][2] = atof(values[7]);
		array1[id][3] = atof(values[10]);
		array1[id][4] = atof(values[9]);
		array1[id][5] = atof(values[8]);
		}

		buf = next + 1;

src/RIGID/fix_rigid.h

+1 −1

Original line number	Diff line number	Diff line
		@@ -141,7 +141,7 @@ class FixRigid : public Fix {
		void set_v();
		void setup_bodies_static();
		void setup_bodies_dynamic();
		void readfile(int, double , double , int );
		void readfile(int, double , double , double , double , int );
		};

		}

src/RIGID/fix_rigid_small.cpp

+15 −2

Original line number	Diff line number	Diff line
		@@ -1820,6 +1820,19 @@ void FixRigidSmall::setup_bodies_static()
		xcm[2] /= body[ibody].mass;
		}

		// set vcm, angmom = 0.0 in case infile is used
		// and doesn't overwrite all body's values
		// since setup_bodies_dynamic() will not be called

		double vcm,angmom;

		for (ibody = 0; ibody < nlocal_body; ibody++) {
		vcm = body[ibody].vcm;
		vcm[0] = vcm[1] = vcm[2] = 0.0;
		angmom = body[ibody].angmom;
		angmom[0] = angmom[1] = angmom[2] = 0.0;
		}

		// overwrite masstotal and center-of-mass with file values
		// inbody[i] = 0/1 if Ith rigid body is initialized by file

		@@ -2282,11 +2295,11 @@ void FixRigidSmall::setup_bodies_dynamic()
		/* ----------------------------------------------------------------------
		read per rigid body info from user-provided file
		which = 0 to read everthing except 6 moments of inertia
		which = 1 to read just 6 moments of inertia, store in array
		which = 1 to read just 6 moments of inertia
		flag inbody = 0 for local bodies this proc initializes from file
		nlines = # of lines of rigid body info, 0 is OK
		one line = rigid-ID mass xcm ycm zcm ixx iyy izz ixy ixz iyz
		and rigid-ID = mol-ID for fix rigid/small
		where rigid-ID = mol-ID for fix rigid/small
		------------------------------------------------------------------------- */

		void FixRigidSmall::readfile(int which, double *array, int inbody)

src/molecule.cpp

+1 −1

Original line number	Diff line number	Diff line
		@@ -156,7 +156,7 @@ void Molecule::compute_mass()
		/* ----------------------------------------------------------------------
		compute com = center of mass of molecule
		could have been set by user, otherwise calculate it
		does NOT account for finite size particles
		works for finite size particles assuming no overlap
		also compute:
		dxcom = displacement of each atom from COM
		comatom = which atom (1-Natom) is nearest the COM

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