Merge pull request #2283 from abhiShandy/soft-test (15cd007d) · Commits · 郑智淋 / lammps

doc/src/pair_fep_soft.rst

+5 −3

Original line number	Original line	Diff line number	Diff line
	@@ -161,11 +161,11 @@ Examples

	pair_style coul/long/soft 1.0 10.0 9.5		pair_style coul/long/soft 1.0 10.0 9.5
	pair_coeff * * 1.0		pair_coeff * * 1.0
	pair_coeff 1 1 1.0 9.5		pair_coeff 1 1 1.0

	pair_style tip4p/long/soft 1 2 7 8 0.15 2.0 0.5 10.0 9.8		pair_style tip4p/long/soft 1 2 7 8 0.15 2.0 0.5 10.0 9.8
	pair_coeff * * 1.0		pair_coeff * * 1.0
	pair_coeff 1 1 1.0 9.5		pair_coeff 1 1 1.0

	pair_style morse/soft 4 0.9 10.0		pair_style morse/soft 4 0.9 10.0
	pair_coeff * * 100.0 2.0 1.5 1.0		pair_coeff * * 100.0 2.0 1.5 1.0
	@@ -284,7 +284,9 @@ core. Hence, if used by themselves, there will be no repulsion to keep two
	oppositely charged particles from overlapping each other. In this case, if		oppositely charged particles from overlapping each other. In this case, if
	:math:`\lambda = 1`, a singularity may occur. These sub-styles are suitable to		:math:`\lambda = 1`, a singularity may occur. These sub-styles are suitable to
	represent charges embedded in the Lennard-Jones radius of another site (for		represent charges embedded in the Lennard-Jones radius of another site (for
	example hydrogen atoms in several water models).		example hydrogen atoms in several water models). The :math:`\lambda` must
			be defined for each pair, and coul/cut/soft can accept an optional cutoff as
			the second coefficient.

	.. note::		.. note::

src/KSPACE/pair_lj_charmm_coul_long.cpp

+2 −2

Original line number	Original line	Diff line number	Diff line
	@@ -689,7 +689,7 @@ void PairLJCharmmCoulLong::init_style()
	int irequest;		int irequest;
	int respa = 0;		int respa = 0;

	if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) {		if (update->whichflag == 1 && utils::strmatch(update->integrate_style,"^respa")) {
	if (((Respa *) update->integrate)->level_inner >= 0) respa = 1;		if (((Respa *) update->integrate)->level_inner >= 0) respa = 1;
	if (((Respa *) update->integrate)->level_middle >= 0) respa = 2;		if (((Respa *) update->integrate)->level_middle >= 0) respa = 2;
	}		}
	@@ -718,7 +718,7 @@ void PairLJCharmmCoulLong::init_style()

	// set & error check interior rRESPA cutoffs		// set & error check interior rRESPA cutoffs

	if (strstr(update->integrate_style,"respa") &&		if (utils::strmatch(update->integrate_style,"^respa") &&
	((Respa *) update->integrate)->level_inner >= 0) {		((Respa *) update->integrate)->level_inner >= 0) {
	cut_respa = ((Respa *) update->integrate)->cutoff;		cut_respa = ((Respa *) update->integrate)->cutoff;
	cut_in_off = cut_respa[0];		cut_in_off = cut_respa[0];

src/KSPACE/pair_lj_cut_coul_long.cpp

+2 −2

Original line number	Original line	Diff line number	Diff line
	@@ -659,7 +659,7 @@ void PairLJCutCoulLong::init_style()
	int irequest;		int irequest;
	int respa = 0;		int respa = 0;

	if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) {		if (update->whichflag == 1 && utils::strmatch(update->integrate_style,"^respa")) {
	if (((Respa *) update->integrate)->level_inner >= 0) respa = 1;		if (((Respa *) update->integrate)->level_inner >= 0) respa = 1;
	if (((Respa *) update->integrate)->level_middle >= 0) respa = 2;		if (((Respa *) update->integrate)->level_middle >= 0) respa = 2;
	}		}
	@@ -676,7 +676,7 @@ void PairLJCutCoulLong::init_style()

	// set rRESPA cutoffs		// set rRESPA cutoffs

	if (strstr(update->integrate_style,"respa") &&		if (utils::strmatch(update->integrate_style,"^respa") &&
	((Respa *) update->integrate)->level_inner >= 0)		((Respa *) update->integrate)->level_inner >= 0)
	cut_respa = ((Respa *) update->integrate)->cutoff;		cut_respa = ((Respa *) update->integrate)->cutoff;
	else cut_respa = NULL;		else cut_respa = NULL;

src/USER-FEP/pair_lj_charmm_coul_long_soft.cpp

+13 −31

Original line number	Original line	Diff line number	Diff line
	@@ -691,38 +691,20 @@ void PairLJCharmmCoulLongSoft::init_style()
	// request regular or rRESPA neighbor lists		// request regular or rRESPA neighbor lists

	int irequest;		int irequest;

	if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) {
	int respa = 0;		int respa = 0;

			if (update->whichflag == 1 && utils::strmatch(update->integrate_style,"^respa")) {
	if (((Respa *) update->integrate)->level_inner >= 0) respa = 1;		if (((Respa *) update->integrate)->level_inner >= 0) respa = 1;
	if (((Respa *) update->integrate)->level_middle >= 0) respa = 2;		if (((Respa *) update->integrate)->level_middle >= 0) respa = 2;
			}

	if (respa == 0) irequest = neighbor->request(this,instance_me);
	else if (respa == 1) {
	irequest = neighbor->request(this,instance_me);		irequest = neighbor->request(this,instance_me);
	neighbor->requests[irequest]->id = 1;
	neighbor->requests[irequest]->half = 0;		if (respa >= 1) {
	neighbor->requests[irequest]->respainner = 1;
	irequest = neighbor->request(this,instance_me);
	neighbor->requests[irequest]->id = 3;
	neighbor->requests[irequest]->half = 0;
	neighbor->requests[irequest]->respaouter = 1;		neighbor->requests[irequest]->respaouter = 1;
	} else {
	irequest = neighbor->request(this,instance_me);
	neighbor->requests[irequest]->id = 1;
	neighbor->requests[irequest]->half = 0;
	neighbor->requests[irequest]->respainner = 1;		neighbor->requests[irequest]->respainner = 1;
	irequest = neighbor->request(this,instance_me);
	neighbor->requests[irequest]->id = 2;
	neighbor->requests[irequest]->half = 0;
	neighbor->requests[irequest]->respamiddle = 1;
	irequest = neighbor->request(this,instance_me);
	neighbor->requests[irequest]->id = 3;
	neighbor->requests[irequest]->half = 0;
	neighbor->requests[irequest]->respaouter = 1;
	}		}
			if (respa == 2) neighbor->requests[irequest]->respamiddle = 1;
	} else irequest = neighbor->request(this,instance_me);

	// require cut_lj_inner < cut_lj		// require cut_lj_inner < cut_lj

	@@ -739,7 +721,7 @@ void PairLJCharmmCoulLongSoft::init_style()

	// set & error check interior rRESPA cutoffs		// set & error check interior rRESPA cutoffs

	if (strstr(update->integrate_style,"respa") &&		if (utils::strmatch(update->integrate_style,"^respa") &&
	((Respa *) update->integrate)->level_inner >= 0) {		((Respa *) update->integrate)->level_inner >= 0) {
	cut_respa = ((Respa *) update->integrate)->cutoff;		cut_respa = ((Respa *) update->integrate)->cutoff;
	if (MIN(cut_lj,cut_coul) < cut_respa[3])		if (MIN(cut_lj,cut_coul) < cut_respa[3])

src/USER-FEP/pair_lj_cut_coul_long_soft.cpp

+10 −28

Original line number	Original line	Diff line number	Diff line
	@@ -634,44 +634,26 @@ void PairLJCutCoulLongSoft::init_style()
	// request regular or rRESPA neighbor lists		// request regular or rRESPA neighbor lists

	int irequest;		int irequest;

	if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) {
	int respa = 0;		int respa = 0;

			if (update->whichflag == 1 && utils::strmatch(update->integrate_style,"^respa")) {
	if (((Respa *) update->integrate)->level_inner >= 0) respa = 1;		if (((Respa *) update->integrate)->level_inner >= 0) respa = 1;
	if (((Respa *) update->integrate)->level_middle >= 0) respa = 2;		if (((Respa *) update->integrate)->level_middle >= 0) respa = 2;
			}

	if (respa == 0) irequest = neighbor->request(this,instance_me);
	else if (respa == 1) {
	irequest = neighbor->request(this,instance_me);		irequest = neighbor->request(this,instance_me);
	neighbor->requests[irequest]->id = 1;
	neighbor->requests[irequest]->half = 0;		if (respa >= 1) {
	neighbor->requests[irequest]->respainner = 1;
	irequest = neighbor->request(this,instance_me);
	neighbor->requests[irequest]->id = 3;
	neighbor->requests[irequest]->half = 0;
	neighbor->requests[irequest]->respaouter = 1;		neighbor->requests[irequest]->respaouter = 1;
	} else {
	irequest = neighbor->request(this,instance_me);
	neighbor->requests[irequest]->id = 1;
	neighbor->requests[irequest]->half = 0;
	neighbor->requests[irequest]->respainner = 1;		neighbor->requests[irequest]->respainner = 1;
	irequest = neighbor->request(this,instance_me);
	neighbor->requests[irequest]->id = 2;
	neighbor->requests[irequest]->half = 0;
	neighbor->requests[irequest]->respamiddle = 1;
	irequest = neighbor->request(this,instance_me);
	neighbor->requests[irequest]->id = 3;
	neighbor->requests[irequest]->half = 0;
	neighbor->requests[irequest]->respaouter = 1;
	}		}
			if (respa == 2) neighbor->requests[irequest]->respamiddle = 1;
	} else irequest = neighbor->request(this,instance_me);

	cut_coulsq = cut_coul * cut_coul;		cut_coulsq = cut_coul * cut_coul;

	// set rRESPA cutoffs		// set rRESPA cutoffs

	if (strstr(update->integrate_style,"respa") &&		if (utils::strmatch(update->integrate_style,"^respa") &&
	((Respa *) update->integrate)->level_inner >= 0)		((Respa *) update->integrate)->level_inner >= 0)
	cut_respa = ((Respa *) update->integrate)->cutoff;		cut_respa = ((Respa *) update->integrate)->cutoff;
	else cut_respa = NULL;		else cut_respa = NULL;

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