A few GLE fixes (a4a97de8) · Commits · 郑智淋 / lammps

doc/fix_gle.html

+15 −1

Original line number	Diff line number	Diff line
		@@ -50,7 +50,8 @@ vibrational modes in the system to inexpensive (approximate)
		modelling of nuclear quantum effects. Contrary to
		<A HREF = "fix_langevin.html">fix langevin</A>, this fix performs both
		thermostatting and evolution of the Hamiltonian equations of motion, so it
		does not need to be used together with <A HREF = "fix_nve.html">fix nve</A>.
		should not be used together with <A HREF = "fix_nve.html">fix nve</A> -- at least not
		on the same atom groups.
		</P>
		<P>Each degree of freedom in the thermostatted group is supplemented
		with Ns additional degrees of freedom s, and the equations of motion
		@@ -93,6 +94,14 @@ generate its own unique seed and its own stream of random numbers.
		Thus the dynamics of the system will not be identical on two runs on
		different numbers of processors.
		</P>
		<P>Note also that the Generalized Langevin Dynamics scheme that is
		implemented by the <A HREF = "fix_gld.html">fix gld</A> scheme is closely related
		to the present one. In fact, it should be always possible to cast the
		Prony series form of the memory kernel used by GLD into an appropriate
		input matrix for <A HREF = "fix_gle.html">fix_gle</A>. While the GLE scheme is more
		general, the form used by <A HREF = "fix_gld.html">fix gld</A> can be more directly
		related to the representation of an implicit solvent environment.
		</P>
		<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
		</P>
		<P>The instantaneous values of the extended variables are written to
		@@ -127,6 +136,11 @@ with rigid bodies, SHAKE or RATTLE. It is expected that all the
		thermostatted degrees of freedom are fully flexible, and the sampled
		ensemble will not be correct otherwise.
		</P>
		<P>In order to perform constant-pressure simulations please use
		<A HREF = "fix_press_berendsen.html">fix press/berendsen</A>, rather than
		<A HREF = "fix_npt.html">fix_npt</A>, to avoid duplicate integration of the
		equations of motion.
		</P>
		<P>This fix is part of the USER-MISC package. It is only enabled if LAMMPS
		was built with that package. See the <A HREF = "Section_start.html#start_3">Making
		LAMMPS</A> section for more info.

doc/fix_gle.txt

+15 −1

Original line number	Diff line number	Diff line
		@@ -40,7 +40,8 @@ vibrational modes in the system to inexpensive (approximate)
		modelling of nuclear quantum effects. Contrary to
		"fix langevin"_fix_langevin.html, this fix performs both
		thermostatting and evolution of the Hamiltonian equations of motion, so it
		does not need to be used together with "fix nve"_fix_nve.html.
		should not be used together with "fix nve"_fix_nve.html -- at least not
		on the same atom groups.

		Each degree of freedom in the thermostatted group is supplemented
		with Ns additional degrees of freedom s, and the equations of motion
		@@ -83,6 +84,14 @@ generate its own unique seed and its own stream of random numbers.
		Thus the dynamics of the system will not be identical on two runs on
		different numbers of processors.

		Note also that the Generalized Langevin Dynamics scheme that is
		implemented by the "fix gld"_fix_gld.html scheme is closely related
		to the present one. In fact, it should be always possible to cast the
		Prony series form of the memory kernel used by GLD into an appropriate
		input matrix for "fix_gle"_fix_gle.html. While the GLE scheme is more
		general, the form used by "fix gld"_fix_gld.html can be more directly
		related to the representation of an implicit solvent environment.

		[Restart, fix_modify, output, run start/stop, minimize info:]

		The instantaneous values of the extended variables are written to
		@@ -117,6 +126,11 @@ with rigid bodies, SHAKE or RATTLE. It is expected that all the
		thermostatted degrees of freedom are fully flexible, and the sampled
		ensemble will not be correct otherwise.

		In order to perform constant-pressure simulations please use
		"fix press/berendsen"_fix_press_berendsen.html, rather than
		"fix_npt"_fix_npt.html, to avoid duplicate integration of the
		equations of motion.

		This fix is part of the USER-MISC package. It is only enabled if LAMMPS
		was built with that package. See the "Making
		LAMMPS"_Section_start.html#start_3 section for more info.

src/USER-MISC/fix_gle.cpp

+7 −1

Original line number	Diff line number	Diff line
		@@ -82,7 +82,13 @@ void StabCholesky(int n, const double* MMt, double* M)
		for (k=0; k<i; ++k) D[i]-=L[midx(n,i,k)]L[midx(n,i,k)]D[k];
		}

		for(i=0; i<n; ++i) D[i]=(D[i]>0.?sqrt(D[i]):0.);
		for(i=0; i<n; ++i)
		{
		#ifdef GLE_DEBUG
		if (D[i]<0) fprintf(stderr,"GLE Cholesky: Negative diagonal term %le, has been set to zero.\n", D[i]);
		#endif
		D[i]=(D[i]>0.?sqrt(D[i]):0.);
		}

		for(i=0; i<n; ++i) for (j=0; j<n; j++) M[midx(n,i,j)]=L[midx(n,i,j)]*D[j];
		}

src/USER-MISC/fix_ipi.cpp

+6 −8

Original line number	Diff line number	Diff line
		@@ -319,12 +319,12 @@ void FixIPI::initial_integrate(int vflag)
		double *boxlo = domain->boxlo;
		double posconv;
		posconv=0.52917721*force->angstrom;
		boxlo[0] = 0;
		boxlo[1] = 0;
		boxlo[2] = 0;
		boxhi[0] = cellh[0]*posconv;
		boxhi[1] = cellh[4]*posconv;
		boxhi[2] = cellh[8]*posconv;
		boxlo[0] = -0.5cellh[0]posconv;
		boxlo[1] = -0.5cellh[4]posconv;
		boxlo[2] = -0.5cellh[8]posconv;
		boxhi[0] = -boxlo[0];
		boxhi[1] = -boxlo[1];
		boxhi[2] = -boxlo[2];
		domain->xy = cellh[1]*posconv;
		domain->xz = cellh[2]*posconv;
		domain->yz = cellh[5]*posconv;
		@@ -421,7 +421,6 @@ void FixIPI::final_integrate()
		error->one(FLERR, "Got EXIT message from i-PI. Now leaving!");

		if (strcmp(header,"GETFORCE ") == 0 ) {

		writebuffer(ipisock,"FORCEREADY ",MSGLEN, error);
		writebuffer(ipisock,(char*) &pot,8, error);
		writebuffer(ipisock,(char*) &nat,4, error);
		@@ -432,7 +431,6 @@ void FixIPI::final_integrate()
		}
		else
		error->one(FLERR, "Wrapper did not ask for forces, I will now die!");

		}

		hasdata=0;

Admin message