-/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
+/*
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*
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*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <math.h>
-#include "typedefs.h"
-#include "gmx_fatal.h"
-#include "mdrun.h"
-#include "md_support.h"
-#include "types/iteratedconstraints.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/legacyheaders/md_support.h"
+#include "gromacs/legacyheaders/md_logging.h"
+#include "gromacs/legacyheaders/types/iteratedconstraints.h"
#ifdef GMX_DOUBLE
#define CONVERGEITER 0.000000001
only some small fraction of the total. */
#define MAX_NUMBER_CLOSE 50
#define FRACTION_CLOSE 0.001
-
+
/* maximum length of cyclic traps to check, emerging from limited numerical precision */
#define CYCLEMAX 20
-void gmx_iterate_init(gmx_iterate_t *iterate,gmx_bool bIterate)
+void gmx_iterate_init(gmx_iterate_t *iterate, gmx_bool bSetIterationActive)
{
int i;
- iterate->iter_i = 0;
- iterate->bIterate = bIterate;
- iterate->num_close = 0;
- for (i=0;i<MAXITERCONST+2;i++)
+ iterate->iter_i = 0;
+ iterate->bIterationActive = bSetIterationActive;
+ iterate->num_close = 0;
+ for (i = 0; i < MAXITERCONST+2; i++)
{
iterate->allrelerr[i] = 0;
}
}
-gmx_bool done_iterating(const t_commrec *cr,FILE *fplog, int nsteps, gmx_iterate_t *iterate, gmx_bool bFirstIterate, real fom, real *newf)
-{
+gmx_bool done_iterating(const t_commrec *cr, FILE *fplog, int nsteps, gmx_iterate_t *iterate, gmx_bool bFirstIterate, real fom, real *newf)
+{
/* monitor convergence, and use a secant search to propose new
- values.
+ values.
x_{i} - x_{i-1}
The secant method computes x_{i+1} = x_{i} - f(x_{i}) * ---------------------
f(x_{i}) - f(x_{i-1})
-
+
The function we are trying to zero is fom-x, where fom is the
"figure of merit" which is the pressure (or the veta value) we
would get by putting in an old value of the pressure or veta into
the incrementor function for the step or half step. I have
verified that this gives the same answer as self consistent
iteration, usually in many fewer steps, especially for small tau_p.
-
+
We could possibly eliminate an iteration with proper use
of the value from the previous step, but that would take a bit
more bookkeeping, especially for veta, since tests indicate the
0.02, which is smaller that would ever be necessary in
practice. Generally, 3-5 iterations will be sufficient */
- real relerr,err,xmin;
- int i;
+ real relerr, err, xmin;
+ int i;
gmx_bool incycle;
-
- if (bFirstIterate)
+
+ if (bFirstIterate)
{
- iterate->x = fom;
- iterate->f = fom-iterate->x;
+ iterate->x = fom;
+ iterate->f = fom-iterate->x;
iterate->xprev = 0;
iterate->fprev = 0;
- *newf = fom;
- }
- else
+ *newf = fom;
+ }
+ else
{
iterate->f = fom-iterate->x; /* we want to zero this difference */
- if ((iterate->iter_i > 1) && (iterate->iter_i < MAXITERCONST))
+ if ((iterate->iter_i > 1) && (iterate->iter_i < MAXITERCONST))
{
- if (iterate->f==iterate->fprev)
+ if (iterate->f == iterate->fprev)
{
*newf = iterate->f;
- }
- else
+ }
+ else
{
- *newf = iterate->x - (iterate->x-iterate->xprev)*(iterate->f)/(iterate->f-iterate->fprev);
+ *newf = iterate->x - (iterate->x-iterate->xprev)*(iterate->f)/(iterate->f-iterate->fprev);
}
- }
- else
+ }
+ else
{
- /* just use self-consistent iteration the first step to initialize, or
+ /* just use self-consistent iteration the first step to initialize, or
if it's not converging (which happens occasionally -- need to investigate why) */
- *newf = fom;
+ *newf = fom;
}
}
/* Consider a slight shortcut allowing us to exit one sooner -- we check the
difference between the closest of x and xprev to the new
value. To be 100% certain, we should check the difference between
the last result, and the previous result, or
-
+
relerr = (fabs((x-xprev)/fom));
-
+
but this is pretty much never necessary under typical conditions.
Checking numerically, it seems to lead to almost exactly the same
trajectories, but there are small differences out a few decimal
places in the pressure, and eventually in the v_eta, but it could
save an interation.
-
+
if (fabs(*newf-x) < fabs(*newf - xprev)) { xmin = x;} else { xmin = xprev;}
relerr = (fabs((*newf-xmin) / *newf));
- */
-
- err = fabs((iterate->f-iterate->fprev));
+ */
+
+ err = fabs((iterate->f-iterate->fprev));
relerr = fabs(err/fom);
iterate->allrelerr[iterate->iter_i] = relerr;
-
- if (iterate->iter_i > 0)
+
+ if (iterate->iter_i > 0)
{
- if (debug)
+ if (debug)
{
- fprintf(debug,"Iterating NPT constraints: %6i %20.12f%14.6g%20.12f\n",
- iterate->iter_i,fom,relerr,*newf);
+ fprintf(debug, "Iterating NPT constraints: %6i %20.12f%14.6g%20.12f\n",
+ iterate->iter_i, fom, relerr, *newf);
}
-
- if ((relerr < CONVERGEITER) || (err < CONVERGEITER) || (fom==0) || ((iterate->x == iterate->xprev) && iterate->iter_i > 1))
+
+ if ((relerr < CONVERGEITER) || (err < CONVERGEITER) || (fom == 0) || ((iterate->x == iterate->xprev) && iterate->iter_i > 1))
{
- iterate->bIterate = FALSE;
- if (debug)
+ iterate->bIterationActive = FALSE;
+ if (debug)
{
- fprintf(debug,"Iterating NPT constraints: CONVERGED\n");
+ fprintf(debug, "Iterating NPT constraints: CONVERGED\n");
}
return TRUE;
}
if (relerr < CLOSE_ENOUGH)
{
incycle = FALSE;
- for (i=1;i<CYCLEMAX;i++) {
+ for (i = 1; i < CYCLEMAX; i++)
+ {
if ((iterate->allrelerr[iterate->iter_i-(1+i)] == iterate->allrelerr[iterate->iter_i-1]) &&
- (iterate->allrelerr[iterate->iter_i-(1+i)] == iterate->allrelerr[iterate->iter_i-(1+2*i)])) {
+ (iterate->allrelerr[iterate->iter_i-(1+i)] == iterate->allrelerr[iterate->iter_i-(1+2*i)]))
+ {
incycle = TRUE;
- if (debug)
+ if (debug)
{
- fprintf(debug,"Exiting from an NPT iterating cycle of length %d\n",i);
+ fprintf(debug, "Exiting from an NPT iterating cycle of length %d\n", i);
}
break;
}
}
-
- if (incycle) {
+
+ if (incycle)
+ {
/* step 1: trapped in a numerical attractor */
/* we are trapped in a numerical attractor, and can't converge any more, and are close to the final result.
Better to give up convergence here than have the simulation die.
- */
+ */
iterate->num_close++;
+ iterate->bIterationActive = FALSE;
return TRUE;
- }
- else
+ }
+ else
{
/* Step #2: test if we are reasonably close for other reasons, then monitor the number. If not, die */
-
+
/* how many close calls have we had? If less than a few, we're OK */
- if (iterate->num_close < MAX_NUMBER_CLOSE)
+ if (iterate->num_close < MAX_NUMBER_CLOSE)
{
- md_print_warn(cr,fplog,"Slight numerical convergence deviation with NPT at step %d, relative error only %10.5g, likely not a problem, continuing\n",nsteps,relerr);
+ md_print_warn(cr, fplog, "Slight numerical convergence deviation with NPT at step %d, relative error only %10.5g, likely not a problem, continuing\n", nsteps, relerr);
iterate->num_close++;
+ iterate->bIterationActive = FALSE;
return TRUE;
/* if more than a few, check the total fraction. If too high, die. */
- } else if (iterate->num_close/(double)nsteps > FRACTION_CLOSE) {
- gmx_fatal(FARGS,"Could not converge NPT constraints, too many exceptions (%d%%\n",iterate->num_close/(double)nsteps);
- }
+ }
+ else if (iterate->num_close/(double)nsteps > FRACTION_CLOSE)
+ {
+ gmx_fatal(FARGS, "Could not converge NPT constraints, too many exceptions (%d%%\n", iterate->num_close/(double)nsteps);
+ }
}
}
- else
+ else
{
- gmx_fatal(FARGS,"Could not converge NPT constraints\n");
+ gmx_fatal(FARGS, "Could not converge NPT constraints\n");
}
}
}
-
+
iterate->xprev = iterate->x;
- iterate->x = *newf;
+ iterate->x = *newf;
iterate->fprev = iterate->f;
iterate->iter_i++;
-
+
return FALSE;
}
-
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff