*/
/*
- * Note that parts of this source code originate from the Simtk release
+ * Note, that parts of this source code originate from the Simtk release
* of OpenMM accelerated Gromacs, for more details see:
* https://simtk.org/project/xml/downloads.xml?group_id=161#package_id600
*/
#include "string2.h"
#include "gmx_gpu_utils.h"
#include "mtop_util.h"
-#include "warninp.h"
#include "openmm_wrapper.h"
* of the respective constant array is taken (GmxOpenMMPlatformOptions#platforms,
* GmxOpenMMPlatformOptions#memtests, GmxOpenMMPlatformOptions#deviceid,
* GmxOpenMMPlatformOptions#force_dev).
- * \param[in] optionString Option string part of the mdrun -deviceoption parameter.
+ * \param[in] optionString Option list part of the mdrun -device parameter.
*/
GmxOpenMMPlatformOptions::GmxOpenMMPlatformOptions(const char *optionString)
{
/*!
- * \brief Returns the value of an option.
+ * \brief Getter function.
* \param[in] opt Name of the option.
+ * \returns Returns the value associated to an option.
*/
string GmxOpenMMPlatformOptions::getOptionValue(const string &opt)
{
/*!
* \brief Runs memtest on the GPU that has alreaby been initialized by OpenMM.
* \param[in] fplog Pointer to gromacs log file.
- * \param[in] devId Device id of the GPU to run the test on. TODO: this can be removed!
+ * \param[in] devId Device id of the GPU to run the test on.
+ Note: as OpenMM previously creates the context,for now this is always -1.
* \param[in] pre_post Contains either "Pre" or "Post" just to be able to differentiate in
* stdout messages/log between memtest carried out before and after simulation.
* \param[in] opt Pointer to platform options object.
*/
static void runMemtest(FILE* fplog, int devId, const char* pre_post, GmxOpenMMPlatformOptions *opt)
{
- char strout_buf[STRLEN];
- int which_test;
- int res = 0;
- string s = opt->getOptionValue("memtest");
- const char * test_type =
- s.c_str();
- /* NOTE: thie code below for some misterious reason does NOT work
- with MSVC, but the above "fix" seems to solve the problem - not sure why though */
- // opt->getOptionValue("memtest").c_str();
-
+ char strout_buf[STRLEN];
+ int which_test;
+ int res = 0;
+ string s = opt->getOptionValue("memtest");
+ const char *test_type = s.c_str();
if (!gmx_strcasecmp(test_type, "off"))
{
fprintf(stdout, "\n%s-simulation %s GPU memtest in progress...", pre_post, test_type);
fflush(fplog);
fflush(stdout);
- res = do_quick_memtest(-1);
+ res = do_quick_memtest(devId);
break; /* case 1 */
case 2: /* full memtest */
fprintf(stdout, "\n%s-simulation %s memtest in progress...", pre_post, test_type);
fflush(fplog);
fflush(stdout);
- res = do_full_memtest(-1);
+ res = do_full_memtest(devId);
break; /* case 2 */
default: /* timed memtest */
fprintf(stdout, "\n%s-simulation ~%ds memtest in progress...", pre_post, which_test);
fflush(fplog);
fflush(stdout);
- res = do_timed_memtest(-1, which_test);
+ res = do_timed_memtest(devId, which_test);
}
- if (which_test != 0 && res != 0)
+ if (which_test != 0)
{
- gmx_fatal(FARGS, MEM_ERR_MSG(pre_post));
- }
- else
- {
- fprintf(fplog, "Memory test completed without errors.\n");
- fflush(fplog);
- fprintf(stdout, "done, no errors detected\n");
- fflush(stdout);
+ if (res != 0)
+ {
+ gmx_fatal(FARGS, MEM_ERR_MSG(pre_post));
+ }
+ else
+ {
+ fprintf(fplog, "Memory test completed without errors.\n");
+ fflush(fplog);
+ fprintf(stdout, "done, no errors detected\n");
+ fflush(stdout);
+ }
}
}
+/*!
+ * \brief Convert Lennard-Jones parameters c12 and c6 to sigma and epsilon.
+ *
+ * \param[in] c12
+ * \param[in] c6
+ * \param[out] sigma
+ * \param[out] epsilon
+ */
+static void convert_c_12_6(double c12, double c6, double *sigma, double *epsilon)
+{
+ if (c12 == 0 && c6 == 0)
+ {
+ *epsilon = 0.0;
+ *sigma = 1.0;
+ }
+ else if (c12 > 0 && c6 > 0)
+ {
+ *epsilon = (c6*c6)/(4.0*c12);
+ *sigma = pow(c12/c6, 1.0/6.0);
+ }
+ else
+ {
+ gmx_fatal(FARGS,"OpenMM only supports c6 > 0 and c12 > 0 or c6 = c12 = 0.");
+ }
+}
+
/*!
* \brief Does gromacs option checking.
*
* Checks the gromacs mdp options for features unsupported in OpenMM, case in which
* interrupts the execution. It also warns the user about pecularities of OpenMM
* implementations.
- * \param[in] ir Gromacs structure for input options, \see ::t_inputrec
- * \param[in] top Gromacs local topology, \see ::gmx_localtop_t
- * \param[in] state Gromacs state structure \see ::t_state
+ * \param[in] fplog Gromacs log file pointer.
+ * \param[in] ir Gromacs input parameters, see ::t_inputrec
+ * \param[in] top Gromacs node local topology, \see gmx_localtop_t
+ * \param[in] state Gromacs state structure \see ::t_state
+ * \param[in] mdatoms Gromacs atom parameters, \see ::t_mdatoms
+ * \param[in] fr \see ::t_forcerec
+ * \param[in] state Gromacs systems state, \see ::t_state
*/
-static void checkGmxOptions(t_inputrec *ir, gmx_localtop_t *top, t_state *state)
+static void checkGmxOptions(FILE* fplog,
+ t_inputrec *ir, gmx_localtop_t *top,
+ t_forcerec *fr, t_state *state)
{
- char warn_buf[STRLEN];
+ char warn_buf[STRLEN];
+ int i, j, natoms;
+ double c6, c12, sigma_ij, sigma_ji, sigma_ii, sigma_jj, sigma_comb,
+ eps_ij, eps_ji, eps_ii, eps_jj, eps_comb;
/* Abort if unsupported critical options are present */
gmx_fatal(FARGS,"OpenMM does not support pulling.");
/* check for restraints */
- int i;
for (i = 0; i < F_EPOT; i++)
{
if (i != F_CONSTR &&
{
gmx_fatal(FARGS,"OpenMM does not support triclinic unit cells.");
}
-
}
-/*!
- * \brief Convert Lennard-Jones parameters c12 and c6 to sigma and epsilon.
- *
- * \param[in] c12
- * \param[in] c6
- * \param[out] sigma
- * \param[out] epsilon
- */
-static void convert_c_12_6(double c12, double c6, double *sigma, double *epsilon)
-{
- if (c12 == 0 && c6 == 0)
- {
- *epsilon = 0.0;
- *sigma = 1.0;
- }
- else if (c12 > 0 && c6 > 0)
- {
- *epsilon = (c6*c6)/(4.0*c12);
- *sigma = pow(c12/c6, 1.0/6.0);
- }
- else
- {
- gmx_fatal(FARGS,"OpenMM only supports c6 > 0 and c12 > 0 or c6 = c12 = 0.");
- }
-}
-
/*!
* \brief Initialize OpenMM, run sanity/consistency checks, and return a pointer to
* the OpenMMData.
* \param[in] fplog Gromacs log file handler.
* \param[in] platformOptStr Platform option string.
* \param[in] ir The Gromacs input parameters, see ::t_inputrec
- * \param[in] top_global Gromacs whole system toppology, \see ::gmx_mtop_t
+ * \param[in] top_global Gromacs system toppology, \see ::gmx_mtop_t
* \param[in] top Gromacs node local topology, \see gmx_localtop_t
* \param[in] mdatoms Gromacs atom parameters, \see ::t_mdatoms
* \param[in] fr \see ::t_forcerec
* \param[in] state Gromacs systems state, \see ::t_state
- *
+ * \returns Pointer to a
+ *
*/
void* openmm_init(FILE *fplog, const char *platformOptStr,
t_inputrec *ir,
}
fprintf(fplog, "\nPlugins loaded from directory %s:\t", usedPluginDir.c_str());
- for (int i = 0; i < loadedPlugins.size(); i++)
+ for (int i = 0; i < (int)loadedPlugins.size(); i++)
{
fprintf(fplog, "%s, ", loadedPlugins[i].c_str());
}
/* parse option string */
GmxOpenMMPlatformOptions *opt = new GmxOpenMMPlatformOptions(platformOptStr);
+ devId = atoi(opt->getOptionValue("deviceid").c_str());
if (debug)
{
}
/* check wheter Gromacs options compatibility with OpenMM */
- checkGmxOptions(ir, top, state);
+ checkGmxOptions(fplog, ir, top, fr, state);
// Create the system.
const t_idef& idef = top->idef;
* If the default ewald_rtol=1e-5 is used we silently adjust the value,
* otherwise a warning is issued about the action taken.
*/
+ double corr_ewald_rtol = 500.0 * ir->ewald_rtol;
if ((ir->ePBC == epbcXYZ) &&
(ir->coulombtype == eelEWALD || ir->coulombtype == eelPME))
{
+ if (debug)
+ {
+ fprintf(debug, ">> ewald_rtol = %e (corrected = %e) \n",
+ ir->ewald_rtol, corr_ewald_rtol);
+ }
+
if (fabs(ir->ewald_rtol - 1e-5) > 1e-10)
{
gmx_warning("OpenMM uses the ewald_rtol parameter with approximate formulas "
"settings close to the ones used in GROMACS. Although the internal correction "
"should work for any reasonable value of ewald_rtol, using values other than "
"the default 1e-5 might cause incorrect behavior.");
+
+ if (corr_ewald_rtol > 1)
+ {
+ gmx_fatal(FARGS, "The ewald_rtol accuracy term is >1 after the "
+ "adjustment for OpenMM (%e)", corr_ewald_rtol);
+ }
}
- nonbondedForce->setEwaldErrorTolerance(500*ir->ewald_rtol);
+ nonbondedForce->setEwaldErrorTolerance(corr_ewald_rtol);
}
for (int i = 0; i < numAtoms; ++i)
else
*/
{
- // Find which platform is it.
- for (int i = 0; i < Platform::getNumPlatforms() && context == NULL; i++)
+ /* which platform should we use */
+ for (int i = 0; i < (int)Platform::getNumPlatforms() && context == NULL; i++)
{
if (isStringEqNCase(opt->getOptionValue("platform"), Platform::getPlatform(i).getName()))
{
const vector<string>& properties = platform.getPropertyNames();
if (debug)
{
- for (int i = 0; i < properties.size(); i++)
+ for (int i = 0; i < (int)properties.size(); i++)
{
- printf(">> %s: %s\n", properties[i].c_str(),
- platform.getPropertyValue(*context, properties[i]).c_str());
- fprintf(fplog, ">> %s: %s\n", properties[i].c_str(),
+ fprintf(debug, ">> %s: %s\n", properties[i].c_str(),
platform.getPropertyValue(*context, properties[i]).c_str());
}
}
{
gmx_fatal(FARGS, "The selected GPU (#%d, %s) is not supported by Gromacs! "
"Most probably you have a low-end GPU which would not perform well, "
- "or new hardware that has not been tested yet with Gromacs-OpenMM. "
+ "or new hardware that has not been tested with the current release. "
"If you still want to try using the device, use the force-device=yes option.",
devId, gpuname);
}
data->removeCM = (ir->nstcomm > 0);
data->platformOpt = opt;
return data;
-
}
catch (std::exception& e)
{
gmx_fatal(FARGS, "OpenMM exception caught while initializating: %s", e.what());
- }
+ }
+ return NULL; /* just to avoid warnings */
}
/*!
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff