int colvarproxy_smp::smp_biases_script_loop()
{
#if defined(_OPENMP)
colvarmodule *cv = cvm::main();
#pragma omp parallel
{
#pragma omp single nowait
{
cv->calc_scripted_forces();
}
#pragma omp for
for (size_t i = 0; i < cv->biases_active()->size(); i++) {
colvarbias *b = (*(cv->biases_active()))[i];
if (cvm::debug()) {
cvm::log("Calculating bias \""+b->name+"\" on thread "+
cvm::to_str(smp_thread_id())+"\n");
}
b->update();
}
}
return cvm::get_error();
#else
return COLVARS_NOT_IMPLEMENTED;
#endif
}
void count_register_thread(unsigned long *p)
{
int idx = smp_thread_id();
spin_lock(&final_mutex);
countarrayp->counterp[idx] = &counter;
spin_unlock(&final_mutex);
}
void *thread_test(void *arg)
{
int myarg = (int)arg;
printf("child thread %d: smp_thread_id() = %d\n",
myarg, smp_thread_id());
return NULL;
}
void count_unregister_thread(int nthreadsexpected)
{
int idx = smp_thread_id();
spin_lock(&final_mutex);
finalcount += *counter;
counterp[idx] = NULL;
spin_unlock(&final_mutex);
}
colvarproxy_smp::~colvarproxy_smp()
{
#if defined(_OPENMP)
if (smp_thread_id() == 0) {
if (omp_lock_state) {
delete reinterpret_cast<omp_lock_t *>(omp_lock_state);
}
}
#endif
}
colvarproxy_smp::colvarproxy_smp()
{
b_smp_active = true; // May be disabled by user option
omp_lock_state = NULL;
#if defined(_OPENMP)
if (smp_thread_id() == 0) {
omp_init_lock(reinterpret_cast<omp_lock_t *>(omp_lock_state));
}
#endif
}
int colvarproxy_lammps::smp_biases_loop()
{
colvarmodule *cv = this->colvars;
#pragma omp parallel for
for (size_t i = 0; i < cv->biases.size(); i++) {
if (cvm::debug()) {
cvm::log("Calculating bias \""+cv->biases[i]->name+"\" on thread "+cvm::to_str(smp_thread_id())+"\n");
}
cv->biases[i]->update();
}
return cvm::get_error();
}
void count_unregister_thread(int nthreadsexpected)
{
struct countarray *cap;
struct countarray *capold;
int idx = smp_thread_id();
cap = malloc(sizeof(*countarrayp));
if (cap == NULL) {
fprintf(stderr, "Out of memory\n");
exit(-1);
}
spin_lock(&final_mutex);
*cap = *countarrayp;
cap->total += counter;
cap->counterp[idx] = NULL;
capold = countarrayp;
rcu_assign_pointer(countarrayp, cap);
spin_unlock(&final_mutex);
synchronize_rcu();
free(capold);
}
colvarproxy_lammps::colvarproxy_lammps(LAMMPS_NS::LAMMPS *lmp,
const char *inp_name,
const char *out_name,
const int seed,
const double temp,
MPI_Comm root2root)
: _lmp(lmp), inter_comm(root2root)
{
if (cvm::debug())
log("Initializing the colvars proxy object.\n");
_random = new LAMMPS_NS::RanPark(lmp,seed);
first_timestep=true;
system_force_requested=false;
previous_step=-1;
t_target=temp;
do_exit=false;
restart_every=0;
// User-scripted forces are not available in LAMMPS
force_script_defined = false;
have_scripts = false;
// set input restart name and strip the extension, if present
input_prefix_str = std::string(inp_name ? inp_name : "");
if (input_prefix_str.rfind(".colvars.state") != std::string::npos)
input_prefix_str.erase(input_prefix_str.rfind(".colvars.state"),
std::string(".colvars.state").size());
// output prefix is always given
output_prefix_str = std::string(out_name);
// not so for restarts
restart_output_prefix_str = std::string("rest");
// check if it is possible to save output configuration
if ((!output_prefix_str.size()) && (!restart_output_prefix_str.size())) {
fatal_error("Error: neither the final output state file or "
"the output restart file could be defined, exiting.\n");
}
// try to extract a restart prefix from a potential restart command.
LAMMPS_NS::Output *outp = _lmp->output;
if ((outp->restart_every_single > 0) && (outp->restart1 != 0)) {
restart_output_prefix_str = std::string(outp->restart1);
} else if ((outp->restart_every_double > 0) && (outp->restart2a != 0)) {
restart_output_prefix_str = std::string(outp->restart2a);
}
// trim off unwanted stuff from the restart prefix
if (restart_output_prefix_str.rfind(".*") != std::string::npos)
restart_output_prefix_str.erase(restart_output_prefix_str.rfind(".*"),2);
#if defined(_OPENMP)
if (smp_thread_id() == 0) {
omp_init_lock(&smp_lock_state);
}
#endif
// initialize multi-replica support, if available
if (replica_enabled()) {
MPI_Comm_rank(inter_comm, &inter_me);
MPI_Comm_size(inter_comm, &inter_num);
}
if (cvm::debug())
log("Done initializing the colvars proxy object.\n");
}
int colvarproxy_lammps::smp_colvars_loop()
{
colvarmodule *cv = this->colvars;
#pragma omp parallel for
for (size_t i = 0; i < cv->colvars_smp.size(); i++) {
if (cvm::debug()) {
cvm::log("Calculating colvar \""+cv->colvars_smp[i]->name+"\" on thread "+cvm::to_str(smp_thread_id())+"\n");
}
cv->colvars_smp[i]->calc_cvcs(cv->colvars_smp_items[i], 1);
}
return cvm::get_error();
}
