From 35394c7e03e00a0086960943be683625a861a5c4 Mon Sep 17 00:00:00 2001
From: "Kurt A. O'Hearn" <ohearnku@msu.edu>
Date: Thu, 10 Dec 2020 10:57:30 -0500
Subject: [PATCH] sPuReMD: fix memory leak with ICHOLT preconditioner (droptol
for OpenMP only) for charge solver. Default to Jacobi preconditioner. Resolve
several compiler warnings around C strings (snprintf, etc.). Other code
clean-up.
---
sPuReMD/src/analyze.c | 34 ++++++++++++++++++++--------------
sPuReMD/src/control.c | 4 ++--
sPuReMD/src/geo_tools.c | 2 +-
sPuReMD/src/lin_alg.c | 7 +++++++
sPuReMD/src/multi_body.c | 10 +++++-----
sPuReMD/src/reset_tools.c | 2 ++
sPuReMD/src/restart.c | 2 +-
7 files changed, 38 insertions(+), 23 deletions(-)
diff --git a/sPuReMD/src/analyze.c b/sPuReMD/src/analyze.c
index c02ac49c..fa831353 100644
--- a/sPuReMD/src/analyze.c
+++ b/sPuReMD/src/analyze.c
@@ -197,12 +197,12 @@ static void Get_Molecule( int atom, molecule *m, int *mark, reax_system *system,
}
-static void Print_Molecule( reax_system *system, molecule *m, int mode, char *s,
- size_t size )
+static void Print_Molecule( reax_system *system, molecule *m, int mode,
+ char *s, size_t s_size, char *s_out, size_t s_out_size )
{
int j, atom;
- s[0] = 0;
+ s[0] = '\0';
if ( mode == 1 )
{
@@ -211,8 +211,9 @@ static void Print_Molecule( reax_system *system, molecule *m, int mode, char *s,
{
if ( m->mtypes[j] )
{
- snprintf( s, size, "%s%14s%3d", s, system->reax_param.sbp[j].name, m->mtypes[j] );
- s[size - 1] = '\0';
+ snprintf( s_out, s_out_size, "%.*s%14s%3d", (int) MAX(s_out_size - 18, 0),
+ s, system->reax_param.sbp[j].name, m->mtypes[j] );
+ s_out[s_out_size - 1] = '\0';
}
}
}
@@ -222,8 +223,10 @@ static void Print_Molecule( reax_system *system, molecule *m, int mode, char *s,
for ( j = 0; j < m->atom_count; ++j )
{
atom = m->atom_list[j];
- snprintf( s, size, "%s%s(%d)",
- s, system->reax_param.sbp[ system->atoms[atom].type ].name, atom );
+ snprintf( s_out, s_out_size, "%.*s%.*s(%d)", (int) MAX((s_out_size - 5) / 2, 0), s,
+ (int) MAX((s_out_size - 5) / 2, 0),
+ system->reax_param.sbp[ system->atoms[atom].type ].name, atom );
+ s_out[s_out_size - 1] = '\0';
}
}
}
@@ -238,6 +241,7 @@ static void Analyze_Molecules( reax_system *system, control_params *control,
int *old_mark = workspace->old_mark;
int num_old, num_new;
char s[MAX_MOLECULE_SIZE * 10];
+ char s_out[MAX_MOLECULE_SIZE * 10];
reax_list *new_bonds = lists[BONDS];
reax_list *old_bonds = lists[OLD_BONDS];
molecule old_molecules[20], new_molecules[20];
@@ -306,8 +310,8 @@ static void Analyze_Molecules( reax_system *system, control_params *control,
fprintf( fout, "old molecules: " );
for ( i = 0; i < num_old; ++i )
{
- Print_Molecule( system, &old_molecules[i], 1, &s[0],
- MAX_MOLECULE_SIZE * 10 );
+ Print_Molecule( system, &old_molecules[i], 1, s,
+ sizeof(s), s_out, sizeof(s_out) );
fprintf( fout, "%s\t", s );
}
fprintf( fout, "\n" );
@@ -315,8 +319,8 @@ static void Analyze_Molecules( reax_system *system, control_params *control,
fprintf( fout, "new molecules: " );
for ( i = 0; i < num_new; ++i )
{
- Print_Molecule( system, &new_molecules[i], 1, &s[0],
- MAX_MOLECULE_SIZE * 10 );
+ Print_Molecule( system, &new_molecules[i], 1, s,
+ sizeof(s), s_out, sizeof(s_out) );
fprintf( fout, "%s\t", s );
}
fprintf( fout, "\n" );
@@ -595,6 +599,7 @@ static void Analyze_Fragments( reax_system *system, control_params *control,
int *mark = workspace->mark;
int num_fragments, num_fragment_types;
char fragment[MAX_ATOM_TYPES];
+ char fragment_out[MAX_ATOM_TYPES];
char fragments[MAX_FRAGMENT_TYPES][MAX_ATOM_TYPES];
int fragment_count[MAX_FRAGMENT_TYPES];
molecule m;
@@ -618,13 +623,14 @@ static void Analyze_Fragments( reax_system *system, control_params *control,
memset( m.mtypes, 0, MAX_ATOM_TYPES * sizeof(int) );
Visit_Bonds( atom, mark, m.mtypes, system, control, new_bonds, ignore );
++num_fragments;
- Print_Molecule( system, &m, 1, fragment, MAX_FRAGMENT_TYPES );
+ Print_Molecule( system, &m, 1, fragment, sizeof(fragment),
+ fragment_out, sizeof(fragment_out) );
/* check if a similar fragment already exists */
flag = 0;
for ( i = 0; i < num_fragment_types; ++i )
{
- if ( !strncmp( fragments[i], fragment, MAX_ATOM_TYPES ) )
+ if ( !strncmp( fragments[i], fragment_out, MAX_ATOM_TYPES ) )
{
++fragment_count[i];
flag = 1;
@@ -635,7 +641,7 @@ static void Analyze_Fragments( reax_system *system, control_params *control,
if ( flag == 0 )
{
/* it is a new one, add to the fragments list */
- strncpy( fragments[num_fragment_types], fragment,
+ strncpy( fragments[num_fragment_types], fragment_out,
sizeof(fragments[num_fragment_types]) - 1 );
fragments[num_fragment_types][sizeof(fragments[num_fragment_types]) - 1] = '\0';
fragment_count[num_fragment_types] = 1;
diff --git a/sPuReMD/src/control.c b/sPuReMD/src/control.c
index b8cceaa7..28978fa2 100644
--- a/sPuReMD/src/control.c
+++ b/sPuReMD/src/control.c
@@ -92,10 +92,10 @@ void Read_Control_File( FILE* fp, reax_system *system, control_params* control,
strncpy( control->cm_init_guess_gd_model, "frozen_model.pb", sizeof(control->cm_init_guess_gd_model) - 1 );
control->cm_init_guess_gd_model[sizeof(control->cm_init_guess_gd_model) - 1] = '\0';
control->cm_init_guess_win_size = 5;
- control->cm_solver_pre_comp_type = ICHOLT_PC;
+ control->cm_solver_pre_comp_type = JACOBI_PC;
control->cm_solver_pre_comp_sweeps = 3;
control->cm_solver_pre_comp_sai_thres = 0.1;
- control->cm_solver_pre_comp_refactor = 100;
+ control->cm_solver_pre_comp_refactor = 1;
control->cm_solver_pre_comp_droptol = 0.01;
control->cm_solver_pre_app_type = TRI_SOLVE_PA;
control->cm_solver_pre_app_jacobi_iters = 50;
diff --git a/sPuReMD/src/geo_tools.c b/sPuReMD/src/geo_tools.c
index 0fef6e03..94472a6d 100644
--- a/sPuReMD/src/geo_tools.c
+++ b/sPuReMD/src/geo_tools.c
@@ -275,7 +275,7 @@ static int Count_Atoms( reax_system *system, FILE *fp, int geo_format )
#if defined(DEBUG)
fprintf( stderr, "[INFO] Count_Atoms: " );
- fprintf( stderr, "N = %d\n", system->N );
+ fprintf( stderr, "N = %d\n", n );
#endif
return n;
diff --git a/sPuReMD/src/lin_alg.c b/sPuReMD/src/lin_alg.c
index 44ddce77..29f4eb8e 100644
--- a/sPuReMD/src/lin_alg.c
+++ b/sPuReMD/src/lin_alg.c
@@ -470,6 +470,13 @@ void Calculate_Droptol( const sparse_matrix * const A,
{
droptol[i] = SQRT( droptol[i] ) * dtol;
}
+
+#if defined(_OPENMP)
+ #pragma omp master
+ {
+ sfree( droptol_local, "Calculate_Droptol::droptol_local" );
+ }
+#endif
}
}
diff --git a/sPuReMD/src/multi_body.c b/sPuReMD/src/multi_body.c
index f1216ac5..1dd047df 100644
--- a/sPuReMD/src/multi_body.c
+++ b/sPuReMD/src/multi_body.c
@@ -66,7 +66,7 @@ void Atom_Energy( reax_system *system, control_params *control,
/* lone-pair Energy */
p_lp2 = sbp_i->p_lp2;
expvd2 = EXP( -75.0 * workspace->Delta_lp[i] );
- inv_expvd2 = 1.0 / (1.0 + expvd2 );
+ inv_expvd2 = 1.0 / (1.0 + expvd2);
/* calculate the energy */
e_lp = p_lp2 * workspace->Delta_lp[i] * inv_expvd2;
@@ -178,16 +178,16 @@ void Atom_Energy( reax_system *system, control_params *control,
exp_ovun2 = EXP( p_ovun2 * Delta_lpcorr );
inv_exp_ovun2 = 1.0 / (1.0 + exp_ovun2);
- DlpVi = 1.0 / (Delta_lpcorr + sbp_i->valency + 1e-8 );
+ DlpVi = 1.0 / (Delta_lpcorr + sbp_i->valency + 1.0e-8 );
CEover1 = Delta_lpcorr * DlpVi * inv_exp_ovun2;
e_ov = sum_ovun1 * CEover1;
data->E_Ov += e_ov;
CEover2 = sum_ovun1 * DlpVi * inv_exp_ovun2
- * ( 1.0 - Delta_lpcorr * ( DlpVi + p_ovun2 * exp_ovun2 * inv_exp_ovun2 ) );
+ * (1.0 - Delta_lpcorr * (DlpVi + p_ovun2 * exp_ovun2 * inv_exp_ovun2));
- CEover3 = CEover2 * (1.0 - dfvl * workspace->dDelta_lp[i] * inv_exp_ovun1 );
+ CEover3 = CEover2 * (1.0 - dfvl * workspace->dDelta_lp[i] * inv_exp_ovun1);
CEover4 = CEover2 * (dfvl * workspace->Delta_lp_temp[i])
* p_ovun4 * exp_ovun1 * SQR(inv_exp_ovun1);
@@ -205,7 +205,7 @@ void Atom_Energy( reax_system *system, control_params *control,
e_un = -p_ovun5 * (1.0 - exp_ovun6) * inv_exp_ovun2n * inv_exp_ovun8;
data->E_Un += e_un;
- CEunder1 = inv_exp_ovun2n * ( p_ovun5 * p_ovun6 * exp_ovun6 * inv_exp_ovun8
+ CEunder1 = inv_exp_ovun2n * (p_ovun5 * p_ovun6 * exp_ovun6 * inv_exp_ovun8
+ p_ovun2 * e_un * exp_ovun2n);
CEunder2 = -e_un * p_ovun8 * exp_ovun8 * inv_exp_ovun8;
CEunder3 = CEunder1 * (1.0 - dfvl * workspace->dDelta_lp[i] * inv_exp_ovun1);
diff --git a/sPuReMD/src/reset_tools.c b/sPuReMD/src/reset_tools.c
index ac2718f8..57ececef 100644
--- a/sPuReMD/src/reset_tools.c
+++ b/sPuReMD/src/reset_tools.c
@@ -27,7 +27,9 @@
void Reset_Pressures( control_params *control, simulation_data *data )
{
+#if defined(_OPENMP)
int i;
+#endif
rtensor_MakeZero( data->flex_bar.P );
data->iso_bar.P = 0.0;
diff --git a/sPuReMD/src/restart.c b/sPuReMD/src/restart.c
index 32b3a622..4afaa367 100644
--- a/sPuReMD/src/restart.c
+++ b/sPuReMD/src/restart.c
@@ -37,7 +37,7 @@ void Write_Binary_Restart( reax_system *system, control_params *control,
restart_header res_header;
restart_atom res_data;
- snprintf( fname, MAX_STR, "%s.res%d", control->sim_name, data->step );
+ snprintf( fname, MAX_STR, "%.*s.res%d", MAX_STR - 12, control->sim_name, data->step );
fres = sfopen( fname, "wb" );
res_header.step = data->step;
--
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