From fec0d8a4023c44c5884707f8c415daa3f8c518b1 Mon Sep 17 00:00:00 2001
From: "Kurt A. O'Hearn" <ohearnk@msu.edu>
Date: Fri, 21 Dec 2018 15:30:41 -0500
Subject: [PATCH] sPuReMD: clean-up geometry file I/O code. Remove a few
compiler warnings.
---
sPuReMD/src/geo_tools.c | 217 +++++++++++++++++++---------------------
sPuReMD/src/init_md.c | 2 +-
2 files changed, 104 insertions(+), 115 deletions(-)
diff --git a/sPuReMD/src/geo_tools.c b/sPuReMD/src/geo_tools.c
index 2e09f60b..df50baa7 100644
--- a/sPuReMD/src/geo_tools.c
+++ b/sPuReMD/src/geo_tools.c
@@ -31,17 +31,17 @@ static void Count_Geo_Atoms( FILE *geo, reax_system *system )
{
int i, serial;
rvec x;
- char element[3], name[9], line[MAX_LINE + 1];
+ char element[3], name[9], line[MAX_LINE];
/* total number of atoms */
- fscanf( geo, " %d", &(system->N) );
+ fscanf( geo, " %d", &system->N );
/* count atoms */
for ( i = 0; i < system->N; ++i )
{
fscanf( geo, CUSTOM_ATOM_FORMAT,
&serial, element, name, &x[0], &x[1], &x[2] );
- Fit_to_Periodic_Box( &(system->box), &x );
+ Fit_to_Periodic_Box( &system->box, &x );
}
fseek( geo, 0, SEEK_SET );
@@ -58,7 +58,7 @@ static int Read_Box_Info( reax_system *system, FILE *geo, int geo_format )
{
int ret, cryst_len;
char *cryst;
- char line[MAX_LINE + 1];
+ char line[MAX_LINE];
char descriptor[9];
char s_a[12], s_b[12], s_c[12], s_alpha[12], s_beta[12], s_gamma[12];
char s_group[12], s_zValue[12];
@@ -83,7 +83,7 @@ static int Read_Box_Info( reax_system *system, FILE *geo, int geo_format )
}
/* locate the cryst line in the geo file, read it and
- initialize the big box */
+ * initialize the big box */
while ( fgets( line, MAX_LINE, geo ) )
{
if ( strncmp( line, cryst, cryst_len ) == 0 )
@@ -91,10 +91,8 @@ static int Read_Box_Info( reax_system *system, FILE *geo, int geo_format )
if ( geo_format == PDB )
{
sscanf( line, PDB_CRYST1_FORMAT,
- &descriptor[0],
- &s_a[0], &s_b[0], &s_c[0],
- &s_alpha[0], &s_beta[0], &s_gamma[0],
- &s_group[0], &s_zValue[0] );
+ descriptor, s_a, s_b, s_c,
+ s_alpha, s_beta, s_gamma, s_group, s_zValue );
/* compute full volume tensor from the angles */
Setup_Box( atof(s_a), atof(s_b), atof(s_c),
@@ -146,15 +144,16 @@ void Read_Geo( const char * const geo_file, reax_system* system, control_params
{
fscanf( geo, CUSTOM_ATOM_FORMAT,
&serial, element, name, &x[0], &x[1], &x[2] );
- Fit_to_Periodic_Box( &(system->box), &x );
+ Fit_to_Periodic_Box( &system->box, &x );
+
#if defined(DEBUG)
fprintf( stderr, "atom%d: %s %s %f %f %f\n",
serial, element, name, x[0], x[1], x[2] );
#endif
- atom = &(system->atoms[top]);
+ atom = &system->atoms[top];
workspace->orig_id[i] = serial;
- atom->type = Get_Atom_Type( &(system->reaxprm), element );
+ atom->type = Get_Atom_Type( &system->reaxprm, element );
strncpy( atom->name, name, 8 );
rvec_Copy( atom->x, x );
rvec_MakeZero( atom->v );
@@ -171,7 +170,7 @@ void Read_Geo( const char * const geo_file, reax_system* system, control_params
static void Count_PDB_Atoms( FILE *geo, reax_system *system )
{
char *endptr = NULL;
- char line[MAX_LINE + 1];
+ char line[MAX_LINE];
char s_x[9], s_y[9], s_z[9];
rvec x;
@@ -251,7 +250,7 @@ void Read_PDB( const char * const pdb_file, reax_system* system, control_params
while ( fgets( s, MAX_LINE, pdb ) )
{
/* read new line and tokenize it */
- strncpy( s1, s, MAX_LINE - 1 );
+ strncpy( s1, s, MAX_LINE );
c1 = Tokenize( s, &tmp );
/* process new line */
@@ -259,75 +258,70 @@ void Read_PDB( const char * const pdb_file, reax_system* system, control_params
{
if ( strncmp(tmp[0], "ATOM", 4) == 0 )
{
- strncpy( &descriptor[0], s1, 6 );
+ strncpy( descriptor, s1, 6 );
descriptor[6] = 0;
- strncpy( &serial[0], s1 + 6, 5 );
+ strncpy( serial, s1 + 6, 5 );
serial[5] = 0;
- strncpy( &atom_name[0], s1 + 12, 4 );
+ strncpy( atom_name, s1 + 12, 4 );
atom_name[4] = 0;
- //strncpy( &serial[0], s1+6, 7 ); serial[7] = 0;
- //strncpy( &atom_name[0], s1+13, 3 ); atom_name[3] = 0;
alt_loc = s1[16];
- strncpy( &res_name[0], s1 + 17, 3 );
+ strncpy( res_name, s1 + 17, 3 );
res_name[3] = 0;
chain_id = s1[21];
- strncpy( &res_seq[0], s1 + 22, 4 );
+ strncpy( res_seq, s1 + 22, 4 );
res_seq[4] = 0;
icode = s1[26];
- strncpy( &s_x[0], s1 + 30, 8 );
+ strncpy( s_x, s1 + 30, 8 );
s_x[8] = 0;
- strncpy( &s_y[0], s1 + 38, 8 );
+ strncpy( s_y, s1 + 38, 8 );
s_y[8] = 0;
- strncpy( &s_z[0], s1 + 46, 8 );
+ strncpy( s_z, s1 + 46, 8 );
s_z[8] = 0;
- strncpy( &occupancy[0], s1 + 54, 6 );
+ strncpy( occupancy, s1 + 54, 6 );
occupancy[6] = 0;
- strncpy( &temp_factor[0], s1 + 60, 6 );
+ strncpy( temp_factor, s1 + 60, 6 );
temp_factor[6] = 0;
- strncpy( &seg_id[0], s1 + 72, 4 );
+ strncpy( seg_id, s1 + 72, 4 );
seg_id[4] = 0;
- strncpy( &element[0], s1 + 76, 2 );
+ strncpy( element, s1 + 76, 2 );
element[2] = 0;
- strncpy( &charge[0], s1 + 78, 2 );
+ strncpy( charge, s1 + 78, 2 );
charge[2] = 0;
}
else if ( strncmp(tmp[0], "HETATM", 6) == 0 )
{
- strncpy( &descriptor[0], s1, 6 );
+ strncpy( descriptor, s1, 6 );
descriptor[6] = 0;
- strncpy( &serial[0], s1 + 6, 5 );
+ strncpy( serial, s1 + 6, 5 );
serial[5] = 0;
- strncpy( &atom_name[0], s1 + 12, 4 );
+ strncpy( atom_name, s1 + 12, 4 );
atom_name[4] = 0;
- //strncpy( &serial[0], s1+6, 7 ); serial[7] = 0;
- //strncpy( &atom_name[0], s1+13, 3 ); atom_name[3] = 0;
alt_loc = s1[16];
- strncpy( &res_name[0], s1 + 17, 3 );
+ strncpy( res_name, s1 + 17, 3 );
res_name[3] = 0;
chain_id = s1[21];
- strncpy( &res_seq[0], s1 + 22, 4 );
+ strncpy( res_seq, s1 + 22, 4 );
res_seq[4] = 0;
icode = s1[26];
- strncpy( &s_x[0], s1 + 30, 8 );
+ strncpy( s_x, s1 + 30, 8 );
s_x[8] = 0;
- strncpy( &s_y[0], s1 + 38, 8 );
+ strncpy( s_y, s1 + 38, 8 );
s_y[8] = 0;
- strncpy( &s_z[0], s1 + 46, 8 );
+ strncpy( s_z, s1 + 46, 8 );
s_z[8] = 0;
- strncpy( &occupancy[0], s1 + 54, 6 );
+ strncpy( occupancy, s1 + 54, 6 );
occupancy[6] = 0;
- strncpy( &temp_factor[0], s1 + 60, 6 );
+ strncpy( temp_factor, s1 + 60, 6 );
temp_factor[6] = 0;
- //strncpy( &seg_id[0], s1+72, 4 ); seg_id[4] = 0;
- strncpy( &element[0], s1 + 76, 2 );
+ strncpy( element, s1 + 76, 2 );
element[2] = 0;
- strncpy( &charge[0], s1 + 78, 2 );
+ strncpy( charge, s1 + 78, 2 );
charge[2] = 0;
}
/* if the point is inside my_box, add it to my lists */
- Make_Point( strtod( &s_x[0], &endptr ), strtod( &s_y[0], &endptr ),
- strtod( &s_z[0], &endptr ), &x );
+ Make_Point( strtod( s_x, &endptr ), strtod( s_y, &endptr ),
+ strtod( s_z, &endptr ), &x );
Fit_to_Periodic_Box( &system->box, &x );
@@ -335,7 +329,7 @@ void Read_PDB( const char * const pdb_file, reax_system* system, control_params
{
/* store orig_id, type, name and coord info of the new atom */
atom = &system->atoms[top];
- pdb_serial = (int) strtod( &serial[0], &endptr );
+ pdb_serial = (int) strtod( serial, &endptr );
workspace->orig_id[top] = pdb_serial;
Trim_Spaces( element, 9 );
@@ -421,18 +415,18 @@ void Write_PDB( reax_system* system, reax_list* bonds, simulation_data *data,
FILE *pdb;
/* Writing Box information */
- gamma = ACOS( (system->box.box[0][0] * system->box.box[1][0] +
- system->box.box[0][1] * system->box.box[1][1] +
- system->box.box[0][2] * system->box.box[1][2]) /
- (system->box.box_norms[0] * system->box.box_norms[1]) );
- beta = ACOS( (system->box.box[0][0] * system->box.box[2][0] +
- system->box.box[0][1] * system->box.box[2][1] +
- system->box.box[0][2] * system->box.box[2][2]) /
- (system->box.box_norms[0] * system->box.box_norms[2]) );
- alpha = ACOS( (system->box.box[2][0] * system->box.box[1][0] +
- system->box.box[2][1] * system->box.box[1][1] +
- system->box.box[2][2] * system->box.box[1][2]) /
- (system->box.box_norms[2] * system->box.box_norms[1]) );
+ gamma = ACOS( (system->box.box[0][0] * system->box.box[1][0]
+ + system->box.box[0][1] * system->box.box[1][1]
+ + system->box.box[0][2] * system->box.box[1][2])
+ / (system->box.box_norms[0] * system->box.box_norms[1]) );
+ beta = ACOS( (system->box.box[0][0] * system->box.box[2][0]
+ + system->box.box[0][1] * system->box.box[2][1]
+ + system->box.box[0][2] * system->box.box[2][2])
+ / (system->box.box_norms[0] * system->box.box_norms[2]) );
+ alpha = ACOS( (system->box.box[2][0] * system->box.box[1][0]
+ + system->box.box[2][1] * system->box.box[1][1]
+ + system->box.box[2][2] * system->box.box[1][2])
+ / (system->box.box_norms[2] * system->box.box_norms[1]) );
/* open pdb and write header */
snprintf( fname, MAX_STR + 9, "%s-%d.pdb", control->sim_name, data->step );
@@ -446,18 +440,17 @@ void Write_PDB( reax_system* system, reax_list* bonds, simulation_data *data,
/* write atom lines to buffer */
for ( i = 0; i < system->N; i++)
{
- p_atom = &(system->atoms[i]);
+ p_atom = &system->atoms[i];
strncpy( name, p_atom->name, 8 );
Trim_Spaces( name, 8 );
memcpy( x, p_atom->x, 3 * sizeof(real) );
- Fit_to_Periodic_Box( &(system->box), &x );
+ Fit_to_Periodic_Box( &system->box, &x );
snprintf( buffer, PDB_ATOM_FORMAT_O_LENGTH, PDB_ATOM_FORMAT_O,
"ATOM ", workspace->orig_id[i], p_atom->name, ' ', "REX", ' ', 1, ' ',
- x[0], x[1], x[2],
- 1.0, 0.0, "0", name, " " );
+ x[0], x[1], x[2], 1.0, 0.0, "0", name, " " );
buffer[PDB_ATOM_FORMAT_O_LENGTH] = '\n';
@@ -494,15 +487,12 @@ void Read_BGF( const char * const bgf_file, reax_system* system, control_params
bgf = sfopen( bgf_file, "r" );
/* allocate memory for tokenizing biograf file lines */
- line = (char*) smalloc( sizeof(char) * MAX_LINE,
- "Read_BGF::line" );
- backup = (char*) smalloc( sizeof(char) * MAX_LINE,
- "Read_BGF::backup" );
- tokens = (char**) smalloc( sizeof(char*) * MAX_TOKENS,
- "Read_BGF::tokens" );
+ line = smalloc( sizeof(char) * MAX_LINE, "Read_BGF::line" );
+ backup = smalloc( sizeof(char) * MAX_LINE, "Read_BGF::backup" );
+ tokens = smalloc( sizeof(char*) * MAX_TOKENS, "Read_BGF::tokens" );
for ( i = 0; i < MAX_TOKENS; i++ )
{
- tokens[i] = (char*) smalloc( sizeof(char) * MAX_TOKEN_LEN,
+ tokens[i] = smalloc( sizeof(char) * MAX_TOKEN_LEN,
"Read_BGF::tokens[i]" );
}
@@ -536,25 +526,25 @@ void Read_BGF( const char * const bgf_file, reax_system* system, control_params
sfclose( bgf, "Read_BGF::bgf" );
/* memory allocations for atoms, atom maps, bond restrictions */
- system->atoms = (reax_atom*) scalloc( system->N, sizeof(reax_atom),
+ system->atoms = scalloc( system->N, sizeof(reax_atom),
"Read_BGF::system->atoms" );
- workspace->map_serials = (int*) scalloc( MAX_ATOM_ID, sizeof(int),
+ workspace->map_serials = scalloc( MAX_ATOM_ID, sizeof(int),
"Read_BGF::workspace->map_serials" );
for ( i = 0; i < MAX_ATOM_ID; ++i )
{
workspace->map_serials[i] = -1;
}
- workspace->orig_id = (int*) scalloc( system->N, sizeof(int),
+ workspace->orig_id = scalloc( system->N, sizeof(int),
"Read_BGF::workspace->orig_id" );
- workspace->restricted = (int*) scalloc( system->N, sizeof(int),
+ workspace->restricted = scalloc( system->N, sizeof(int),
"Read_BGF::workspace->restricted" );
- workspace->restricted_list = (int**) scalloc( system->N, sizeof(int*),
+ workspace->restricted_list = scalloc( system->N, sizeof(int*),
"Read_BGF::workspace->restricted_list" );
for ( i = 0; i < system->N; ++i )
{
- workspace->restricted_list[i] = (int*) scalloc( MAX_RESTRICT, sizeof(int),
+ workspace->restricted_list[i] = scalloc( MAX_RESTRICT, sizeof(int),
"Read_BGF::workspace->restricted_list[i]" );
}
@@ -566,7 +556,7 @@ void Read_BGF( const char * const bgf_file, reax_system* system, control_params
while ( fgets( line, MAX_LINE, bgf ) )
{
/* read new line and tokenize it */
- strncpy( backup, line, MAX_LINE - 1 );
+ strncpy( backup, line, MAX_LINE );
token_cnt = Tokenize( line, &tokens );
/* process new line */
@@ -574,80 +564,80 @@ void Read_BGF( const char * const bgf_file, reax_system* system, control_params
{
if ( !strncmp(tokens[0], "ATOM", 4) )
{
- strncpy( &descriptor[0], backup, 6 );
+ strncpy( descriptor, backup, 6 );
descriptor[6] = 0;
- strncpy( &serial[0], backup + 7, 5 );
+ strncpy( serial, backup + 7, 5 );
serial[5] = 0;
- strncpy( &atom_name[0], backup + 13, 5 );
+ strncpy( atom_name, backup + 13, 5 );
atom_name[5] = 0;
- strncpy( &res_name[0], backup + 19, 3 );
+ strncpy( res_name, backup + 19, 3 );
res_name[3] = 0;
chain_id = backup[23];
- strncpy( &res_seq[0], backup + 25, 5 );
+ strncpy( res_seq, backup + 25, 5 );
res_seq[5] = 0;
- strncpy( &s_x[0], backup + 30, 10 );
+ strncpy( s_x, backup + 30, 10 );
s_x[10] = 0;
- strncpy( &s_y[0], backup + 40, 10 );
+ strncpy( s_y, backup + 40, 10 );
s_y[10] = 0;
- strncpy( &s_z[0], backup + 50, 10 );
+ strncpy( s_z, backup + 50, 10 );
s_z[10] = 0;
- strncpy( &element[0], backup + 61, 5 );
+ strncpy( element, backup + 61, 5 );
element[5] = 0;
- strncpy( &occupancy[0], backup + 66, 3 );
+ strncpy( occupancy, backup + 66, 3 );
occupancy[3] = 0;
- strncpy( &temp_factor[0], backup + 69, 2 );
+ strncpy( temp_factor, backup + 69, 2 );
temp_factor[2] = 0;
- strncpy( &charge[0], backup + 72, 8 );
+ strncpy( charge, backup + 72, 8 );
charge[8] = 0;
}
else if ( !strncmp(tokens[0], "HETATM", 6) )
{
/* bgf hetatm:
(7x,i5,1x,a5,1x,a3,1x,a1,1x,a5,3f10.5,1x,a5,i3,i2,1x,f8.5) */
- strncpy( &descriptor[0], backup, 6 );
+ strncpy( descriptor, backup, 6 );
descriptor[6] = 0;
- strncpy( &serial[0], backup + 7, 5 );
+ strncpy( serial, backup + 7, 5 );
serial[5] = 0;
- strncpy( &atom_name[0], backup + 13, 5 );
+ strncpy( atom_name, backup + 13, 5 );
atom_name[5] = 0;
- strncpy( &res_name[0], backup + 19, 3 );
+ strncpy( res_name, backup + 19, 3 );
res_name[3] = 0;
chain_id = backup[23];
- strncpy( &res_seq[0], backup + 25, 5 );
+ strncpy( res_seq, backup + 25, 5 );
res_seq[5] = 0;
- strncpy( &s_x[0], backup + 30, 10 );
+ strncpy( s_x, backup + 30, 10 );
s_x[10] = 0;
- strncpy( &s_y[0], backup + 40, 10 );
+ strncpy( s_y, backup + 40, 10 );
s_y[10] = 0;
- strncpy( &s_z[0], backup + 50, 10 );
+ strncpy( s_z, backup + 50, 10 );
s_z[10] = 0;
- strncpy( &element[0], backup + 61, 5 );
+ strncpy( element, backup + 61, 5 );
element[5] = 0;
- strncpy( &occupancy[0], backup + 66, 3 );
+ strncpy( occupancy, backup + 66, 3 );
occupancy[3] = 0;
- strncpy( &temp_factor[0], backup + 69, 2 );
+ strncpy( temp_factor, backup + 69, 2 );
temp_factor[2] = 0;
- strncpy( &charge[0], backup + 72, 8 );
+ strncpy( charge, backup + 72, 8 );
charge[8] = 0;
}
/* add to mapping */
- bgf_serial = strtod( &serial[0], &endptr );
+ bgf_serial = strtod( serial, &endptr );
Check_Input_Range( bgf_serial, 0, MAX_ATOM_ID, "Invalid bgf serial" );
workspace->map_serials[ bgf_serial ] = atom_cnt;
workspace->orig_id[ atom_cnt ] = bgf_serial;
// fprintf( stderr, "map %d --> %d\n", bgf_serial, atom_cnt );
/* copy atomic positions */
- system->atoms[atom_cnt].x[0] = strtod( &s_x[0], &endptr );
- system->atoms[atom_cnt].x[1] = strtod( &s_y[0], &endptr );
- system->atoms[atom_cnt].x[2] = strtod( &s_z[0], &endptr );
+ system->atoms[atom_cnt].x[0] = strtod( s_x, &endptr );
+ system->atoms[atom_cnt].x[1] = strtod( s_y, &endptr );
+ system->atoms[atom_cnt].x[2] = strtod( s_z, &endptr );
/* atom name and type */
strncpy( system->atoms[atom_cnt].name, atom_name, 8 );
Trim_Spaces( element, 10 );
system->atoms[atom_cnt].type =
- Get_Atom_Type( &(system->reaxprm), element );
+ Get_Atom_Type( &system->reaxprm, element );
/* fprintf( stderr,
"a:%3d(%1d) c:%10.5f%10.5f%10.5f q:%10.5f occ:%s temp:%s seg_id:%s element:%s\n",
@@ -659,18 +649,17 @@ void Read_BGF( const char * const bgf_file, reax_system* system, control_params
atom_cnt++;
}
- else if (!strncmp( tokens[0], "CRYSTX", 6 ))
+ else if ( !strncmp( tokens[0], "CRYSTX", 6 ) )
{
- sscanf( backup, BGF_CRYSTX_FORMAT, &descriptor[0],
- &s_a[0], &s_b[0], &s_c[0],
- &s_alpha[0], &s_beta[0], &s_gamma[0] );
+ sscanf( backup, BGF_CRYSTX_FORMAT, descriptor,
+ s_a, s_b, s_c, s_alpha, s_beta, s_gamma );
/* Compute full volume tensor from the angles */
Setup_Box( atof(s_a), atof(s_b), atof(s_c),
atof(s_alpha), atof(s_beta), atof(s_gamma),
- &(system->box) );
+ &system->box );
}
- else if (!strncmp( tokens[0], "CONECT", 6 ))
+ else if ( !strncmp( tokens[0], "CONECT", 6 ) )
{
/* check number of restrictions */
Check_Input_Range( token_cnt - 2, 0, MAX_RESTRICT,
@@ -687,8 +676,8 @@ void Read_BGF( const char * const bgf_file, reax_system* system, control_params
{
if ( is_Valid_Serial( workspace, bgf_serial = atoi(tokens[i]) ) )
{
- workspace->restricted_list[ ratom ][ i - 2 ] =
- workspace->map_serials[ bgf_serial ];
+ workspace->restricted_list[ratom][i - 2] =
+ workspace->map_serials[bgf_serial];
}
}
diff --git a/sPuReMD/src/init_md.c b/sPuReMD/src/init_md.c
index e0899c70..2195900e 100644
--- a/sPuReMD/src/init_md.c
+++ b/sPuReMD/src/init_md.c
@@ -907,7 +907,7 @@ static void Init_Out_Controls( reax_system *system, control_params *control,
if ( control->ensemble == aNPT || control->ensemble == iNPT
|| control->ensemble == sNPT )
{
- strncpy( temp, control->sim_name, MAX_STR );
+ strncpy( temp, control->sim_name, TEMP_SIZE );
strcat( temp, ".prs" );
out_control->prs = sfopen( temp, "w" );
fprintf( out_control->prs, "%-6s%13s%13s%13s%13s%13s%13s%13s%13s\n",
--
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