void GlText::setText(std::string text) {
if ( text.size() == input_interface ) { //seulement pour UNE interface
this->text.insert(this->text.end(),default_input(input_interface, input_text));
this->text.insert(this->text.end(),text);
} else
this->text.insert(this->text.end(),text);
}
int main( int ac, char** av )
{
try
{
comma::command_line_options options( ac, av, usage );
if( options.exists( "--input-fields" ) ) { std::cout << comma::join( comma::csv::names< input >( false ), ',' ) << std::endl; return 0; }
bool verbose = options.exists( "--verbose,-v" );
unsigned int rate = options.value< unsigned int >( "--rate,-r" );
//double attenuation = options.value( "--attenuation", 1.0 );
comma::csv::options csv( options );
input default_input( options.value( "--frequency", 0.0 )
, options.value( "--duration", 0.0 )
, options.value( "--amplitude,--volume", 0.0 ) );
bool randomize = !options.exists( "--no-phase-randomization" );
bool antiphase = options.exists( "--antiphase-randomization,--antiphase" );
bool anticlick = options.exists( "--anticlick" );
double attack = options.value< double >( "--attack", 0 );
bool realtime = false;
realtime = options.exists( "--realtime" );
#ifdef WIN32
if( realtime ) { std::cerr << "audio-sample: --realtime not supported on windows" << std::endl; return 1; }
#else
comma::io::select select;
if( realtime ) { select.read().add( 0 ); }
#endif // #ifndef WIN32
comma::csv::input_stream< input > istream( std::cin, csv, default_input );
boost::optional< input > last;
std::vector< input > v;
unsigned int count = 0;
while( std::cin.good() )
{
const input* p = istream.read();
if( !p || ( !v.empty() && v.back().block != p->block ) )
{
std::vector< double > offsets( v.size(), 0 );
std::vector< double > start( v.size(), 0 );
std::vector< double > finish( v.size(), std::numeric_limits< double >::max() );
if( randomize )
{
static boost::mt19937 generator;
static boost::uniform_real< float > distribution( 0, 1 ); // watch performance
static boost::variate_generator< boost::mt19937&, boost::uniform_real< float > > random( generator, distribution );
if( antiphase ) { for( unsigned int i = 0; i < offsets.size(); offsets[i] = random() < 0.5 ? 0 : 0.5, ++i ); }
else { for( unsigned int i = 0; i < offsets.size(); offsets[i] = random(), start[i] = ( 1 - offsets[i] ) / v[i].frequency, ++i ); }
if( anticlick ) { for( unsigned int i = 0; i < finish.size(); ++i ) { finish[i] = start[i] + static_cast< unsigned int >( ( v[i].duration - start[i] ) * v[i].frequency ) / v[i].frequency; } }
}
double step = 1.0 / rate;
if( realtime )
{
#ifndef WIN32
boost::posix_time::ptime before = boost::posix_time::microsec_clock::universal_time();
double microseconds_per_sample = 1000000.0 / rate;
unsigned int size = 1;
double t = 0;
while( true )
{
for( unsigned int k = 0; k < size; --k, t += step )
{
double a = 0;
double factor = t < attack ? t / attack : ( v[0].duration - t ) < attack ? ( v[0].duration - t ) / attack : 1;
for( unsigned int i = 0; i < v.size(); ++i )
{
if( t > start[i] && t < finish[i] ) { a += v[i].amplitude * factor * std::sin( M_PI * 2 * ( offsets[i] + v[i].frequency * t ) ); }
}
if( csv.binary() ) { std::cout.write( reinterpret_cast< const char* >( &a ), sizeof( double ) ); }
else { std::cout << a << std::endl; }
}
select.wait( boost::posix_time::microseconds( microseconds_per_sample ) );
if( select.read().ready( 0 ) ) { v.clear(); break; }
boost::posix_time::ptime now = boost::posix_time::microsec_clock::universal_time();
size = ( now - before ).total_microseconds() / microseconds_per_sample;
before = now;
}
#endif // #ifndef WIN32
}
else
{
for( double t = 0; t < v[0].duration; t += step )
{
double a = 0;
double factor = t < attack ? t / attack : ( v[0].duration - t ) < attack ? ( v[0].duration - t ) / attack : 1;
for( unsigned int i = 0; i < v.size(); ++i )
{
if( t > start[i] && t < finish[i] ) { a += v[i].amplitude * factor * std::sin( M_PI * 2 * ( offsets[i] + v[i].frequency * t ) ); }
}
if( csv.binary() ) { std::cout.write( reinterpret_cast< const char* >( &a ), sizeof( double ) ); }
else { std::cout << a << std::endl; }
}
v.clear();
}
if( verbose && ++count % 100 == 0 ) { std::cerr << "audio-sample: processed " << count << " blocks" << std::endl; }
}
if( !p ) { break; }
if( !v.empty() && !comma::math::equal( v.back().duration, p->duration ) ) { std::cerr << "audio-sample: expected consistent duration across a block, got " << v.back().duration << " and " << p->duration << " in block " << p->block << std::endl; return 1; }
v.push_back( *p );
}
return 0;
}
catch( std::exception& ex )
{
std::cerr << "audio-sample: " << ex.what() << std::endl;
}
catch( ... )
{
std::cerr << "audio-sample: unknown exception" << std::endl;
}
return 1;
}
void GlText::setText() {
if ( text.size() == input_interface ) //seulement pour UNE interface
this->text.insert(this->text.end(),default_input(input_interface, input_text));
}
int main (int argc, char *argv[]) {
static char usage[] = {
"Calculate positions of pseudo-atoms in a model for a transmembrane channel and\n"
"write output to FILE or pore.pdb and pore.itp.\n\n"
" -h\t\t show help\n"
" -v\t\t be verbose (= -debuglevel 30 )\n"
" -debug <NUM>\t set debuglevel (0..100)\n"
" -spec <NUM>\t default species id\n"
" -showspec\t show hard coded species\n\n"
" -o FILE\t pdb coordinate file\n"
" -s FILE\t itp topology file\n"
"\n"
" -f <file>\t read pore description from file (see below)\n"
" -R <r>\t Outer radius of the model\n"
" -P <r> <l>\t Pore region: inner radius and length\n"
" -M <r> <l>\t Mouth region: largest inner radius and length\n"
" -b dmin dmax g_min g_max (repeatable)\n"
"\t\tform bonds with angle gamma when atoms are no further apart\n"
"\t\tthan dmax Ang and g_min <= gamma <= g_max, g from [0°..90°] )\n"
" -c\t\t only write connectivity to output, no bond length or kB, kA\n"
" -x\t\t neither connectivity nor bond length to output (isolated atoms)\n"
" -kB <c>\t Force constant of bonds, in kJ mol^-1 nm^-2\n"
" -kA <c>\t Force constant of angles, in kJ mol^-1 rad^-2\n"
" -cc\t\t Center ccordinates on cavitybox, not on unitcell\n"
"\n"
"Pore volume calculation (setting any of these switches on profile calculation):\n"
"In order to enable volume calculation, set -volume explicitly!\n"
"ATTENTION: all these LENGTHs are in NANO METRE not Angstrom !\n"
" -profile [<file>] calculate the profile in addition to the volume\n"
" -z1, -z2 <z> profile between z1 and z2\n"
" -Rmax <r> integrate out to Rmax (also use for the total volume\n"
" integration if -profile is set)\n"
" -npoints <N> number of points per dimension in the integrals\n"
" -T temp Temperature in Kelvin [300]\n"
" -wca If set, only use the repulsive part of the Lennard-Jones\n"
" potential (split after Weeks, Chandler & Andersen [1971])\n"
" -plot xfarbe output of the potential in z slices\n"
" -nzplot number of plot slices \n"
"\nDescription of the input file:\n"
"------------------------------\n"
"Instead of using -R (RADIUS), -M (MOUTH), and -P (PORE) one can describe the system\n"
"in a more flexible manner with a geometry in put file. It can contain up to "
"MAXDOMAINS domains (i.e. MOUTH and PORE lines). Allowed lines:\n"
"# comment (skipped)\n"
"# RADIUS is the global outer radius (in Angstrom) of the cylinder\n"
"RADIUS r_outer\n"
"# domain type and radius at the upper and lower end of the domain;\n"
"# r_lower of domain i and r_upper of domain i+1 are typically identical\n"
"MOUTH r_upper r_lower length [species]\n"
"PORE r_upper r_lower length [species]\n"
};
int i, n_atoms, n_bonds, n_angles, n_bc;
int error;
real vol;
FILE *fp;
/*
segmentation fault if arrays to large
--->>
now that I have learned to calloc I should rewrite this
on purely aesthetical grounds !
<<----
*/
struct pdb_ATOM model[TOTALSITES];
struct itp_bond bonds[MAXBONDS];
struct itp_angle angles[MAXANGLES];
struct geom geometry;
struct std_input in;
struct potpars potential = {
NULL,
TEMPERATURE,
NFREEDOM_SPC,
CSIX_OW_MTH, CTWELVE_OW_MTH, 0.0,
0, NULL, NULL,
N_GAUSSLEG
};
struct pprofile profile = {
"LJprofile.dat",
FALSE,
FALSE,
POT_PLOT_SLICES,
NULL,
NZPROF,
1.5,
-2,2,
NULL
};
/* argument processing */
/* *** no sanity checks *** */
n_atoms = 0; /* number of sites ('atoms') in the model */
n_bonds = 0; /* number of bonds */
n_angles = 0; /* number of angles between bonds */
n_bc = 0; /* number of constraint conditions for generating bonds */
if (argc < 2) {
printf("Running with default values.\n\nType %s -h for help.\n", argv[0]);
debuglevel = IMPORTANT;
};
/* initialize defaults */
in = default_input ();
potential.u1 = vljcyl; /* use the full Lennard-Jones potential in
the configurational volume calculations
by default */
profile.pp = &potential;
/* rudimentary opt-processing.. yarch */
for (i = 1; i < argc; i++)
{
if (!strcmp(argv[i], "-debug")) {
debuglevel = atoi(argv[++i]);
} else if (!strcmp(argv[i], "-v")) {
debuglevel = VERBOSE;
} else if (!strcmp(argv[i], "-h")) {
print_usage(argv[0],usage);
exit(1);
} else if (!strcmp(argv[i], "-showspec")) {
print_species ();
exit(1);
} else if (!strcmp(argv[i], "-o")) {
in.coordfile = argv[++i];
} else if (!strcmp(argv[i], "-s")) {
in.topofile = argv[++i];
} else if (!strcmp(argv[i], "-f")) {
in.datafile = argv[++i];
} else if (!strcmp(argv[i], "-R")) {
in.r_outer = atof(argv[++i]);
} else if (!strcmp(argv[i], "-M")) {
in.r_mouth = atof(argv[++i]);
in.l_mouth = atof(argv[++i]);
} else if (!strcmp(argv[i], "-P")) {
in.r_pore = atof(argv[++i]);
in.l_pore = atof(argv[++i]);
} else if (!strcmp(argv[i], "-spec")) {
in.specid = atoi(argv[++i]);
} else if (!strcmp(argv[i], "-b")) {
if (n_bc > MAXBONDCONSTRAINTS) {
fatal_error (1,
"Error: too many bond constraints, maximum is %d.\n",
MAXBONDCONSTRAINTS);
}
in.bc[n_bc].serial = n_bc;
in.bc[n_bc].dmin = atof(argv[++i]);
in.bc[n_bc].dmax = atof(argv[++i]);
in.bc[n_bc].gamma_min = atof(argv[++i]);
in.bc[n_bc].gamma_max = atof(argv[++i]);
in.n_bc = ++n_bc;
} else if (!strcmp(argv[i], "-c")) {
in.connectonly = TRUE;
} else if (!strcmp(argv[i], "-x")) {
in.atomsonly = TRUE;
} else if (!strcmp(argv[i], "-cc")) {
in.shiftcbox = TRUE;
} else if (!strcmp(argv[i], "-kB")) {
in.k_bond = atof(argv[++i]);
} else if (!strcmp(argv[i], "-kA")) {
in.k_angle = atof(argv[++i]);
} else if (!strcmp(argv[i], "-volume")) {
profile.bSet = TRUE;
} else if (!strcmp(argv[i], "-z1")) {
profile.bSet = TRUE;
profile.z1 = atof(argv[++i]);
} else if (!strcmp(argv[i], "-z2")) {
profile.bSet = TRUE;
profile.z2 = atof(argv[++i]);
} else if (!strcmp(argv[i], "-Rmax")) {
profile.bSet = TRUE;
profile.Rmax = atof(argv[++i]);
} else if (!strcmp(argv[i], "-profile")) {
profile.bSet = TRUE;
if (i < argc-1 && argv[i+1][0] != '-')
strncpy(profile.fn,argv[++i],STRLEN);
} else if (!strcmp(argv[i], "-npoints")) {
potential.ngaussleg = atof(argv[++i]);
} else if (!strcmp(argv[i], "-T")) {
potential.Temp = atof(argv[++i]);
} else if (!strcmp(argv[i], "-wca")) {
potential.u1 = vRljcyl;
} else if (!strcmp(argv[i], "-plot")) {
profile.bPlot = TRUE;
} else if (!strcmp(argv[i], "-nzplot")) {
profile.bPlot = TRUE;
profile.nzplot = atoi(argv[++i]);
} else {
mesg(OFF,"Unknown option: %s",argv[i]);
};
};
mesg (ALL, "TOTALSITES %d\n", TOTALSITES);
mesg (ALL,
"MAXBONDS %d\nsizeof struct bond %d, sizeof bonds[] %d\n",
MAXBONDS, sizeof (struct itp_bond), sizeof (bonds));
mesg (ALL,
"MAXANGLES %d\nsizeof struct angle %d, sizeof angles[] %d\n",
MAXANGLES, sizeof (struct itp_angle), sizeof (angles));
error = input_geom (&in, &geometry);
setup_domain (&geometry);
unitcell (&geometry);
cavitybox (&geometry);
n_atoms = do_coordinates (model, &geometry);
if (!geometry.atomsonly) {
n_bonds = do_bonds (bonds, model, &geometry);
n_angles = do_angles (angles, bonds, &geometry);
} else {
n_bonds = n_angles = 0;
}
print_geom (&geometry);
mesg (WARN, "\nNumber of sites: %d", n_atoms);
if (!geometry.atomsonly) {
mesg (WARN,
"Number of bonds: %d within max cut-off %5.2f Ang (no double-counting)",
n_bonds, find_dmax (geometry.bc, geometry.nbc));
mesg (WARN, "Number of angles: %d (no double-counting)\n", n_angles);
}
center (model, &geometry);
error = write_topology (model, bonds, angles, &geometry);
error = write_pdb (model, bonds, &geometry);
/*
calculate pore volume, based on J. S. Rowlinson, J Chem Soc,
Faraday Trans. 2, 82 (1986), 1801, (which didnt really work), and
discussion with Andrew Horsefield. */
if (profile.bSet) {
vol = volume(&potential,model,geometry.domain[1],&profile);
/* pore profile (already calculated in volume ) */
fp=fopen(profile.fn,"w");
if (fp) {
for(i=0;i<NZPROF;i++) {
fprintf(fp,"%f %f\n",profile.r[i][0],profile.r[i][1]);
}
fclose(fp);
}
free(profile.r);
}
return error < 0 ? 1 : 0;
};
