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Commit ce7baae5 by Francois Gygi
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removed trailing blanks in *.[Ch] *.mk Makefile 


git-svn-id: http://qboxcode.org/svn/qb/trunk@515 cba15fb0-1239-40c8-b417-11db7ca47a34
parent 14e9be36
Showing with 807 additions and 807 deletions
src/AndersonMixer.C
......@@ -3,7 +3,7 @@
// AndersonMixer.C
//
////////////////////////////////////////////////////////////////////////////////
// $Id: AndersonMixer.C,v 1.4 2007-03-17 01:14:00 fgygi Exp $
// $Id: AndersonMixer.C,v 1.5 2007-10-19 16:24:03 fgygi Exp $
#include "AndersonMixer.h"
#include "blas.h"
......@@ -28,13 +28,13 @@ void AndersonMixer::update(const double* f, double* theta, double* fbar)
// tmp0 = delta_F = f - flast
for ( int i = 0; i < n_; i++ )
tmp0[i] = f[i] - flast_[i];
// a = delta_F * F
double a = ddot(&n_, &tmp0[0], &ione, f, &ione);
// b = delta_F * delta_F
double b = ddot(&n_, &tmp0[0], &ione, &tmp0[0], &ione);
if ( pctxt_ != 0 )
{
double work[2] = { a, b };
......@@ -47,16 +47,16 @@ void AndersonMixer::update(const double* f, double* theta, double* fbar)
*theta = - a / b;
else
*theta = 0.0;
// test if residual has increased
if ( *theta <= -1.0 )
{
*theta = theta_nc_;
}
*theta = min(theta_max_,*theta);
}
// fbar = f + theta * ( f - flast )
// flast_ = f_
for ( int i = 0; i < n_; i++ )
......@@ -64,6 +64,6 @@ void AndersonMixer::update(const double* f, double* theta, double* fbar)
const double ftmp = f[i];
fbar[i] = ftmp + *theta * ( ftmp - flast_[i] );
flast_[i] = ftmp;
}
}
extrapolate_ = true;
}
src/AndersonMixer.h
......@@ -3,7 +3,7 @@
// AndersonMixer.h
//
////////////////////////////////////////////////////////////////////////////////
// $Id: AndersonMixer.h,v 1.4 2007-03-17 01:14:00 fgygi Exp $
// $Id: AndersonMixer.h,v 1.5 2007-10-19 16:24:03 fgygi Exp $
#ifndef ANDERSONMIXER_H
#define ANDERSONMIXER_H
......@@ -18,7 +18,7 @@ class AndersonMixer
const Context* const pctxt_; // pointer to relevant Context, null if local
double theta_max_; // maximum extrapolation
double theta_nc_; // negative curvature value
std::valarray<double> flast_; // last residual
bool extrapolate_; // state variable
......
src/AngleCmd.h
......@@ -3,7 +3,7 @@
// AngleCmd.h:
//
////////////////////////////////////////////////////////////////////////////////
// $Id: AngleCmd.h,v 1.1 2005-06-27 22:35:26 fgygi Exp $
// $Id: AngleCmd.h,v 1.2 2007-10-19 16:24:03 fgygi Exp $
#ifndef ANGLECMD_H
#define ANGLECMD_H
......@@ -24,7 +24,7 @@ class AngleCmd : public Cmd
char *name(void) const { return "angle"; }
char *help_msg(void) const
{
return
return
"\n angle\n\n"
" syntax: angle name1 name2 name3\n\n"
" The angle command prints the angle defined by three atoms.\n\n";
......@@ -40,15 +40,15 @@ class AngleCmd : public Cmd
}
return 1;
}
string name1(argv[1]);
string name2(argv[2]);
string name3(argv[3]);
Atom* a1 = s->atoms.findAtom(name1);
Atom* a2 = s->atoms.findAtom(name2);
Atom* a3 = s->atoms.findAtom(name3);
if ( a1 == 0 || a2 == 0 || a3 == 0 )
{
string name1(argv[1]);
string name2(argv[2]);
string name3(argv[3]);
Atom* a1 = s->atoms.findAtom(name1);
Atom* a2 = s->atoms.findAtom(name2);
Atom* a3 = s->atoms.findAtom(name3);
if ( a1 == 0 || a2 == 0 || a3 == 0 )
{
if ( ui->onpe0() )
{
if ( a1 == 0 )
......@@ -63,28 +63,28 @@ class AngleCmd : public Cmd
}
return 1;
}
if ( a1 == a2 || a2 == a3 || a3 == a1 )
{
if ( a1 == a2 || a2 == a3 || a3 == a1 )
{
if ( ui->onpe0() )
{
cout << " <!-- AngleCmd: replicated atoms in " << name1
<< " " << name2 << " " << name3 << " -->" << endl;
cout << " <!-- AngleCmd: replicated atoms in " << name1
<< " " << name2 << " " << name3 << " -->" << endl;
}
return 1;
}
D3vector r12(a1->position()-a2->position());
D3vector r32(a3->position()-a2->position());
if ( norm(r12) == 0.0 || norm(r32) == 0.0 )
{
{
if ( ui->onpe0() )
{
cout << " <!-- AngleCmd: atoms are too close -->" << endl;
}
return 1;
}
const double sp = normalized(r12) * normalized(r32);
const double c = max(-1.0,min(1.0,sp));
const double a = (180.0/M_PI)*acos(c);
......@@ -92,9 +92,9 @@ class AngleCmd : public Cmd
{
cout.setf(ios::fixed,ios::floatfield);
cout << " <!-- angle " << name1 << "-" << name2 << "-" << name3
<< ": "
<< setprecision(3)
<< a << " (deg) -->" << endl;
<< ": "
<< setprecision(3)
<< a << " (deg) -->" << endl;
}
return 0;
}
......
src/AngleConstraint.C
......@@ -3,7 +3,7 @@
// AngleConstraint.C
//
////////////////////////////////////////////////////////////////////////////////
// $Id: AngleConstraint.C,v 1.2 2005-09-16 23:08:11 fgygi Exp $
// $Id: AngleConstraint.C,v 1.3 2007-10-19 16:24:03 fgygi Exp $
#include "AngleConstraint.h"
#include "AtomSet.h"
......@@ -26,7 +26,7 @@ void AngleConstraint::setup(const AtomSet& atoms)
m1_ = atoms.species_list[is1_]->mass() * 1822.89;
assert(m1_>0.0);
m1_inv_ = 1.0 / m1_;
is2_ = atoms.is(name2_);
ia2_ = atoms.ia(name2_);
assert(is2_>=0);
......@@ -34,7 +34,7 @@ void AngleConstraint::setup(const AtomSet& atoms)
m2_ = atoms.species_list[is2_]->mass() * 1822.89;
assert(m2_>0.0);
m2_inv_ = 1.0 / m2_;
is3_ = atoms.is(name3_);
ia3_ = atoms.ia(name3_);
assert(is3_>=0);
......@@ -63,7 +63,7 @@ vector<vector<double> > &rp) const
double* pr1p = &rp[is1_][3*ia1_];
double* pr2p = &rp[is2_][3*ia2_];
double* pr3p = &rp[is3_][3*ia3_];
D3vector r1(pr1);
D3vector r2(pr2);
D3vector r3(pr3);
......@@ -72,7 +72,7 @@ vector<vector<double> > &rp) const
const double a = bond_angle(r1,r2,r3);
double ng = g1*g1 + g2*g2 + g3*g3;
assert(ng>=0.0);
D3vector r1p(pr1p);
D3vector r2p(pr2p);
D3vector r3p(pr3p);
......@@ -81,7 +81,7 @@ vector<vector<double> > &rp) const
const double ap = bond_angle(r1p,r2p,r3p);
const double ngp = g1p*g1p + g2p*g2p + g3p*g3p;
assert(ngp>=0.0);
const double err = fabs(ap-angle_);
if ( ng == 0.0 )
......@@ -119,25 +119,25 @@ vector<vector<double> > &rp) const
// no action necessary
}
}
// test alignment of the gradient at r and at rp
// compute scalar product of normalized gradients
const double sp = ( g1*g1p + g2*g2p + g3*g3p ) / sqrt( ng * ngp );
if ( fabs(sp) < 0.5*sqrt(3.0) )
{
g1 = g1p;
g2 = g2p;
g3 = g3p;
g1 = g1p;
g2 = g2p;
g3 = g3p;
}
const double den = m1_inv_ * g1 * g1p +
const double den = m1_inv_ * g1 * g1p +
m2_inv_ * g2 * g2p +
m3_inv_ * g3 * g3p;
#if DEBUG_CONSTRAINTS
cout << " <!-- ";
cout << " AngleConstraint::enforce_r: "
cout << " AngleConstraint::enforce_r: "
<< name1_ << " " << name2_ << " " << name3_
<< " angle = " << ap << endl;
cout << " AngleConstraint::enforce_r: r1 = " << r1 << endl;
......@@ -159,25 +159,25 @@ vector<vector<double> > &rp) const
cout << " -->" << endl;
#endif
if ( err < tol_ ) return true;
// make one shake iteration
assert(fabs(den)>0.0);
const double lambda = - sigma(r1p,r2p,r3p) / den;
pr1p[0] += m1_inv_ * lambda * g1.x;
pr1p[1] += m1_inv_ * lambda * g1.y;
pr1p[2] += m1_inv_ * lambda * g1.z;
pr2p[0] += m2_inv_ * lambda * g2.x;
pr2p[1] += m2_inv_ * lambda * g2.y;
pr2p[2] += m2_inv_ * lambda * g2.z;
pr3p[0] += m3_inv_ * lambda * g3.x;
pr3p[1] += m3_inv_ * lambda * g3.y;
pr3p[2] += m3_inv_ * lambda * g3.z;
return false;
}
......@@ -191,30 +191,30 @@ vector<vector<double> > &v0) const
double* pv1 = &v0[is1_][3*ia1_];
double* pv2 = &v0[is2_][3*ia2_];
double* pv3 = &v0[is3_][3*ia3_];
D3vector r1(pr1);
D3vector r2(pr2);
D3vector r3(pr3);
D3vector g1,g2,g3;
grad_sigma(r1,r2,r3,g1,g2,g3);
D3vector v1(pv1);
D3vector v2(pv2);
D3vector v3(pv3);
const double proj = v1*g1 + v2*g2 + v3*g3;
const double norm2 = g1*g1 + g2*g2 + g3*g3;
// if the gradient is too small, do not attempt correction
if ( norm2 < 1.e-6 ) return true;
const double err = fabs(proj)/sqrt(norm2);
#if DEBUG_CONSTRAINTS
cout << " <!-- ";
cout << " AngleConstraint::enforce_v: "
cout << " AngleConstraint::enforce_v: "
<< name1_ << " " << name2_ << " " << name3_ << endl;
cout << " AngleConstraint::enforce_v: tol = " << tol_ << endl;
cout << " AngleConstraint::enforce_v: err = " << err << endl;
......@@ -224,27 +224,27 @@ vector<vector<double> > &v0) const
cout << " -->" << endl;
#endif
if ( err < tol_ ) return true;
// make one shake iteration
const double den = m1_inv_ * g1 * g1 +
const double den = m1_inv_ * g1 * g1 +
m2_inv_ * g2 * g2 +
m3_inv_ * g3 * g3;
assert(den>0.0);
const double eta = -proj / den;
pv1[0] += m1_inv_ * eta * g1.x;
pv1[1] += m1_inv_ * eta * g1.y;
pv1[2] += m1_inv_ * eta * g1.z;
pv2[0] += m2_inv_ * eta * g2.x;
pv2[1] += m2_inv_ * eta * g2.y;
pv2[2] += m2_inv_ * eta * g2.z;
pv3[0] += m3_inv_ * eta * g3.x;
pv3[1] += m3_inv_ * eta * g3.y;
pv3[2] += m3_inv_ * eta * g3.z;
return false;
}
......@@ -258,30 +258,30 @@ void AngleConstraint::compute_force(const vector<vector<double> > &r0,
const double* pf1 = &f[is1_][3*ia1_];
const double* pf2 = &f[is2_][3*ia2_];
const double* pf3 = &f[is3_][3*ia3_];
D3vector r1(pr1);
D3vector r2(pr2);
D3vector r3(pr3);
D3vector g1,g2,g3;
grad_sigma(r1,r2,r3,g1,g2,g3);
D3vector f1(pf1);
D3vector f2(pf2);
D3vector f3(pf3);
const double norm2 = g1*g1 + g2*g2 + g3*g3;
if ( norm2 == 0.0 )
{
force_ = 0.0;
return;
}
const double proj = f1*g1 + f2*g2 + f3*g3;
force_ = -proj/norm2;
// compute weight
const double z = m1_inv_ * g1 * g1 +
const double z = m1_inv_ * g1 * g1 +
m2_inv_ * g2 * g2 +
m3_inv_ * g3 * g3;
assert(z > 0.0);
......@@ -292,10 +292,10 @@ void AngleConstraint::compute_force(const vector<vector<double> > &r0,
const double r32s = norm(r3-r2);
const double fac = 180.0/M_PI;
const double cos_theta = normalized(r1-r2)*normalized(r3-r2);
const double zcheck = fac*fac *
const double zcheck = fac*fac *
( m1_inv_ / r12s +
m2_inv_ * ( (r12s+r32s-2*sqrt(r12s*r32s)*cos_theta) /(r12s*r32s) ) +
m3_inv_ / r32s
m3_inv_ / r32s
);
cout << " <!-- AngleConstraint: z=" << z << " zcheck=" << zcheck << " -->"
<< endl;
......@@ -310,7 +310,7 @@ double AngleConstraint::sigma(D3vector a, D3vector b, D3vector c) const
}
////////////////////////////////////////////////////////////////////////////////
void AngleConstraint::grad_sigma(const D3vector &r1, const D3vector &r2,
void AngleConstraint::grad_sigma(const D3vector &r1, const D3vector &r2,
const D3vector &r3,
D3vector &g1, D3vector &g2, D3vector &g3) const
{
......@@ -321,7 +321,7 @@ void AngleConstraint::grad_sigma(const D3vector &r1, const D3vector &r2,
D3vector e12(normalized(r12));
D3vector e32(normalized(r32));
const double ss = length(e12^e32);
// use simplified expression if the angle is smaller than 0.2 degrees
if ( ss < sin(0.2*(M_PI/180.0) ) )
{
......@@ -351,43 +351,43 @@ void AngleConstraint::grad_sigma(const D3vector &r1, const D3vector &r2,
{
// angle is large enough. Use finite differences
//cout << " ========= grad_sigma using finite differences" << endl;
const double r12_inv = 1.0/length(r12);
const double r32_inv = 1.0/length(r32);
const double a = bond_angle(r1,r2,r3);
const double l12 = length(r1-r2);
const double l32 = length(r3-r2);
// displacement h causes changes in angle of less than 0.05 degrees
const double h = 0.05 * (M_PI/180.0) * min(l12,l32);
const double fac = 0.5 / h;
D3vector dx(h,0,0), dy(0,h,0), dz(0,0,h);
// compute gradient at r
g1.x = fac * ( sigma(r1+dx,r2,r3) - sigma(r1-dx,r2,r3) );
g1.y = fac * ( sigma(r1+dy,r2,r3) - sigma(r1-dy,r2,r3) );
g1.z = fac * ( sigma(r1+dz,r2,r3) - sigma(r1-dz,r2,r3) );
g2.x = fac * ( sigma(r1,r2+dx,r3) - sigma(r1,r2-dx,r3) );
g2.y = fac * ( sigma(r1,r2+dy,r3) - sigma(r1,r2-dy,r3) );
g2.z = fac * ( sigma(r1,r2+dz,r3) - sigma(r1,r2-dz,r3) );
g3.x = fac * ( sigma(r1,r2,r3+dx) - sigma(r1,r2,r3-dx) );
g3.y = fac * ( sigma(r1,r2,r3+dy) - sigma(r1,r2,r3-dy) );
g3.z = fac * ( sigma(r1,r2,r3+dz) - sigma(r1,r2,r3-dz) );
}
}
}
////////////////////////////////////////////////////////////////////////////////
double AngleConstraint::bond_angle(D3vector a, D3vector b, D3vector c) const
{
// compute the bond angle defined by vectors a,b,c
D3vector e12(normalized(a-b));
D3vector e32(normalized(c-b));
const double ss = length(e12^e32);
const double cc = e12*e32;
double an = (180.0/M_PI) * atan2(ss,cc);
const double ss = length(e12^e32);
const double cc = e12*e32;
double an = (180.0/M_PI) * atan2(ss,cc);
return an;
}
......
src/AngleConstraint.h
......@@ -3,7 +3,7 @@
// AngleConstraint.h
//
////////////////////////////////////////////////////////////////////////////////
// $Id: AngleConstraint.h,v 1.3 2007-03-17 01:14:00 fgygi Exp $
// $Id: AngleConstraint.h,v 1.4 2007-10-19 16:24:03 fgygi Exp $
#ifndef ANGLECONSTRAINT_H
#define ANGLECONSTRAINT_H
......@@ -24,16 +24,16 @@ class AngleConstraint : public Constraint
void grad_sigma(const D3vector &r1, const D3vector &r2, const D3vector &r3,
D3vector &g1, D3vector &g2,D3vector &g3) const;
double bond_angle(D3vector a, D3vector b, D3vector c) const;
public:
AngleConstraint(std::string name, std::string name1,
AngleConstraint(std::string name, std::string name1,
std::string name2, std::string name3,
double angle, double velocity, double tolerance):
name1_(name1), name2_(name2), name3_(name3),
name1_(name1), name2_(name2), name3_(name3),
velocity_(velocity),
tol_(tolerance), m1_(0.0), m2_(0.0), m3_(0.0)
{
{
set_value(angle);
name_ = name;
names_.resize(3);
......@@ -43,7 +43,7 @@ class AngleConstraint : public Constraint
force_ = 0.0;
weight_ = 1.0;
}
std::string type(void) const { return "angle"; }
double value(void) const { return angle_; }
double velocity(void) const { return velocity_; }
......@@ -60,7 +60,7 @@ class AngleConstraint : public Constraint
{
velocity_ = velocity;
}
void setup(const AtomSet& atoms);
void update(double dt);
bool enforce_r(const std::vector<std::vector<double> > &r0,
......@@ -70,6 +70,6 @@ class AngleConstraint : public Constraint
void compute_force(const std::vector<std::vector<double> > &r0,
const std::vector<std::vector<double> > &f);
std::ostream& print( std::ostream& os );
};
#endif
src/Atom.h
......@@ -3,7 +3,7 @@
// Atom.h:
//
////////////////////////////////////////////////////////////////////////////////
// $Id: Atom.h,v 1.3 2007-03-17 01:14:00 fgygi Exp $
// $Id: Atom.h,v 1.4 2007-10-19 16:24:03 fgygi Exp $
#ifndef ATOM_H
#define ATOM_H
......@@ -14,7 +14,7 @@
class Atom
{
private:
std::string name_;
std::string species_;
D3vector position_;
......@@ -22,7 +22,7 @@ class Atom
public:
Atom (std::string name, std::string species,
Atom (std::string name, std::string species,
D3vector position, D3vector velocity);
std::string name(void) { return name_; };
std::string species(void) { return species_; };
......
src/AtomCmd.h
......@@ -3,7 +3,7 @@
// AtomCmd.h:
//
////////////////////////////////////////////////////////////////////////////////
// $Id: AtomCmd.h,v 1.7 2007-03-17 01:14:00 fgygi Exp $
// $Id: AtomCmd.h,v 1.8 2007-10-19 16:24:03 fgygi Exp $
#ifndef ATOMCMD_H
#define ATOMCMD_H
......@@ -25,7 +25,7 @@ class AtomCmd : public Cmd
char *name(void) const { return "atom"; }
char *help_msg(void) const
{
return
return
"\n atom\n\n"
" syntax: atom name species x y z [vx vy vz]\n\n"
" The atom command defines a new atom and adds it to the atom list.\n"
......@@ -41,7 +41,7 @@ class AtomCmd : public Cmd
string species;
D3vector position;
D3vector velocity;
// atom must be defined with either 3 or 6 arguments
if ( argc != 6 && argc != 9 )
{
......@@ -49,7 +49,7 @@ class AtomCmd : public Cmd
cout << " use: atom name species x y z [vx vy vz]" << endl;
return 1;
}
name = argv[1];
species = argv[2];
position.x = atof(argv[3]);
......@@ -61,10 +61,10 @@ class AtomCmd : public Cmd
velocity.y = atof(argv[7]);
velocity.z = atof(argv[8]);
}
Atom *a = new Atom(name,species,position,velocity);
const int atoms_nel_before = s->atoms.nel();
const int atoms_nel_before = s->atoms.nel();
if ( !(s->atoms.addAtom( a ) ) )
{
if ( ui->onpe0() )
......@@ -73,9 +73,9 @@ class AtomCmd : public Cmd
return 1;
}
const int atoms_nel_after = s->atoms.nel();
const int delta_nel = atoms_nel_after - atoms_nel_before;
const int delta_nel = atoms_nel_after - atoms_nel_before;
const int wf_nel = s->wf.nel();
s->wf.set_nel(wf_nel+delta_nel);
s->wf.update_occ(0.0);
if ( s->wfv != 0 )
......@@ -83,7 +83,7 @@ class AtomCmd : public Cmd
s->wfv->set_nel(wf_nel+delta_nel);
s->wfv->clear();
}
return 0;
}
};
......
src/AtomSet.C
......@@ -3,7 +3,7 @@
// AtomSet.C
//
////////////////////////////////////////////////////////////////////////////////
// $Id: AtomSet.C,v 1.16 2007-10-16 18:23:20 fgygi Exp $
// $Id: AtomSet.C,v 1.17 2007-10-19 16:24:03 fgygi Exp $
#include "AtomSet.h"
#include "Species.h"
......@@ -23,10 +23,10 @@ bool AtomSet::addSpecies(Species* sp, string name)
<< " is already defined" << endl;
return false;
}
const double rcps = 1.0;
sp->initialize(rcps);
// create new entry in species list
species_list.push_back(sp);
spname.push_back(name);
......@@ -34,7 +34,7 @@ bool AtomSet::addSpecies(Species* sp, string name)
na_.insert(map<string,int>::value_type(name,0));
atom_list.resize(atom_list.size()+1);