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colvartypes.h File Reference

#include <cmath>

Go to the source code of this file.

Classes

class  colvarmodule::rvector
 1-dimensional vector of real numbers with three components More...
class  colvarmodule::vector1d< T, length >
 Arbitrary size array (one dimensions) suitable for linear algebra operations (i.e. for floating point numbers it can be used with library functions). More...
class  colvarmodule::matrix2d< T, outer_length, inner_length >
 Arbitrary size array (two dimensions) suitable for linear algebra operations (i.e. for floating point numbers it can be used with library functions). More...
class  colvarmodule::rmatrix
 2-dimensional array of real numbers with three components along each dimension (works with colvarmodule::rvector) More...
class  colvarmodule::quaternion
 1-dimensional vector of real numbers with four components and a quaternion algebra More...
class  colvarmodule::rotation
 A rotation between two sets of coordinates (for the moment a wrapper for colvarmodule::quaternion). More...

Defines

#define PI   3.14159265358979323846

Functions

cvm::rvector operator * (cvm::rmatrix const &m, cvm::rvector const &r)
void jacobi (cvm::real **a, int n, cvm::real d[], cvm::real **v, int *nrot)
 Numerical recipes diagonalization.
void eigsrt (cvm::real d[], cvm::real **v, int n)
 Eigenvector sort.
void transpose (cvm::real **v, int n)
 Transpose the matrix.

Define Documentation

#define PI   3.14159265358979323846
 

Definition at line 7 of file colvartypes.h.

Referenced by colvar::dihedPC::apply_force(), colvar::dihedral::calc_force_invgrads(), colvar::angle::calc_Jacobian_derivative(), colvar::dihedPC::calc_value(), calcOverlap(), colvar::colvar(), colvarbias_meta::colvarbias_meta(), CrosstermElem::computeForce(), colvarmodule::rotation::cos_theta(), crossterm_setup(), colvarmodule::quaternion::dist2(), colvarmodule::quaternion::dist2_grad(), ComputeLCPO::doForce(), ComputeEField::doForce(), colvarmodule::rotation::dspin_angle_dq(), GromacsTopFile::GromacsTopFile(), proc_getdihedral(), colvarbias_meta::read_hill(), and vec_rotation_matrix().

Function Documentation

void eigsrt (  cvm::real  d[],
cvm::real **  v,
int  n
) 
 

Eigenvector sort.

Definition at line 1326 of file colvarmodule.C.

References j.

01327 {
01328   int k,j,i;
01329   cvm::real p;
01330 
01331   for (i=0;i<n;i++) {
01332     p=d[k=i];
01333     for (j=i+1;j<n;j++)
01334       if (d[j] >= p) p=d[k=j];
01335     if (k != i) {
01336       d[k]=d[i];
01337       d[i]=p;
01338       for (j=0;j<n;j++) {
01339         p=v[j][i];
01340         v[j][i]=v[j][k];
01341         v[j][k]=p;
01342       }
01343     }
01344   }
01345 }

void jacobi (  cvm::real **  a,
int  n,
cvm::real  d[],
cvm::real **  v,
int *  nrot
) 
 

Numerical recipes diagonalization.

Definition at line 1245 of file colvarmodule.C.

References colvarmodule::fatal_error(), j, and ROTATE.

01246 {
01247   int j,iq,ip,i;
01248   cvm::real tresh,theta,tau,t,sm,s,h,g,c;
01249 
01250   std::vector<cvm::real> b (n, 0.0);
01251   std::vector<cvm::real> z (n, 0.0);
01252 
01253   for (ip=0;ip<n;ip++) {
01254     for (iq=0;iq<n;iq++) v[ip][iq]=0.0;
01255     v[ip][ip]=1.0;
01256   }
01257   for (ip=0;ip<n;ip++) {
01258     b[ip]=d[ip]=a[ip][ip];
01259     z[ip]=0.0;
01260   }
01261   *nrot=0;
01262   for (i=0;i<=50;i++) {
01263     sm=0.0;
01264     for (ip=0;ip<n-1;ip++) {
01265       for (iq=ip+1;iq<n;iq++)
01266         sm += std::fabs(a[ip][iq]);
01267     }
01268     if (sm == 0.0) {
01269       return;
01270     }
01271     if (i < 4)
01272       tresh=0.2*sm/(n*n);
01273     else
01274       tresh=0.0;
01275     for (ip=0;ip<n-1;ip++) {
01276       for (iq=ip+1;iq<n;iq++) {
01277         g=100.0*std::fabs(a[ip][iq]);
01278         if (i > 4 && (cvm::real)(std::fabs(d[ip])+g) == (cvm::real)std::fabs(d[ip])
01279             && (cvm::real)(std::fabs(d[iq])+g) == (cvm::real)std::fabs(d[iq]))
01280           a[ip][iq]=0.0;
01281         else if (std::fabs(a[ip][iq]) > tresh) {
01282           h=d[iq]-d[ip];
01283           if ((cvm::real)(std::fabs(h)+g) == (cvm::real)std::fabs(h))
01284             t=(a[ip][iq])/h;
01285           else {
01286             theta=0.5*h/(a[ip][iq]);
01287             t=1.0/(std::fabs(theta)+std::sqrt(1.0+theta*theta));
01288             if (theta < 0.0) t = -t;
01289           }
01290           c=1.0/std::sqrt(1+t*t);
01291           s=t*c;
01292           tau=s/(1.0+c);
01293           h=t*a[ip][iq];
01294           z[ip] -= h;
01295           z[iq] += h;
01296           d[ip] -= h;
01297           d[iq] += h;
01298           a[ip][iq]=0.0;
01299           for (j=0;j<=ip-1;j++) {
01300             ROTATE(a,j,ip,j,iq)
01301               }
01302           for (j=ip+1;j<=iq-1;j++) {
01303             ROTATE(a,ip,j,j,iq)
01304               }
01305           for (j=iq+1;j<n;j++) {
01306             ROTATE(a,ip,j,iq,j)
01307               }
01308           for (j=0;j<n;j++) {
01309             ROTATE(v,j,ip,j,iq)
01310               }
01311           ++(*nrot);
01312         }
01313       }
01314     }
01315     for (ip=0;ip<n;ip++) {
01316       b[ip] += z[ip];
01317       d[ip]=b[ip];
01318       z[ip]=0.0;
01319     }
01320   }
01321   cvm::fatal_error ("Too many iterations in routine jacobi.\n");
01322 }

cvm::rvector operator * (  cvm::rmatrix const &  m,
cvm::rvector const &  r
)  [inline]
 

Definition at line 531 of file colvartypes.h.

References colvarmodule::rmatrix::xx(), colvarmodule::rmatrix::xy(), colvarmodule::rmatrix::xz(), colvarmodule::rmatrix::yx(), colvarmodule::rmatrix::yy(), colvarmodule::rmatrix::yz(), colvarmodule::rmatrix::zx(), colvarmodule::rmatrix::zy(), and colvarmodule::rmatrix::zz().

00533 {
00534   return cvm::rvector (m.xx()*r.x + m.xy()*r.y + m.xz()*r.z,
00535                        m.yx()*r.x + m.yy()*r.y + m.yz()*r.z,
00536                        m.zx()*r.x + m.zy()*r.y + m.zz()*r.z);
00537 }

void transpose (  cvm::real **  v,
int  n
) 
 

Transpose the matrix.

Definition at line 1348 of file colvarmodule.C.

References j.

01349 {
01350   cvm::real p;
01351   for (int i=0;i<n;i++) {
01352     for (int j=i+1;j<n;j++) {
01353       p=v[i][j];
01354       v[i][j]=v[j][i];
01355       v[j][i]=p;
01356     }
01357   }
01358 }

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