NamdOneTools.h File Reference

#include "common.h"
#include "NamdTypes.h"
#include "Vector.h"
#include "PDB.h"
#include "Molecule.h"

Go to the source code of this file.

Functions
void	read_binary_coors (char *fname, PDB *pdbobj)
void	read_binary_file (const char *fname, Vector *vels, int n)
void	vec_rotation_matrix (BigReal angle, Vector v, BigReal m[])
Vector	mat_multiply_vec (const Vector &v, BigReal m[])

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Function Documentation

Vector mat_multiply_vec (  const Vector &  v, BigReal  m[] )

Definition at line 232 of file NamdOneTools.C. References Vector::x, Vector::y, and Vector::z. Referenced by ComputeRestraints::doForce(). { return Vector( m[0]*v.x + m[1]*v.y + m[2]*v.z, m[3]*v.x + m[4]*v.y + m[5]*v.z, m[6]*v.x + m[7]*v.y + m[8]*v.z ); }

void read_binary_coors (  char *  fname, PDB *  pdbobj )

Copyright (c) 1995, 1996, 1997, 1998, 1999, 2000 by The Board of Trustees of the University of Illinois. All rights reserved. Definition at line 34 of file NamdOneTools.C. { Vector *newcoords; // Array of vectors to hold coordinates from file // Allocate an array to hold the new coordinates newcoords = new Vector[pdbobj->num_atoms()]; // Read the coordinate from the file read_binary_file(fname,newcoords,pdbobj->num_atoms()); // Set the coordinates in the PDB object to the new coordinates pdbobj->set_all_positions(newcoords); // Clean up delete [] newcoords; } // END OF FUNCTION read_binary_coors()

void read_binary_file (  const char *  fname, Vector *  vels, int  n )

Definition at line 52 of file NamdOneTools.C. References Fclose(), Fopen(), iINFO(), int32, iout, iWARN(), and NAMD_die(). Referenced by read_binary_coors(). { int32 filen; // Number of atoms read from file FILE *fp; // File descriptor int needToFlip = 0; iout << iINFO << "Reading from binary file " << fname << "\n" << endi; // Open the file and die if the open fails if ( (fp = Fopen(fname, "rb")) == NULL) { char errmsg[256]; sprintf(errmsg, "Unable to open binary file %s", fname); NAMD_die(errmsg); } // read the number of coordinates in this file if (fread(&filen, sizeof(int32), 1, fp) != (size_t)1) { char errmsg[256]; sprintf(errmsg, "Error reading binary file %s", fname); NAMD_die(errmsg); } // read the number of coordinates in this file // check for palindromic number of atoms char lenbuf[4]; memcpy(lenbuf, (const char *)&filen, 4); char tmpc; tmpc = lenbuf[0]; lenbuf[0] = lenbuf[3]; lenbuf[3] = tmpc; tmpc = lenbuf[1]; lenbuf[1] = lenbuf[2]; lenbuf[2] = tmpc; if ( ! memcmp((const char *)&filen, lenbuf, 4) ) { iout << iWARN << "Number of atoms in binary file " << fname << " is palindromic, assuming same endian.\n" << endi; } // Die if this doesn't match the number in our system if (filen != n) { needToFlip = 1; memcpy((char *)&filen, lenbuf, 4); } if (filen != n) { char errmsg[256]; sprintf(errmsg, "Incorrect atom count in binary file %s", fname); NAMD_die(errmsg); } if (fread(data, sizeof(Vector), n, fp) != (size_t)n) { char errmsg[256]; sprintf(errmsg, "Error reading binary file %s", fname); NAMD_die(errmsg); } Fclose(fp); if (needToFlip) { iout << iWARN << "Converting binary file " << fname << "\n" << endi; int i; char *cdata = (char *) data; for ( i=0; i<3*n; ++i, cdata+=8 ) { char tmp0, tmp1, tmp2, tmp3; tmp0 = cdata[0]; tmp1 = cdata[1]; tmp2 = cdata[2]; tmp3 = cdata[3]; cdata[0] = cdata[7]; cdata[1] = cdata[6]; cdata[2] = cdata[5]; cdata[3] = cdata[4]; cdata[7] = tmp0; cdata[6] = tmp1; cdata[5] = tmp2; cdata[4] = tmp3; } } }

void vec_rotation_matrix (  BigReal  angle, Vector  v, BigReal  m[] )

Definition at line 132 of file NamdOneTools.C. References BigReal, Vector::length(), PI, Vector::x, Vector::y, and Vector::z. Referenced by ComputeRestraints::doForce(). { /* This function contributed by Erich Boleyn (erich@uruk.org) */ BigReal mag, s, c; BigReal xx, yy, zz, xy, yz, zx, xs, ys, zs, one_c; s = sin(angle * PI/180.0); c = cos(angle * PI/180.0); mag = v.length(); if (mag == 0.0) { /* generate an identity matrix and return */ for ( int i = 0; i < 9; ++i ) m[i] = 0.0; m[0] = m[4] = m[8] = 1.0; return; } // normalize the vector v /= mag; /* * Arbitrary axis rotation matrix. * * This is composed of 5 matrices, Rz, Ry, T, Ry', Rz', multiplied * like so: Rz * Ry * T * Ry' * Rz'. T is the final rotation * (which is about the X-axis), and the two composite transforms * Ry' * Rz' and Rz * Ry are (respectively) the rotations necessary * from the arbitrary axis to the X-axis then back. They are * all elementary rotations. * * Rz' is a rotation about the Z-axis, to bring the axis vector * into the x-z plane. Then Ry' is applied, rotating about the * Y-axis to bring the axis vector parallel with the X-axis. The * rotation about the X-axis is then performed. Ry and Rz are * simply the respective inverse transforms to bring the arbitrary * axis back to it's original orientation. The first transforms * Rz' and Ry' are considered inverses, since the data from the * arbitrary axis gives you info on how to get to it, not how * to get away from it, and an inverse must be applied. * * The basic calculation used is to recognize that the arbitrary * axis vector (x, y, z), since it is of unit length, actually * represents the sines and cosines of the angles to rotate the * X-axis to the same orientation, with theta being the angle about * Z and phi the angle about Y (in the order described above) * as follows: * * cos ( theta ) = x / sqrt ( 1 - z^2 ) * sin ( theta ) = y / sqrt ( 1 - z^2 ) * * cos ( phi ) = sqrt ( 1 - z^2 ) * sin ( phi ) = z * * Note that cos ( phi ) can further be inserted to the above * formulas: * * cos ( theta ) = x / cos ( phi ) * sin ( theta ) = y / sin ( phi ) * * ...etc. Because of those relations and the standard trigonometric * relations, it is pssible to reduce the transforms down to what * is used below. It may be that any primary axis chosen will give the * same results (modulo a sign convention) using thie method. * * Particularly nice is to notice that all divisions that might * have caused trouble when parallel to certain planes or * axis go away with care paid to reducing the expressions. * After checking, it does perform correctly under all cases, since * in all the cases of division where the denominator would have * been zero, the numerator would have been zero as well, giving * the expected result. */ // store matrix in (row, col) form, i.e., m(row,col) = m[row*3+col] xx = v.x * v.x; yy = v.y * v.y; zz = v.z * v.z; xy = v.x * v.y; yz = v.y * v.z; zx = v.z * v.x; xs = v.x * s; ys = v.y * s; zs = v.z * s; one_c = 1.0 - c; m[0] = (one_c * xx) + c; m[1] = (one_c * xy) - zs; m[2] = (one_c * zx) + ys; m[3] = (one_c * xy) + zs; m[4] = (one_c * yy) + c; m[5] = (one_c * yz) - xs; m[6] = (one_c * zx) - ys; m[7] = (one_c * yz) + xs; m[8] = (one_c * zz) + c; }

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