// Converts the RESIDUE_POINTER block into an array, index by atom, that
// provides the residue number (starting at 0) for each atom.
func makeResidueMap(mol *amber.System) []int {
residueList := amber.VectorAsIntArray(mol.Blocks["RESIDUE_POINTER"])
residueMap := make([]int, mol.NumAtoms()) // len(residueList) == #resideus
for res_i := 1; res_i < len(residueList); res_i++ {
a := residueList[res_i-1] - 1 // Fortran starts counting at 1
b := residueList[res_i] - 1
for i := a; i < b; i++ {
residueMap[i] = res_i - 1
}
}
// RESIDUE_POINTER doesn't specify the last residue because that's implied
numResidues := mol.NumResidues()
for i := residueList[numResidues-1] - 1; i < len(residueMap); i++ {
residueMap[i] = numResidues - 1
}
return residueMap
}
// Calculates the nonbonded energies for a single snapshot.
// Results are returned through reqOutCh.
func calcSingleTrjFrame(mol *amber.System, params NonbondedParamsCache, coords []float32, frame int, bondType []uint8, residueMap []int, reqOutCh chan []float64, ch chan int) {
var request EnergyCalcRequest
request.Molecule = mol
request.Frame = frame
request.NBParams = params
request.Coords = coords
request.BondType = bondType
request.ResidueMap = residueMap
var ok bool
request.Decomp = <-decompFreeList
if !ok {
fmt.Println("Allocating a new decomposition matrix buffer.")
request.Decomp = make([]float64, mol.NumResidues()*mol.NumResidues())
}
// Since we're reusing buffers, we need to zero them out
for i := 0; i < len(request.Decomp); i++ {
request.Decomp[i] = 0.0
}
/* //DEBUG: print first few coordinates
fmt.Printf("%d [%d]:", frame, len(coords));
for i := 0; i < 6; i++ {
fmt.Printf(" %f", coords[i]);
}
fmt.Println();
*/
elec := Electro(&request)
vdw := LennardJones(&request)
if math.IsNaN(elec) || math.IsNaN(vdw) {
fmt.Println("Weird energies. Does your trajectory have boxes but your prmtop doesn't, or vice versa?")
os.Exit(1)
}
fmt.Printf("%d: Electrostatic: %f vdW: %f Total: %f\n", frame, elec, vdw, elec+vdw)
// Release coords buffer so it can be reused
amber.ReleaseCoordsBuffer(coords)
// Send request to listening something that will probably average the decomp matrix
// but could in theory do whatever it wants.
reqOutCh <- request.Decomp
// Return frame ID through channel
//ch <- frame
}
// We want to be able to quickly look up if two atoms are bonded.
// To do this, make a matrix for all atom pairs such that
// M[numAtoms*i+j] & bondtypeflag != 0
func makeBondTypeTable(mol *amber.System) []uint8 {
numAtoms := mol.NumAtoms()
bondType := make([]uint8, numAtoms*numAtoms)
bondsBlocks := []string{"BONDS_INC_HYDROGEN", "BONDS_WITHOUT_HYDROGEN"}
for _, blockName := range bondsBlocks {
bonds := amber.VectorAsIntArray(mol.Blocks[blockName])
// atom_i atom_j indexintostuff
// These are actually coordinate array indices, not atom indices
for i := 0; i < len(bonds); i += 3 {
a, b := bonds[i]/3, bonds[i+1]/3
bondType[numAtoms*a+b] |= BOND
bondType[numAtoms*b+a] |= BOND
}
}
angleBlocks := []string{"ANGLES_WITHOUT_HYDROGEN", "ANGLES_INC_HYDROGEN"}
for _, blockName := range angleBlocks {
angles := amber.VectorAsIntArray(mol.Blocks[blockName])
// atom_i atom_j atom_k indexintostuff
for i := 0; i < len(angles); i += 4 {
a, b := angles[i]/3, angles[i+2]/3
bondType[numAtoms*a+b] |= ANGLE
bondType[numAtoms*b+a] |= ANGLE
}
}
dihedBlocks := []string{"DIHEDRALS_INC_HYDROGEN", "DIHEDRALS_WITHOUT_HYDROGEN"}
for _, blockName := range dihedBlocks {
diheds := amber.VectorAsIntArray(mol.Blocks[blockName])
// atom_i atom_j atom_k atom_l indexintostuff
for i := 0; i < len(diheds); i += 5 {
// Fourth coordinate index is negative if this is an improper
a, b := amber.Abs(diheds[i]/3), amber.Abs(diheds[i+3]/3)
bondType[numAtoms*a+b] |= DIHEDRAL
bondType[numAtoms*b+a] |= DIHEDRAL
}
}
return bondType
}