//RotatorToNewY takes a set of coordinates (mol) and a vector (y). It returns
//a rotation matrix that, when applied to mol, will rotate it around the Z axis
//in such a way that the projection of newy in the XY plane will be aligned with
//the Y axis.
func RotatorAroundZToNewY(newy *v3.Matrix) (*v3.Matrix, error) {
nr, nc := newy.Dims()
if nc != 3 || nr != 1 {
return nil, CError{"Wrong newy vector", []string{"RotatorAroundZtoNewY"}}
}
if nc != 3 {
return nil, CError{"Wrong mol vector", []string{"RotatorAroundZtoNewY"}} //this one doesn't seem reachable
}
gamma := math.Atan2(newy.At(0, 0), newy.At(0, 1))
singamma := math.Sin(gamma)
cosgamma := math.Cos(gamma)
operator := []float64{cosgamma, singamma, 0,
-singamma, cosgamma, 0,
0, 0, 1}
return v3.NewMatrix(operator)
}
//writePDBLine writes a line in PDB format from the data passed as a parameters. It takes the chain of the previous atom
//and returns the written line, the chain of the just-written atom, and error or nil.
func writePDBLine(atom *Atom, coord *v3.Matrix, bfact float64, chainprev string) (string, string, error) {
var ter string
var out string
if atom.Chain != chainprev {
ter = fmt.Sprint(out, "TER\n")
chainprev = atom.Chain
}
first := "ATOM"
if atom.Het {
first = "HETATM"
}
formatstring := "%-6s%5d %-3s %-4s%1s%4d %8.3f%8.3f%8.3f%6.2f%6.2f %2s \n"
//4 chars for the atom name are used when hydrogens are included.
//This has not been tested
if len(atom.Name) == 4 {
formatstring = strings.Replace(formatstring, "%-3s ", "%-4s", 1)
} else if len(atom.Name) > 4 {
return "", chainprev, CError{"Cant print PDB line", []string{"writePDBLine"}}
}
//"%-6s%5d %-3s %3s %1c%4d %8.3f%8.3f%8.3f%6.2f%6.2f %2s \n"
out = fmt.Sprintf(formatstring, first, atom.ID, atom.Name, atom.Molname, atom.Chain,
atom.MolID, coord.At(0, 0), coord.At(0, 1), coord.At(0, 2), atom.Occupancy, bfact, atom.Symbol)
out = strings.Join([]string{ter, out}, "")
return out, chainprev, nil
}
//RotatorToNewZ takes a matrix a row vector (newz).
//It returns a linear operator such that, when applied to a matrix mol ( with the operator on the right side)
//it will rotate mol such that the z axis is aligned with newz.
func RotatorToNewZ(newz *v3.Matrix) *v3.Matrix {
r, c := newz.Dims()
if c != 3 || r != 1 {
panic("Wrong newz vector")
}
normxy := math.Sqrt(math.Pow(newz.At(0, 0), 2) + math.Pow(newz.At(0, 1), 2))
theta := math.Atan2(normxy, newz.At(0, 2)) //Around the new y
phi := math.Atan2(newz.At(0, 1), newz.At(0, 0)) //First around z
psi := 0.000000000000 // second around z
sinphi := math.Sin(phi)
cosphi := math.Cos(phi)
sintheta := math.Sin(theta)
costheta := math.Cos(theta)
sinpsi := math.Sin(psi)
cospsi := math.Cos(psi)
operator := []float64{cosphi*costheta*cospsi - sinphi*sinpsi, -sinphi*cospsi - cosphi*costheta*sinpsi, cosphi * sintheta,
sinphi*costheta*cospsi + cosphi*sinpsi, -sinphi*costheta*sinpsi + cosphi*cospsi, sintheta * sinphi,
-sintheta * cospsi, sintheta * sinpsi, costheta}
finalop, _ := v3.NewMatrix(operator) //we are hardcoding opperator so it must have the right dimensions.
return finalop
}
//MakeWater Creates a water molecule at distance Angstroms from a2, in a direction that is angle radians from the axis defined by a1 and a2.
//Notice that the exact position of the water is not well defined when angle is not zero. One can always use the RotateAbout
//function to move the molecule to the desired location. If oxygen is true, the oxygen will be pointing to a2. Otherwise,
//one of the hydrogens will.
func MakeWater(a1, a2 *v3.Matrix, distance, angle float64, oxygen bool) *v3.Matrix {
water := v3.Zeros(3)
const WaterOHDist = 0.96
const WaterAngle = 52.25
const deg2rad = 0.0174533
w := water.VecView(0) //we first set the O coordinates
w.Copy(a2)
w.Sub(w, a1)
w.Unit(w)
dist := v3.Zeros(1)
dist.Sub(a1, a2)
a1a2dist := dist.Norm(0)
fmt.Println("ala2dist", a1a2dist, distance) ////////////////7777
w.Scale(distance+a1a2dist, w)
w.Add(w, a1)
for i := 0; i <= 1; i++ {
o := water.VecView(0)
w = water.VecView(i + 1)
w.Copy(o)
fmt.Println("w1", w) ////////
w.Sub(w, a2)
fmt.Println("w12", w) ///////////////
w.Unit(w)
fmt.Println("w4", w)
w.Scale(WaterOHDist+distance, w)
fmt.Println("w3", w, WaterOHDist, distance)
o.Sub(o, a2)
t, _ := v3.NewMatrix([]float64{0, 0, 1})
upp := v3.Zeros(1)
upp.Cross(w, t)
fmt.Println("upp", upp, w, t)
upp.Add(upp, o)
upp.Add(upp, a2)
//water.SetMatrix(3,0,upp)
w.Add(w, a2)
o.Add(o, a2)
sign := 1.0
if i == 1 {
sign = -1.0
}
temp, _ := RotateAbout(w, o, upp, deg2rad*WaterAngle*sign)
w.SetMatrix(0, 0, temp)
}
var v1, v2 *v3.Matrix
if angle != 0 {
v1 = v3.Zeros(1)
v2 = v3.Zeros(1)
v1.Sub(a2, a1)
v2.Copy(v1)
v2.Set(0, 2, v2.At(0, 2)+1) //a "random" modification. The idea is that its not colinear with v1
v3 := cross(v1, v2)
v3.Add(v3, a2)
water, _ = RotateAbout(water, a2, v3, angle)
}
if oxygen {
return water
}
//we move things so an hydrogen points to a2 and modify the distance acordingly.
e1 := water.VecView(0)
e2 := water.VecView(1)
e3 := water.VecView(2)
if v1 == nil {
v1 = v3.Zeros(1)
}
if v2 == nil {
v2 = v3.Zeros(1)
}
v1.Sub(e2, e1)
v2.Sub(e3, e1)
axis := cross(v1, v2)
axis.Add(axis, e1)
water, _ = RotateAbout(water, e1, axis, deg2rad*(180-WaterAngle))
v1.Sub(e1, a2)
v1.Unit(v1)
v1.Scale(WaterOHDist, v1)
water.AddVec(water, v1)
return water
}
//BuildInput builds an input for NWChem based int the data in atoms, coords and C.
//returns only error.
func (O *NWChemHandle) BuildInput(coords *v3.Matrix, atoms chem.AtomMultiCharger, Q *Calc) error {
//Only error so far
if atoms == nil || coords == nil {
return Error{ErrMissingCharges, NWChem, O.inputname, "", []string{"BuildInput"}, true}
}
if Q.Basis == "" {
log.Printf("no basis set assigned for NWChem calculation, will use the default %s, \n", O.defbasis)
Q.Basis = O.defbasis
}
if Q.Method == "" {
log.Printf("no method assigned for NWChem calculation, will use the default %s, \n", O.defmethod)
Q.Method = O.defmethod
Q.RI = true
}
if O.inputname == "" {
O.inputname = "gochem"
}
//The initial guess
vectors := fmt.Sprintf("output %s.movecs", O.inputname) //The initial guess
switch Q.Guess {
case "":
case "hcore": //This option is not a great idea, apparently.
vectors = fmt.Sprintf("input hcore %s", vectors)
default:
if !Q.OldMO {
//If the user gives something in Q.Guess but DOES NOT want an old MO to be used, I assume he/she wants to put whatever
//is in Q.Guess directly in the vector keyword. If you want the default put an empty string in Q.Guess.
vectors = fmt.Sprintf("%s %s", Q.Guess, vectors)
break
}
//I assume the user gave a basis set name in Q.Guess which I can use to project vectors from a previous run.
moname := getOldMO(O.previousMO)
if moname == "" {
break
}
if strings.ToLower(Q.Guess) == strings.ToLower(Q.Basis) {
//Useful if you only change functionals.
vectors = fmt.Sprintf("input %s %s", moname, vectors)
} else {
//This will NOT work if one assigns different basis sets to different atoms.
vectors = fmt.Sprintf("input project %s %s %s", strings.ToLower(Q.Guess), moname, vectors)
}
}
vectors = "vectors " + vectors
disp, ok := nwchemDisp[Q.Dispersion]
if !ok {
disp = "vdw 3"
}
tightness := ""
switch Q.SCFTightness {
case 1:
tightness = "convergence energy 5.000000E-08\n convergence density 5.000000E-09\n convergence gradient 1E-05"
case 2:
//NO idea if this will work, or the criteria will be stronger than the criteria for the intergral evaluation
//and thus the SCF will never converge. Delete when properly tested.
tightness = "convergence energy 1.000000E-10\n convergence density 5.000000E-11\n convergence gradient 1E-07"
}
//For now, the only convergence help I trust is to run a little HF calculation before and use the orbitals as a guess.
//It works quite nicely. When the NWChem people get their shit together and fix the bugs with cgmin and RI and cgmin and
//COSMO, cgmin will be a great option also.
scfiters := "iterations 60"
prevscf := ""
if Q.SCFConvHelp > 0 {
scfiters = "iterations 200"
if Q.Guess == "" {
prevscf = fmt.Sprintf("\nbasis \"3-21g\"\n * library 3-21g\nend\nset \"ao basis\" 3-21g\nscf\n maxiter 200\n vectors output hf.movecs\n %s\nend\ntask scf energy\n\n", strings.ToLower(mopacMultiplicity[atoms.Multi()]))
vectors = fmt.Sprintf("vectors input project \"3-21g\" hf.movecs output %s.movecs", O.inputname)
}
}
grid, ok := nwchemGrid[Q.Grid]
if !ok {
grid = "medium"
}
if Q.SCFTightness > 0 { //We need this if we want the SCF to converge.
grid = "xfine"
}
grid = fmt.Sprintf("grid %s", grid)
var err error
//Only cartesian constraints supported by now.
constraints := ""
if len(Q.CConstraints) > 0 {
constraints = "constraints\n fix atom"
for _, v := range Q.CConstraints {
constraints = fmt.Sprintf("%s %d", constraints, v+1) //goChem numbering starts from 0, apparently NWChem starts from 1, hence the v+1
}
constraints = constraints + "\nend"
}
cosmo := ""
if Q.Dielectric > 0 {
//SmartCosmo in a single-point means that do_gasphase False is used, nothing fancy.
if Q.Job.Opti || O.smartCosmo {
cosmo = fmt.Sprintf("cosmo\n dielec %4.1f\n do_gasphase False\nend", Q.Dielectric)
} else {
cosmo = fmt.Sprintf("cosmo\n dielec %4.1f\n do_gasphase True\nend", Q.Dielectric)
}
}
memory := ""
if Q.Memory != 0 {
memory = fmt.Sprintf("memory total %d mb", Q.Memory)
}
m := strings.ToLower(Q.Method)
method, ok := nwchemMethods[m]
if !ok {
method = "xtpss03 ctpss03"
}
method = fmt.Sprintf("xc %s", method)
task := "dft energy"
driver := ""
preopt := ""
jc := jobChoose{}
jc.opti = func() {
eprec := "" //The available presition is set to default except if tighter SCF convergene criteria are being used.
if Q.SCFTightness > 0 {
eprec = " eprec 1E-7\n"
}
if Q.Dielectric > 0 && O.smartCosmo {
//If COSMO is used, and O.SmartCosmo is enabled, we start the optimization with a rather loose SCF (the default).
//and use that denisty as a starting point for the next calculation. The idea is to
//avoid the gas phase calculation in COSMO.
//This procedure doesn't seem to help at all, and just using do_gasphase False appears to be good enough in my tests.
preopt = fmt.Sprintf("cosmo\n dielec %4.1f\n do_gasphase True\nend\n", Q.Dielectric)
preopt = fmt.Sprintf("%sdft\n iterations 100\n %s\n %s\n print low\nend\ntask dft energy\n", preopt, vectors, method)
vectors = fmt.Sprintf("vectors input %s.movecs output %s.movecs", O.inputname, O.inputname) //We must modify the initial guess so we use the vectors we have just generated
}
//The NWCHem optimizer is horrible. To try to get something out of it we use this 3-step optimization scheme where we try to compensate for the lack of
//variable trust radius in nwchem.
task = "dft optimize"
//First an optimization with very loose convergency and the standard trust radius.
driver = fmt.Sprintf("driver\n maxiter 200\n%s trust 0.3\n gmax 0.0500\n grms 0.0300\n xmax 0.1800\n xrms 0.1200\n xyz %s_prev\nend\ntask dft optimize", eprec, O.inputname)
//Then a second optimization with a looser convergency and a 0.1 trust radius
driver = fmt.Sprintf("%s\ndriver\n maxiter 200\n%s trust 0.1\n gmax 0.009\n grms 0.001\n xmax 0.04 \n xrms 0.02\n xyz %s_prev2\nend\ntask dft optimize", driver, eprec, O.inputname)
//Then the final optimization with a small trust radius and the NWChem default convergence criteria.
driver = fmt.Sprintf("%s\ndriver\n maxiter 200\n%s trust 0.05\n xyz %s\nend\n", driver, eprec, O.inputname)
//Old criteria (ORCA): gmax 0.003\n grms 0.0001\n xmax 0.004 \n xrms 0.002\n
}
Q.Job.Do(jc)
//////////////////////////////////////////////////////////////
//Now lets write the thing. Ill process/write the basis later
//////////////////////////////////////////////////////////////
file, err := os.Create(fmt.Sprintf("%s.nw", O.inputname))
if err != nil {
return Error{err.Error(), NWChem, O.inputname, "", []string{"os.Create", "BuildInput"}, true}
}
defer file.Close()
start := "start"
if O.restart {
start = "restart"
}
_, err = fmt.Fprintf(file, "%s %s\n", start, O.inputname)
//after this check its assumed that the file is ok.
if err != nil {
return Error{err.Error(), NWChem, O.inputname, "", []string{"fmt.Fprintf", "BuildInput"}, true}
}
fmt.Fprint(file, "echo\n") //echo input in the output.
fmt.Fprintf(file, "charge %d\n", atoms.Charge())
if memory != "" {
fmt.Fprintf(file, "%s\n", memory) //the memory
}
//Now the geometry:
//If we have cartesian constraints we give the directive noautoz to optimize in cartesian coordinates.
autoz := ""
if len(Q.CConstraints) > 0 {
autoz = "noautoz"
}
fmt.Fprintf(file, "geometry units angstroms noautosym %s\n", autoz)
elements := make([]string, 0, 5) //I will collect the different elements that are in the molecule using the same loop as the geometry.
for i := 0; i < atoms.Len(); i++ {
symbol := atoms.Atom(i).Symbol
//In the following if/else I try to set up basis for specific atoms. Not SO sure it works.
if isInInt(Q.HBAtoms, i) {
symbol = symbol + "1"
} else if isInInt(Q.LBAtoms, i) {
symbol = symbol + "2"
}
fmt.Fprintf(file, " %-2s %8.3f%8.3f%8.3f \n", symbol, coords.At(i, 0), coords.At(i, 1), coords.At(i, 2))
if !isInString(elements, symbol) {
elements = append(elements, symbol)
}
}
fmt.Fprintf(file, "end\n")
fmt.Fprintf(file, prevscf) //The preeliminar SCF if exists.
//The basis. First the ao basis (required)
decap := strings.ToLower //hoping to make the next for loop less ugly
basis := make([]string, 1, 2)
basis[0] = "\"ao basis\""
fmt.Fprintf(file, "basis \"large\" spherical\n") //According to the manual this fails with COSMO. The calculations dont crash. Need to compare energies and geometries with Turbomole in order to be sure.
for _, el := range elements {
if isInString(Q.HBElements, el) || strings.HasSuffix(el, "1") {
fmt.Fprintf(file, " %-2s library %s\n", el, decap(Q.HighBasis))
} else if isInString(Q.LBElements, el) || strings.HasSuffix(el, "2") {
fmt.Fprintf(file, " %-2s library %s\n", el, decap(Q.LowBasis))
} else {
fmt.Fprintf(file, " %-2s library %s\n", el, decap(Q.Basis))
}
}
fmt.Fprintf(file, "end\n")
fmt.Fprintf(file, "set \"ao basis\" large\n")
//Only Ahlrichs basis are supported for RI. USE AHLRICHS BASIS, PERKELE! :-)
//The only Ahlrichs J basis in NWchem appear to be equivalent to def2-TZVPP/J (orca nomenclature). I suppose that they are still faster
//than not using RI if the main basis is SVP. One can also hope that they are good enough if the main basis is QZVPP or something.
//(about the last point, it appears that in Turbomole, the aux basis also go up to TZVPP).
//This comment is based on the H, Be and C basis.
if Q.RI {
fmt.Fprint(file, "basis \"cd basis\"\n * library \"Ahlrichs Coulomb Fitting\"\nend\n")
}
//Now the geometry constraints. I kind of assume they are
if constraints != "" {
fmt.Fprintf(file, "%s\n", constraints)
}
fmt.Fprintf(file, preopt)
if cosmo != "" {
fmt.Fprintf(file, "%s\n", cosmo)
}
//The DFT block
fmt.Fprint(file, "dft\n")
fmt.Fprintf(file, " %s\n", vectors)
fmt.Fprintf(file, " %s\n", scfiters)
if tightness != "" {
fmt.Fprintf(file, " %s\n", tightness)
}
fmt.Fprintf(file, " %s\n", grid)
fmt.Fprintf(file, " %s\n", method)
if disp != "" {
fmt.Fprintf(file, " disp %s\n", disp)
}
if Q.Job.Opti {
fmt.Fprintf(file, " print convergence\n")
}
//task part
fmt.Fprintf(file, " mult %d\n", atoms.Multi())
fmt.Fprint(file, "end\n")
fmt.Fprintf(file, "%s", driver)
fmt.Fprintf(file, "task %s\n", task)
return nil
}
//BuildInput builds an input for Fermions++ based int the data in atoms, coords and C.
//returns only error.
func (O *FermionsHandle) BuildInput(coords *v3.Matrix, atoms chem.AtomMultiCharger, Q *Calc) error {
//Only error so far
if atoms == nil || coords == nil {
return Error{ErrMissingCharges, Fermions, O.inputname, "", []string{"BuildInput"}, true}
}
if Q.Basis == "" {
log.Printf("no basis set assigned for Fermions++ calculation, will used the default %s, \n", O.defbasis)
Q.Basis = O.defbasis
}
if Q.Method == "" {
log.Printf("no method assigned for Fermions++ calculation, will used the default %s, \n", O.defmethod)
Q.Method = O.defmethod
}
disp, ok := fermionsDisp[strings.ToLower(Q.Dispersion)]
if !ok {
disp = "disp_corr D3"
}
grid, ok := fermionsGrid[Q.Grid]
if !ok {
grid = "M3"
}
grid = fmt.Sprintf("GRID_RAD_TYPE %s", grid)
var err error
m := strings.ToLower(Q.Method)
method, ok := fermionsMethods[m]
if !ok {
method = "EXC XC_GGA_X_PBE_R\n ECORR XC_GGA_C_PBE"
}
task := "SinglePoint"
dloptions := ""
jc := jobChoose{}
jc.opti = func() {
task = "DLF_OPTIMIZE"
dloptions = fmt.Sprintf("*start::dlfind\n JOB std\n method l-bfgs\n trust_radius energy\n dcd %s.dcd\n maxcycle 300\n maxene 200\n coord_type cartesian\n*end\n", O.inputname)
//Only cartesian constraints supported by now.
if len(Q.CConstraints) > 0 {
dloptions = fmt.Sprintf("%s\n*start::dlf_constraints\n", dloptions)
for _, v := range Q.CConstraints {
dloptions = fmt.Sprintf("%s cart %d\n", dloptions, v+1) //fortran numbering, starts with 1.
}
dloptions = fmt.Sprintf("%s*end\n", dloptions)
}
}
Q.Job.Do(jc)
cosmo := ""
if Q.Dielectric > 0 {
cosmo = fmt.Sprintf("*start::solvate\n pcm_model cpcm\n epsilon %f\n cavity_model bondi\n*end\n", Q.Dielectric)
}
//////////////////////////////////////////////////////////////
//Now lets write the thing.
//////////////////////////////////////////////////////////////
file, err := os.Create(fmt.Sprintf("%s.in", O.inputname))
if err != nil {
return Error{ErrCantInput, Fermions, O.inputname, err.Error(), []string{"os.Create", "BuildInput"}, true}
}
defer file.Close()
//Start with the geometry part (coords, charge and multiplicity)
fmt.Fprintf(file, "*start::geo\n")
fmt.Fprintf(file, "%d %d\n", atoms.Charge(), atoms.Multi())
for i := 0; i < atoms.Len(); i++ {
fmt.Fprintf(file, "%-2s %8.3f%8.3f%8.3f\n", atoms.Atom(i).Symbol, coords.At(i, 0), coords.At(i, 1), coords.At(i, 2))
}
fmt.Fprintf(file, "*end\n\n")
fmt.Fprintf(file, "*start::sys\n")
fmt.Fprintf(file, " TODO %s\n", task)
fmt.Fprintf(file, " BASIS %s\n PC pure\n", strings.ToLower(Q.Basis))
fmt.Fprintf(file, " %s\n", method)
fmt.Fprintf(file, " %s\n", grid)
fmt.Fprintf(file, " %s\n", disp)
fmt.Fprintf(file, " %s\n", O.gpu)
if !Q.Job.Opti {
fmt.Fprintf(file, " INFO 2\n")
}
fmt.Fprintf(file, "*end\n\n")
fmt.Fprintf(file, "%s\n", cosmo)
fmt.Fprintf(file, "%s\n", dloptions)
return nil
}
//BuildInput builds an input for ORCA based int the data in atoms, coords and C.
//returns only error.
func (O *MopacHandle) BuildInput(coords *v3.Matrix, atoms chem.AtomMultiCharger, Q *Calc) error {
if strings.Contains(Q.Others, "RI") {
Q.Others = ""
}
//Only error so far
if atoms == nil || coords == nil {
return Error{ErrMissingCharges, Mopac, O.inputname, "", []string{"BuildInput"}, true}
}
ValidMethods := []string{"PM3", "PM6", "PM7", "AM1"}
if Q.Method == "" || !isInString(ValidMethods, Q.Method[0:3]) { //not found
log.Printf("no method assigned for MOPAC calculation, will used the default %s, \n", O.defmethod)
Q.Method = O.defmethod
}
opt := "" //Empty string means optimize
jc := jobChoose{}
jc.sp = func() {
opt = "1SCF"
}
jc.opti = func() {}
Q.Job.Do(jc)
//If this flag is set we'll look for a suitable MO file.
//If not found, we'll just use the default ORCA guess
hfuhf := "RHF"
if atoms.Multi() != 1 {
hfuhf = "UHF"
}
cosmo := ""
if Q.Dielectric > 0 {
cosmo = fmt.Sprintf("EPS=%2.1f RSOLV=1.3 LET DDMIN=0.0", Q.Dielectric) //The DDMIN ensures that the optimization continues when cosmo is used. From the manual I understand that it is OK
}
strict := ""
if Q.SCFTightness > 0 {
strict = "GNORM=0.01 RELSCF=0.00001"
}
multi := mopacMultiplicity[atoms.Multi()]
charge := fmt.Sprintf("CHARGE=%d", atoms.Charge())
MainOptions := []string{hfuhf, Q.Method, strict, opt, cosmo, charge, multi, Q.Others, "BONDS AUX\n"}
mainline := strings.Join(MainOptions, " ")
//Now lets write the thing
if O.inputname == "" {
O.inputname = "input"
}
file, err := os.Create(fmt.Sprintf("%s.mop", O.inputname))
if err != nil {
return Error{ErrCantInput, Mopac, O.inputname, "", []string{"os.Create", "BuildInput"}, true}
}
defer file.Close()
if _, err = fmt.Fprint(file, "* ===============================\n* Input file for Mopac\n* ===============================\n"); err != nil {
return Error{ErrCantInput, Mopac, O.inputname, "", []string{"BuildInput"}, true}
//After this check I just assume the file is ok and dont check again.
}
fmt.Fprint(file, mainline)
fmt.Fprint(file, "\n")
fmt.Fprint(file, "Mopac file generated by gochem :-)\n")
//now the coordinates
for i := 0; i < atoms.Len(); i++ {
tag := 1
if isInInt(Q.CConstraints, i) {
tag = 0
}
// fmt.Println(atoms.Atom(i).Symbol)
fmt.Fprintf(file, "%-2s %8.5f %d %8.5f %d %8.5f %d\n", atoms.Atom(i).Symbol, coords.At(i, 0), tag, coords.At(i, 1), tag, coords.At(i, 2), tag)
}
fmt.Fprintf(file, "\n")
return nil
}