Python printAtomsXYZ示例

示例#1

文件： minpermdist_stochastic.py 项目： cjforman/pele

def test(X1, X2, lj, atomtypes=None, fname="lj.xyz", minPermDist=MinPermDistCluster()): # pragma: no cover
    if not atomtypes: atomtypes = ["LA"]
    import copy
    natoms = len(X1) / 3
        
    X1i = copy.copy(X1)
    X2i = copy.copy(X2)
    
    printlist = []
    printlist.append((X2.copy(), "X2 initial"))
    printlist.append((X1.copy(), "X1 initial"))


    distinit = np.linalg.norm(X1-X2)
    print "distinit", distinit

    (dist, X1, X2) = minPermDist(X1,X2)
    distfinal = np.linalg.norm(X1-X2)
    print "dist returned    ", dist
    print "dist from coords ", distfinal
    print "initial energies (post quench)", lj.getEnergy(X1i), lj.getEnergy(X2i)
    print "final energies                ", lj.getEnergy(X1), lj.getEnergy(X2)

    printlist.append((X1.copy(), "X1 final"))
    printlist.append((X2.copy(), "X2 final"))


    import pele.printing.print_atoms_xyz as printxyz
    with open(fname, "w") as fout:
        for xyz, line2 in printlist:
            printxyz.printAtomsXYZ(fout, xyz, line2=line2 +" "+ str(lj.getEnergy(xyz)))

示例#2

文件： minpermdist_stochastic.py 项目： borislavujo/pele

def test(X1, X2, lj, atomtypes=["LA"], permlist = None, fname = "lj.xyz",
         minPermDist=minPermDistStochastic):
    import copy
    natoms = len(X1) / 3
    if permlist == None:
        permlist = [range(natoms)]
    
    X1i = copy.copy(X1)
    X2i = copy.copy(X2)
    
    printlist = []
    printlist.append((X2.copy(), "X2 initial"))
    printlist.append((X1.copy(), "X1 initial"))


    distinit = np.linalg.norm(X1-X2)
    print "distinit", distinit

    (dist, X1, X2) = minPermDist(X1,X2, permlist=permlist)
    distfinal = np.linalg.norm(X1-X2)
    print "dist returned    ", dist
    print "dist from coords ", distfinal
    print "initial energies (post quench)", lj.getEnergy(X1i), lj.getEnergy(X2i)
    print "final energies                ", lj.getEnergy(X1), lj.getEnergy(X2)

    printlist.append((X1.copy(), "X1 final"))
    printlist.append((X2.copy(), "X2 final"))


    import pele.printing.print_atoms_xyz as printxyz
    with open(fname, "w") as fout:
        for xyz, line2 in printlist:
            printxyz.printAtomsXYZ(fout, xyz, line2=line2 +" "+ str(lj.getEnergy(xyz)))

示例#3

文件： minpermdist_rbmol.py 项目： jdf43/pele

def test(coords1, coords2, mysys, permlist):
    printlist = []
    printlist.append((coords1.copy(), "after quench"))
    printlist.append((coords2.copy(), "after quench"))
    coords2in = coords2.copy()
    coords1in = coords1.copy()

    distinit = getDistaa(coords1, coords2, mysys)
    print "distinit", distinit

    (dist, coords1, coords2) = minPermDistRBMol(coords1, coords2, mysys, permlist=permlist)
    distfinal = getDistaa(coords1, coords2, mysys)
    print "dist returned    ", dist
    print "dist from coords ", distfinal
    print "coords2 initial energy", mysys.getEnergy(coords2in)
    print "coords2 final energy  ", mysys.getEnergy(coords2)
    print "coords1 initial energy", mysys.getEnergy(coords1in)
    print "coords1 final energy  ", mysys.getEnergy(coords1)

    printlist.append((coords1.copy(), "coords1 after mindist"))
    printlist.append((coords2.copy(), "coords2 after mindist"))
    import pele.printing.print_atoms_xyz as printxyz

    with open("otp.xyz", "w") as fout:
        for coords, line2 in printlist:
            xyz = mysys.getxyz(coords)
            printxyz.printAtomsXYZ(fout, xyz, line2=line2, atom_type=["N", "O", "O"])

    return dist, coords1, coords2

示例#4

文件： minpermdist.py 项目： borislavujo/pele

def main():
    natoms = 9
    X1 = np.random.uniform(-1,1,[natoms*3])*(float(natoms))**(1./3)
    X2 = np.random.uniform(-1,1,[natoms*3])*(float(natoms))**(1./3)

    #X1 = np.array( [ 0., 0., 0., 1., 0., 0., 0., 0., 1.,] )
    #X2 = np.array( [ 0., 0., 0., 1., 0., 0., 0., 1., 0.,] )
    import copy
    X1i = copy.copy(X1)
    X2i = copy.copy(X2)

    distinit = np.linalg.norm(X1-X2)
    print "distinit", distinit

    (dist, X1, X2) = minPermDistLong(X1,X2)
    distfinal = np.linalg.norm(X1-X2)
    print "dist returned    ", dist
    print "dist from coords ", distfinal

    import pele.printing.print_atoms_xyz as printxyz
    with open("out.xyz", "w") as fout:
        CoMToOrigin(X1i)
        CoMToOrigin(X2i)
        printxyz.printAtomsXYZ(fout, X1i )
        printxyz.printAtomsXYZ(fout, X2i )
        printxyz.printAtomsXYZ(fout, X1 )
        printxyz.printAtomsXYZ(fout, X2 )

示例#5

def test(X1,
         X2,
         lj,
         atomtypes=None,
         fname="lj.xyz",
         minPermDist=MinPermDistCluster()):  # pragma: no cover
    if not atomtypes: atomtypes = ["LA"]
    import copy
    natoms = len(X1) / 3

    X1i = copy.copy(X1)
    X2i = copy.copy(X2)

    printlist = []
    printlist.append((X2.copy(), "X2 initial"))
    printlist.append((X1.copy(), "X1 initial"))

    distinit = np.linalg.norm(X1 - X2)
    print("distinit", distinit)

    (dist, X1, X2) = minPermDist(X1, X2)
    distfinal = np.linalg.norm(X1 - X2)
    print("dist returned    ", dist)
    print("dist from coords ", distfinal)
    print("initial energies (post quench)", lj.getEnergy(X1i),
          lj.getEnergy(X2i))
    print("final energies                ", lj.getEnergy(X1), lj.getEnergy(X2))

    printlist.append((X1.copy(), "X1 final"))
    printlist.append((X2.copy(), "X2 final"))

    import pele.printing.print_atoms_xyz as printxyz
    with open(fname, "w") as fout:
        for xyz, line2 in printlist:
            printxyz.printAtomsXYZ(fout,
                                   xyz,
                                   line2=line2 + " " + str(lj.getEnergy(xyz)))