diff --git a/doc/src/compute_orientorder_atom.txt b/doc/src/compute_orientorder_atom.txt index 7327a7b1d3..da14c866bd 100644 --- a/doc/src/compute_orientorder_atom.txt +++ b/doc/src/compute_orientorder_atom.txt @@ -19,6 +19,8 @@ keyword = {cutoff} or {nnn} or {degrees} or {components} {cutoff} value = distance cutoff {nnn} value = number of nearest neighbors {degrees} values = nlvalues, l1, l2,... + {wl} value = yes or no + {wl/hat} value = yes or no {components} value = ldegree :pre :ule @@ -27,7 +29,8 @@ keyword = {cutoff} or {nnn} or {degrees} or {components} compute 1 all orientorder/atom compute 1 all orientorder/atom degrees 5 4 6 8 10 12 nnn NULL cutoff 1.5 -compute 1 all orientorder/atom degrees 4 6 components 6 nnn NULL cutoff 3.0 :pre +compute 1 all orientorder/atom wl/hat yes +compute 1 all orientorder/atom components 6 :pre [Description:] @@ -48,7 +51,7 @@ neighbors of the central atom. The angles theta and phi are the standard spherical polar angles defining the direction of the bond vector {rij}. The second equation defines {Ql}, which is a -rotationally invariant scalar quantity obtained by summing +rotationally invariant non-negative amplitude obtained by summing over all the components of degree {l}. The optional keyword {cutoff} defines the distance cutoff @@ -63,7 +66,7 @@ specified distance cutoff are used. The optional keyword {degrees} defines the list of order parameters to be computed. The first argument {nlvalues} is the number of order -parameters. This is followed by that number of integers giving the +parameters. This is followed by that number of non-negative integers giving the degree of each order parameter. Because {Q}2 and all odd-degree order parameters are zero for atoms in cubic crystals (see "Steinhardt"_#Steinhardt), the default order parameters are {Q}4, @@ -71,7 +74,20 @@ parameters are zero for atoms in cubic crystals (see = sqrt(7/3)/8 = 0.19094.... The numerical values of all order parameters up to {Q}12 for a range of commonly encountered high-symmetry structures are given in Table I of "Mickel et -al."_#Mickel. +al."_#Mickel, and these can be reproduced with this compute + +The optional keyword {wl} will output the third-order invariants {Wl} +(see Eq. 1.4 in "Steinhardt"_#Steinhardt) for the same degrees as +for the {Ql} parameters. For the FCC crystal with {nnn} =12, +{W}4 = -sqrt(14/143).(49/4096)/Pi^1.5 = -0.0006722136... + +The optional keyword {wl/hat} will output the normalized third-order +invariants {Wlhat} (see Eq. 2.2 in "Steinhardt"_#Steinhardt) +for the same degrees as for the {Ql} parameters. For the FCC crystal +with {nnn} =12, {W}4hat = -7/3*sqrt(2/429) = -0.159317...The numerical +values of {Wlhat} for a range of commonly encountered high-symmetry +structures are given in Table I of "Steinhardt"_#Steinhardt, and these +can be reproduced with this keyword. The optional keyword {components} will output the components of the normalized complex vector {Ybar_lm} of degree {ldegree}, which must be @@ -82,7 +98,7 @@ particles, as discussed in "ten Wolde"_#tenWolde2. The value of {Ql} is set to zero for atoms not in the specified compute group, as well as for atoms that have less than -{nnn} neighbors within the distance cutoff. +{nnn} neighbors within the distance cutoff, unless {nnn} is NULL. The neighbor list needed to compute this quantity is constructed each time the calculation is performed (i.e. each time a snapshot of atoms @@ -108,6 +124,12 @@ This compute calculates a per-atom array with {nlvalues} columns, giving the {Ql} values for each atom, which are real numbers on the range 0 <= {Ql} <= 1. +If the keyword {wl} is set to yes, then the {Wl} values for each +atom will be added to the output array, which are real numbers. + +If the keyword {wl/hat} is set to yes, then the {Wl_hat} +values for each atom will be added to the output array, which are real numbers. + If the keyword {components} is set, then the real and imaginary parts of each component of (normalized) {Ybar_lm} will be added to the output array in the following order: Re({Ybar_-m}) Im({Ybar_-m}) @@ -130,7 +152,8 @@ hexorder/atom"_compute_hexorder_atom.html [Default:] The option defaults are {cutoff} = pair style cutoff, {nnn} = 12, -{degrees} = 5 4 6 8 10 12 i.e. {Q}4, {Q}6, {Q}8, {Q}10, and {Q}12. +{degrees} = 5 4 6 8 10 12 i.e. {Q}4, {Q}6, {Q}8, {Q}10, and {Q}12, +{wl} = no, {wl/hat} = no, and {components} off :line diff --git a/examples/steinhardt/in.bcc b/examples/steinhardt/in.bcc new file mode 100644 index 0000000000..a0348fdcd9 --- /dev/null +++ b/examples/steinhardt/in.bcc @@ -0,0 +1,91 @@ +# Steinhardt-Nelson bond orientational order parameters for BCC + +variable rcut equal 3.0 + +boundary p p p + +atom_style atomic +neighbor 0.3 bin +neigh_modify delay 5 + +# create geometry + +lattice bcc 1.0 +region box block 0 3 0 3 0 3 +create_box 1 box +create_atoms 1 box + +mass 1 1.0 + +# LJ potentials + +pair_style lj/cut ${rcut} +pair_coeff * * 1.0 1.0 ${rcut} + +# 14 neighbors, perfect crystal + +compute qlwlhat all orientorder/atom degrees 6 2 4 6 8 10 12 nnn 14 wl/hat yes +compute avql all reduce ave c_qlwlhat[1] c_qlwlhat[2] c_qlwlhat[3] c_qlwlhat[4] c_qlwlhat[5] c_qlwlhat[6] +compute avwlhat all reduce ave c_qlwlhat[7] c_qlwlhat[8] c_qlwlhat[9] c_qlwlhat[10] c_qlwlhat[11] c_qlwlhat[12] + +thermo_style custom step temp epair etotal c_avql[*] c_avwlhat[*] + +run 0 + +# check Q_l values + +print " " +print "*******************************************************************" +print " " +print "Comparison with reference values of Q_l " +print " [Table I in W. Mickel, S. C. Kapfer," +print " G. E. Schroeder-Turkand, K. Mecke, " +print " J. Chem. Phys. 138, 044501 (2013).]" +print " " + +variable q2ref equal 0.0 +variable q4ref equal 0.036 +variable q6ref equal 0.511 +variable q8ref equal 0.429 +variable q10ref equal 0.195 +variable q12ref equal 0.405 + +variable q2 equal c_avql[1] +variable q4 equal c_avql[2] +variable q6 equal c_avql[3] +variable q8 equal c_avql[4] +variable q10 equal c_avql[5] +variable q12 equal c_avql[6] + +print "q2 = $(v_q2:%10.6f) delta = $(v_q2-v_q2ref:%10.4f)" +print "q4 = $(v_q4:%10.6f) delta = $(v_q4-v_q4ref:%10.4f)" +print "q6 = $(v_q6:%10.6f) delta = $(v_q6-v_q6ref:%10.4f)" +print "q8 = $(v_q8:%10.6f) delta = $(v_q8-v_q8ref:%10.4f)" +print "q10 = $(v_q10:%10.6f) delta = $(v_q10-v_q10ref:%10.4f)" +print "q12 = $(v_q12:%10.6f) delta = $(v_q12-v_q12ref:%10.4f)" + +# check W_l_hat values + +print " " +print "Comparison with reference values of W_l_hat" +print " [Table I in P. Steinhardt, D. Nelson, and M. Ronchetti, " +print " Phys. Rev. B 28, 784 (1983).]" +print " " + +variable w4hatref equal 0.159317 +variable w6hatref equal 0.013161 +variable w8hatref equal -0.058455 +variable w10hatref equal -0.090130 + +variable w4hat equal c_avwlhat[2] +variable w6hat equal c_avwlhat[3] +variable w8hat equal c_avwlhat[4] +variable w10hat equal c_avwlhat[5] + +print "w4hat = $(v_w4hat:%10.6f) delta = $(v_w4hat-v_w4hatref:%10.6f)" +print "w6hat = $(v_w6hat:%10.6f) delta = $(v_w6hat-v_w6hatref:%10.6f)" +print "w8hat = $(v_w8hat:%10.6f) delta = $(v_w8hat-v_w8hatref:%10.6f)" +print "w10hat = $(v_w10hat:%10.6f) delta = $(v_w10hat-v_w10hatref:%10.6f)" +print " " +print "*******************************************************************" +print " " diff --git a/examples/steinhardt/in.fcc b/examples/steinhardt/in.fcc new file mode 100644 index 0000000000..6d2775d0bb --- /dev/null +++ b/examples/steinhardt/in.fcc @@ -0,0 +1,88 @@ +# Steinhardt-Nelson bond orientational order parameters for FCC + +variable rcut equal 3.0 + +boundary p p p + +atom_style atomic +neighbor 0.3 bin +neigh_modify delay 5 + +# create geometry + +lattice fcc 1.0 +region box block 0 3 0 3 0 3 +create_box 1 box +create_atoms 1 box + +mass 1 1.0 + +# LJ potentials + +pair_style lj/cut ${rcut} +pair_coeff * * 1.0 1.0 ${rcut} + +# 12 neighbors, perfect crystal + +compute qlwlhat all orientorder/atom wl/hat yes +compute avql all reduce ave c_qlwlhat[1] c_qlwlhat[2] c_qlwlhat[3] c_qlwlhat[4] c_qlwlhat[5] +compute avwlhat all reduce ave c_qlwlhat[6] c_qlwlhat[7] c_qlwlhat[8] c_qlwlhat[9] c_qlwlhat[10] + +thermo_style custom step temp epair etotal c_avql[*] c_avwlhat[*] + +run 0 + +# check Q_l values + +print " " +print "*******************************************************************" +print " " +print "Comparison with reference values of Q_l " +print " [Table I in W. Mickel, S. C. Kapfer," +print " G. E. Schroeder-Turkand, K. Mecke, " +print " J. Chem. Phys. 138, 044501 (2013).]" +print " " + +variable q4ref equal 0.190 +variable q6ref equal 0.575 +variable q8ref equal 0.404 +variable q10ref equal 0.013 +variable q12ref equal 0.600 + +variable q4 equal c_avql[1] +variable q6 equal c_avql[2] +variable q8 equal c_avql[3] +variable q10 equal c_avql[4] +variable q12 equal c_avql[5] + +print "q4 = $(v_q4:%10.6f) delta = $(v_q4-v_q4ref:%10.4f)" +print "q6 = $(v_q6:%10.6f) delta = $(v_q6-v_q6ref:%10.4f)" +print "q8 = $(v_q8:%10.6f) delta = $(v_q8-v_q8ref:%10.4f)" +print "q10 = $(v_q10:%10.6f) delta = $(v_q10-v_q10ref:%10.4f)" +print "q12 = $(v_q12:%10.6f) delta = $(v_q12-v_q12ref:%10.4f)" + +# check W_l_hat values + +print " " +print "Comparison with reference values of W_l_hat" +print " [Table I in P. Steinhardt, D. Nelson, and M. Ronchetti, " +print " Phys. Rev. B 28, 784 (1983).]" +print " " + +variable w4hatref equal -0.159316 +variable w6hatref equal -0.013161 +variable w8hatref equal 0.058454 +variable w10hatref equal -0.090128 + +variable w4hat equal c_avwlhat[1] +variable w6hat equal c_avwlhat[2] +variable w8hat equal c_avwlhat[3] +variable w10hat equal c_avwlhat[4] + +print "w4hat = $(v_w4hat:%10.6f) delta = $(v_w4hat-v_w4hatref:%10.6f)" +print "w6hat = $(v_w6hat:%10.6f) delta = $(v_w6hat-v_w6hatref:%10.6f)" +print "w8hat = $(v_w8hat:%10.6f) delta = $(v_w8hat-v_w8hatref:%10.6f)" +print "w10hat = $(v_w10hat:%10.6f) delta = $(v_w10hat-v_w10hatref:%10.6f)" +print " " +print "*******************************************************************" +print " " diff --git a/examples/steinhardt/in.icos b/examples/steinhardt/in.icos new file mode 100644 index 0000000000..d0d61a902d --- /dev/null +++ b/examples/steinhardt/in.icos @@ -0,0 +1,106 @@ +# Steinhardt-Nelson bond orientational order parameters for icosahedral cluster +# W_6_hat is sensitive to icosohedral order + +variable rcut equal 1.2 # a bit bigger than LJ Rmin +variable rcutred equal 0.75 # a bit bigger than 1/sqrt(2) + +# create a perfect fcc crystallite + +atom_style atomic +boundary s s s +lattice fcc 1.0 # neighbors at LJ Rmin +region box block 0 2 0 2 0 2 +create_box 1 box +create_atoms 1 box +mass 1 1.0 + +region centralatom sphere 1 1 1 0.0 side in +group centralatom region centralatom + +region mysphere sphere 1 1 1 ${rcutred} side out +delete_atoms region mysphere + +# LJ potential + +pair_style lj/cut 100.0 +pair_coeff * * 1.0 1.0 100.0 + +# define output for central atom + +compute qlwlhat all orientorder/atom wl/hat yes cutoff ${rcut} nnn NULL +compute avql centralatom reduce ave c_qlwlhat[1] c_qlwlhat[2] c_qlwlhat[3] c_qlwlhat[4] c_qlwlhat[5] +compute avwlhat centralatom reduce ave c_qlwlhat[6] c_qlwlhat[7] c_qlwlhat[8] c_qlwlhat[9] c_qlwlhat[10] +variable q6 equal c_avql[2] +variable w6hat equal c_avwlhat[2] + +compute mype all pe/atom +compute centralatompe centralatom reduce ave c_mype + +# gently equilibrate the crystallite + +velocity all create 0.001 482748 +fix 1 all nve +neighbor 0.3 bin +neigh_modify every 1 check no delay 0 +timestep 0.003 +thermo_style custom step temp epair etotal c_centralatompe v_q6 v_w6hat +thermo 10 + +run 10 + +# quench to icosehedral cluster + +minimize 1.0e-10 1.0e-6 100 1000 + +# check Q_l values + +print " " +print "*******************************************************************" +print " " +print "Comparison with reference values of Q_l " +print " [Table I in W. Mickel, S. C. Kapfer," +print " G. E. Schroeder-Turkand, K. Mecke, " +print " J. Chem. Phys. 138, 044501 (2013).]" +print " " + +variable q4ref equal 0.0 +variable q6ref equal 0.663 +variable q8ref equal 0.0 +variable q10ref equal 0.363 +variable q12ref equal 0.585 + +variable q4 equal c_avql[1] +variable q6 equal c_avql[2] +variable q8 equal c_avql[3] +variable q10 equal c_avql[4] +variable q12 equal c_avql[5] + +print "q4 = $(v_q4:%10.6f) delta = $(v_q4-v_q4ref:%10.4f)" +print "q6 = $(v_q6:%10.6f) delta = $(v_q6-v_q6ref:%10.4f)" +print "q8 = $(v_q8:%10.6f) delta = $(v_q8-v_q8ref:%10.4f)" +print "q10 = $(v_q10:%10.6f) delta = $(v_q10-v_q10ref:%10.4f)" +print "q12 = $(v_q12:%10.6f) delta = $(v_q12-v_q12ref:%10.4f)" + +# check W_l_hat values + +print " " +print "Comparison with reference values of W_l_hat" +print " [Table I in P. Steinhardt, D. Nelson, and M. Ronchetti, " +print " Phys. Rev. B 28, 784 (1983).]" +print " " + +variable w6hatref equal -0.169754 +variable w10hatref equal -0.093967 + +variable w4hat equal c_avwlhat[1] +variable w6hat equal c_avwlhat[2] +variable w8hat equal c_avwlhat[3] +variable w10hat equal c_avwlhat[4] +variable w12hat equal c_avwlhat[5] + +print "w6hat = $(v_w6hat:%10.6f) delta = $(v_w6hat-v_w6hatref:%10.6f)" +print "w10hat = $(v_w10hat:%10.6f) delta = $(v_w10hat-v_w10hatref:%10.6f)" +print " " +print "*******************************************************************" +print " " + diff --git a/src/compute_orientorder_atom.cpp b/src/compute_orientorder_atom.cpp index 266df575f9..0a78356127 100644 --- a/src/compute_orientorder_atom.cpp +++ b/src/compute_orientorder_atom.cpp @@ -43,12 +43,14 @@ using namespace std; #define MY_EPSILON (10.0*2.220446049250313e-16) #endif +#define QEPSILON 1.0e-6 + /* ---------------------------------------------------------------------- */ ComputeOrientOrderAtom::ComputeOrientOrderAtom(LAMMPS *lmp, int narg, char **arg) : Compute(lmp, narg, arg), qlist(NULL), distsq(NULL), nearest(NULL), rlist(NULL), - qnarray(NULL), qnm_r(NULL), qnm_i(NULL) + qnarray(NULL), qnm_r(NULL), qnm_i(NULL), cglist(NULL) { if (narg < 3 ) error->all(FLERR,"Illegal compute orientorder/atom command"); @@ -56,6 +58,8 @@ ComputeOrientOrderAtom::ComputeOrientOrderAtom(LAMMPS *lmp, int narg, char **arg nnn = 12; cutsq = 0.0; + wlflag = 0; + wlhatflag = 0; qlcompflag = 0; // specify which orders to request @@ -96,27 +100,39 @@ ComputeOrientOrderAtom::ComputeOrientOrderAtom(LAMMPS *lmp, int narg, char **arg if (iarg+nqlist > narg) error->all(FLERR,"Illegal compute orientorder/atom command"); qmax = 0; - for (int iw = 0; iw < nqlist; iw++) { - qlist[iw] = force->numeric(FLERR,arg[iarg+iw]); - if (qlist[iw] < 0) + for (int il = 0; il < nqlist; il++) { + qlist[il] = force->numeric(FLERR,arg[iarg+il]); + if (qlist[il] < 0) error->all(FLERR,"Illegal compute orientorder/atom command"); - if (qlist[iw] > qmax) qmax = qlist[iw]; + if (qlist[il] > qmax) qmax = qlist[il]; } iarg += nqlist; + } else if (strcmp(arg[iarg],"wl") == 0) { + if (iarg+2 > narg) + error->all(FLERR,"Illegal compute orientorder/atom command"); + if (strcmp(arg[iarg+1],"yes") == 0) wlflag = 1; + else if (strcmp(arg[iarg+1],"no") == 0) wlflag = 0; + else error->all(FLERR,"Illegal compute orientorder/atom command"); + iarg += 2; + } else if (strcmp(arg[iarg],"wl/hat") == 0) { + if (iarg+2 > narg) + error->all(FLERR,"Illegal compute orientorder/atom command"); + if (strcmp(arg[iarg+1],"yes") == 0) wlhatflag = 1; + else if (strcmp(arg[iarg+1],"no") == 0) wlhatflag = 0; + else error->all(FLERR,"Illegal compute orientorder/atom command"); + iarg += 2; } else if (strcmp(arg[iarg],"components") == 0) { qlcompflag = 1; if (iarg+2 > narg) error->all(FLERR,"Illegal compute orientorder/atom command"); qlcomp = force->numeric(FLERR,arg[iarg+1]); - if (qlcomp <= 0) - error->all(FLERR,"Illegal compute orientorder/atom command"); iqlcomp = -1; - for (int iw = 0; iw < nqlist; iw++) - if (qlcomp == qlist[iw]) { - iqlcomp = iw; + for (int il = 0; il < nqlist; il++) + if (qlcomp == qlist[il]) { + iqlcomp = il; break; } - if (iqlcomp < 0) + if (iqlcomp == -1) error->all(FLERR,"Illegal compute orientorder/atom command"); iarg += 2; } else if (strcmp(arg[iarg],"cutoff") == 0) { @@ -130,8 +146,10 @@ ComputeOrientOrderAtom::ComputeOrientOrderAtom(LAMMPS *lmp, int narg, char **arg } else error->all(FLERR,"Illegal compute orientorder/atom command"); } - if (qlcompflag) ncol = nqlist + 2*(2*qlcomp+1); - else ncol = nqlist; + ncol = nqlist; + if (wlflag) ncol += nqlist; + if (wlhatflag) ncol += nqlist; + if (qlcompflag) ncol += 2*(2*qlcomp+1); peratom_flag = 1; size_peratom_cols = ncol; @@ -151,7 +169,7 @@ ComputeOrientOrderAtom::~ComputeOrientOrderAtom() memory->destroy(qlist); memory->destroy(qnm_r); memory->destroy(qnm_i); - + memory->destroy(cglist); } /* ---------------------------------------------------------------------- */ @@ -166,8 +184,8 @@ void ComputeOrientOrderAtom::init() error->all(FLERR,"Compute orientorder/atom cutoff is " "longer than pairwise cutoff"); - memory->create(qnm_r,qmax,2*qmax+1,"orientorder/atom:qnm_r"); - memory->create(qnm_i,qmax,2*qmax+1,"orientorder/atom:qnm_i"); + memory->create(qnm_r,nqlist,2*qmax+1,"orientorder/atom:qnm_r"); + memory->create(qnm_i,nqlist,2*qmax+1,"orientorder/atom:qnm_i"); // need an occasional full neighbor list @@ -183,6 +201,8 @@ void ComputeOrientOrderAtom::init() if (strcmp(modify->compute[i]->style,"orientorder/atom") == 0) count++; if (count > 1 && comm->me == 0) error->warning(FLERR,"More than one compute orientorder/atom"); + + if (wlflag || wlhatflag) init_clebsch_gordan(); } /* ---------------------------------------------------------------------- */ @@ -274,8 +294,8 @@ void ComputeOrientOrderAtom::compute_peratom() // if not nnn neighbors, order parameter = 0; if ((ncount == 0) || (ncount < nnn)) { - for (int iw = 0; iw < nqlist; iw++) - qn[iw] = 0.0; + for (int jj = 0; jj < ncol; jj++) + qn[jj] = 0.0; continue; } @@ -287,6 +307,7 @@ void ComputeOrientOrderAtom::compute_peratom() } calc_boop(rlist, ncount, qn, qlist, nqlist); + } } } @@ -403,13 +424,12 @@ void ComputeOrientOrderAtom::select3(int k, int n, double *arr, int *iarr, doubl void ComputeOrientOrderAtom::calc_boop(double **rlist, int ncount, double qn[], int qlist[], int nqlist) { - for (int iw = 0; iw < nqlist; iw++) { - int n = qlist[iw]; - qn[iw] = 0.0; - for(int m = 0; m < 2*n+1; m++) { - qnm_r[iw][m] = 0.0; - qnm_i[iw][m] = 0.0; + for (int il = 0; il < nqlist; il++) { + int l = qlist[il]; + for(int m = 0; m < 2*l+1; m++) { + qnm_r[il][m] = 0.0; + qnm_i[il][m] = 0.0; } } @@ -433,24 +453,24 @@ void ComputeOrientOrderAtom::calc_boop(double **rlist, expphi_i *= rxymaginv; } - for (int iw = 0; iw < nqlist; iw++) { - int n = qlist[iw]; + for (int il = 0; il < nqlist; il++) { + int l = qlist[il]; - qnm_r[iw][n] += polar_prefactor(n, 0, costheta); + qnm_r[il][l] += polar_prefactor(l, 0, costheta); double expphim_r = expphi_r; double expphim_i = expphi_i; - for(int m = 1; m <= +n; m++) { - double prefactor = polar_prefactor(n, m, costheta); + for(int m = 1; m <= +l; m++) { + double prefactor = polar_prefactor(l, m, costheta); double c_r = prefactor * expphim_r; double c_i = prefactor * expphim_i; - qnm_r[iw][m+n] += c_r; - qnm_i[iw][m+n] += c_i; + qnm_r[il][m+l] += c_r; + qnm_i[il][m+l] += c_i; if(m & 1) { - qnm_r[iw][-m+n] -= c_r; - qnm_i[iw][-m+n] += c_i; + qnm_r[il][-m+l] -= c_r; + qnm_i[il][-m+l] += c_i; } else { - qnm_r[iw][-m+n] += c_r; - qnm_i[iw][-m+n] -= c_i; + qnm_r[il][-m+l] += c_r; + qnm_i[il][-m+l] -= c_i; } double tmp_r = expphim_r*expphi_r - expphim_i*expphi_i; double tmp_i = expphim_r*expphi_i + expphim_i*expphi_r; @@ -461,30 +481,110 @@ void ComputeOrientOrderAtom::calc_boop(double **rlist, } } - double fac = sqrt(MY_4PI) / ncount; - double normfac = 0.0; - for (int iw = 0; iw < nqlist; iw++) { - int n = qlist[iw]; - double qm_sum = 0.0; - for(int m = 0; m < 2*n+1; m++) { - qm_sum += qnm_r[iw][m]*qnm_r[iw][m] + qnm_i[iw][m]*qnm_i[iw][m]; - // printf("Ylm^2 = %d %d %g\n",n,m, - // qnm_r[iw][m]*qnm_r[iw][m] + qnm_i[iw][m]*qnm_i[iw][m]); - } - qn[iw] = fac * sqrt(qm_sum / (2*n+1)); - if (qlcompflag && iqlcomp == iw) normfac = 1.0/sqrt(qm_sum); + // convert sums to averages + double facn = 1.0 / ncount; + for (int il = 0; il < nqlist; il++) { + int l = qlist[il]; + for(int m = 0; m < 2*l+1; m++) { + qnm_r[il][m] *= facn; + qnm_i[il][m] *= facn; + } } - // output of the complex vector + // calculate Q_l + // NOTE: optional W_l_hat and components of Q_qlcomp use these stored Q_l values + + int jj = 0; + for (int il = 0; il < nqlist; il++) { + int l = qlist[il]; + double qnormfac = sqrt(MY_4PI/(2*l+1)); + double qm_sum = 0.0; + for(int m = 0; m < 2*l+1; m++) + qm_sum += qnm_r[il][m]*qnm_r[il][m] + qnm_i[il][m]*qnm_i[il][m]; + qn[jj++] = qnormfac * sqrt(qm_sum); + } + + // TODO: + // 1. [done]Need to allocate extra memory in qnarray[] for this option + // 2. [done]Need to add keyword option + // 3. [done]Need to caclulate Clebsch-Gordan/Wigner 3j coefficients + // (Can try getting them from boop.py first) + // 5. [done]Compare to bcc values in /Users/athomps/netapp/codes/MatMiner/matminer/matminer/featurizers/boop.py + // 6. [done]I get the right answer for W_l, but need to make sure that factor of 1/sqrt(l+1) is right for cglist + // 7. Add documentation + // 8. [done] run valgrind + // 9. [done] Add Wlhat + // 10. Update memory_usage() + // 11. Add exact FCC values for W_4, W_4_hat + + // calculate W_l + + if (wlflag) { + int idxcg_count = 0; + for (int il = 0; il < nqlist; il++) { + int l = qlist[il]; + double wlsum = 0.0; + for(int m1 = 0; m1 < 2*l+1; m1++) { + for(int m2 = MAX(0,l-m1); m2 < MIN(2*l+1,3*l-m1+1); m2++) { + int m = m1 + m2 - l; + double qm1qm2_r = qnm_r[il][m1]*qnm_r[il][m2] - qnm_i[il][m1]*qnm_i[il][m2]; + double qm1qm2_i = qnm_r[il][m1]*qnm_i[il][m2] + qnm_i[il][m1]*qnm_r[il][m2]; + wlsum += (qm1qm2_r*qnm_r[il][m] + qm1qm2_i*qnm_i[il][m])*cglist[idxcg_count]; + idxcg_count++; + } + } + qn[jj++] = wlsum/sqrt(2*l+1); + } + } + + // calculate W_l_hat + + if (wlhatflag) { + int idxcg_count = 0; + for (int il = 0; il < nqlist; il++) { + int l = qlist[il]; + double wlsum = 0.0; + for(int m1 = 0; m1 < 2*l+1; m1++) { + for(int m2 = MAX(0,l-m1); m2 < MIN(2*l+1,3*l-m1+1); m2++) { + int m = m1 + m2 - l; + double qm1qm2_r = qnm_r[il][m1]*qnm_r[il][m2] - qnm_i[il][m1]*qnm_i[il][m2]; + double qm1qm2_i = qnm_r[il][m1]*qnm_i[il][m2] + qnm_i[il][m1]*qnm_r[il][m2]; + wlsum += (qm1qm2_r*qnm_r[il][m] + qm1qm2_i*qnm_i[il][m])*cglist[idxcg_count]; + idxcg_count++; + } + } + // Whats = [w/(q/np.sqrt(np.pi * 4 / (2 * l + 1)))**3 if abs(q) > 1.0e-6 else 0.0 for l,q,w in zip(range(1,max_l+1),Qs,Ws)] + if (qn[il] < QEPSILON) + qn[jj++] = 0.0; + else { + double qnormfac = sqrt(MY_4PI/(2*l+1)); + double qnfac = qnormfac/qn[il]; + qn[jj++] = wlsum/sqrt(2*l+1)*(qnfac*qnfac*qnfac); + } + } + } + + // Calculate components of Q_l, for l=qlcomp if (qlcompflag) { - int j = nqlist; - for(int m = 0; m < 2*qlcomp+1; m++) { - qn[j++] = qnm_r[iqlcomp][m] * normfac; - qn[j++] = qnm_i[iqlcomp][m] * normfac; + int il = iqlcomp; + int l = qlcomp; + if (qn[il] < QEPSILON) + for(int m = 0; m < 2*l+1; m++) { + qn[jj++] = 0.0; + qn[jj++] = 0.0; + } + else { + double qnormfac = sqrt(MY_4PI/(2*l+1)); + double qnfac = qnormfac/qn[il]; + for(int m = 0; m < 2*l+1; m++) { + qn[jj++] = qnm_r[il][m] * qnfac; + qn[jj++] = qnm_i[il][m] * qnfac; + } } } + } /* ---------------------------------------------------------------------- @@ -542,3 +642,258 @@ double ComputeOrientOrderAtom::associated_legendre(int l, int m, double x) return p; } + +/* ---------------------------------------------------------------------- + assign Clebsch-Gordan coefficients + using the quasi-binomial formula VMK 8.2.1(3) + specialized for case j1=j2=j=l +------------------------------------------------------------------------- */ + +void ComputeOrientOrderAtom::init_clebsch_gordan() +{ + double sum,dcg,sfaccg, sfac1, sfac2; + int m, aa2, bb2, cc2; + int ifac, idxcg_count; + + idxcg_count = 0; + for (int il = 0; il < nqlist; il++) { + int l = qlist[il]; + for(int m1 = 0; m1 < 2*l+1; m1++) + for(int m2 = MAX(0,l-m1); m2 < MIN(2*l+1,3*l-m1+1); m2++) + idxcg_count++; + } + idxcg_max = idxcg_count; + memory->create(cglist, idxcg_max, "computeorientorderatom:cglist"); + + idxcg_count = 0; + for (int il = 0; il < nqlist; il++) { + int l = qlist[il]; + for(int m1 = 0; m1 < 2*l+1; m1++) { + aa2 = m1 - l; + for(int m2 = MAX(0,l-m1); m2 < MIN(2*l+1,3*l-m1+1); m2++) { + bb2 = m2 - l; + m = aa2 + bb2 + l; + + sum = 0.0; + for (int z = MAX(0, MAX(-aa2, bb2)); + z <= MIN(l, MIN(l - aa2, l + bb2)); z++) { + ifac = z % 2 ? -1 : 1; + sum += ifac / + (factorial(z) * + factorial(l - z) * + factorial(l - aa2 - z) * + factorial(l + bb2 - z) * + factorial(aa2 + z) * + factorial(-bb2 + z)); + } + + cc2 = m - l; + sfaccg = sqrt(factorial(l + aa2) * + factorial(l - aa2) * + factorial(l + bb2) * + factorial(l - bb2) * + factorial(l + cc2) * + factorial(l - cc2) * + (2*l + 1)); + + sfac1 = factorial(3*l + 1); + sfac2 = factorial(l); + dcg = sqrt(sfac2*sfac2*sfac2 / sfac1); + + cglist[idxcg_count] = sum * dcg * sfaccg; + idxcg_count++; + } + } + } +} + +/* ---------------------------------------------------------------------- + factorial n, wrapper for precomputed table +------------------------------------------------------------------------- */ + +double ComputeOrientOrderAtom::factorial(int n) +{ + if (n < 0 || n > nmaxfactorial) { + char str[128]; + sprintf(str, "Invalid argument to factorial %d", n); + error->all(FLERR, str); + } + + return nfac_table[n]; +} + +/* ---------------------------------------------------------------------- + factorial n table, size SNA::nmaxfactorial+1 +------------------------------------------------------------------------- */ + +const double ComputeOrientOrderAtom::nfac_table[] = { + 1, + 1, + 2, + 6, + 24, + 120, + 720, + 5040, + 40320, + 362880, + 3628800, + 39916800, + 479001600, + 6227020800, + 87178291200, + 1307674368000, + 20922789888000, + 355687428096000, + 6.402373705728e+15, + 1.21645100408832e+17, + 2.43290200817664e+18, + 5.10909421717094e+19, + 1.12400072777761e+21, + 2.5852016738885e+22, + 6.20448401733239e+23, + 1.5511210043331e+25, + 4.03291461126606e+26, + 1.08888694504184e+28, + 3.04888344611714e+29, + 8.8417619937397e+30, + 2.65252859812191e+32, + 8.22283865417792e+33, + 2.63130836933694e+35, + 8.68331761881189e+36, + 2.95232799039604e+38, + 1.03331479663861e+40, + 3.71993326789901e+41, + 1.37637530912263e+43, + 5.23022617466601e+44, + 2.03978820811974e+46, + 8.15915283247898e+47, + 3.34525266131638e+49, + 1.40500611775288e+51, + 6.04152630633738e+52, + 2.65827157478845e+54, + 1.1962222086548e+56, + 5.50262215981209e+57, + 2.58623241511168e+59, + 1.24139155925361e+61, + 6.08281864034268e+62, + 3.04140932017134e+64, + 1.55111875328738e+66, + 8.06581751709439e+67, + 4.27488328406003e+69, + 2.30843697339241e+71, + 1.26964033536583e+73, + 7.10998587804863e+74, + 4.05269195048772e+76, + 2.35056133128288e+78, + 1.3868311854569e+80, + 8.32098711274139e+81, + 5.07580213877225e+83, + 3.14699732603879e+85, + 1.98260831540444e+87, + 1.26886932185884e+89, + 8.24765059208247e+90, + 5.44344939077443e+92, + 3.64711109181887e+94, + 2.48003554243683e+96, + 1.71122452428141e+98, + 1.19785716699699e+100, + 8.50478588567862e+101, + 6.12344583768861e+103, + 4.47011546151268e+105, + 3.30788544151939e+107, + 2.48091408113954e+109, + 1.88549470166605e+111, + 1.45183092028286e+113, + 1.13242811782063e+115, + 8.94618213078297e+116, + 7.15694570462638e+118, + 5.79712602074737e+120, + 4.75364333701284e+122, + 3.94552396972066e+124, + 3.31424013456535e+126, + 2.81710411438055e+128, + 2.42270953836727e+130, + 2.10775729837953e+132, + 1.85482642257398e+134, + 1.65079551609085e+136, + 1.48571596448176e+138, + 1.3520015276784e+140, + 1.24384140546413e+142, + 1.15677250708164e+144, + 1.08736615665674e+146, + 1.03299784882391e+148, + 9.91677934870949e+149, + 9.61927596824821e+151, + 9.42689044888324e+153, + 9.33262154439441e+155, + 9.33262154439441e+157, + 9.42594775983835e+159, + 9.61446671503512e+161, + 9.90290071648618e+163, + 1.02990167451456e+166, + 1.08139675824029e+168, + 1.14628056373471e+170, + 1.22652020319614e+172, + 1.32464181945183e+174, + 1.44385958320249e+176, + 1.58824554152274e+178, + 1.76295255109024e+180, + 1.97450685722107e+182, + 2.23119274865981e+184, + 2.54355973347219e+186, + 2.92509369349301e+188, + 3.3931086844519e+190, + 3.96993716080872e+192, + 4.68452584975429e+194, + 5.5745857612076e+196, + 6.68950291344912e+198, + 8.09429852527344e+200, + 9.8750442008336e+202, + 1.21463043670253e+205, + 1.50614174151114e+207, + 1.88267717688893e+209, + 2.37217324288005e+211, + 3.01266001845766e+213, + 3.8562048236258e+215, + 4.97450422247729e+217, + 6.46685548922047e+219, + 8.47158069087882e+221, + 1.118248651196e+224, + 1.48727070609069e+226, + 1.99294274616152e+228, + 2.69047270731805e+230, + 3.65904288195255e+232, + 5.01288874827499e+234, + 6.91778647261949e+236, + 9.61572319694109e+238, + 1.34620124757175e+241, + 1.89814375907617e+243, + 2.69536413788816e+245, + 3.85437071718007e+247, + 5.5502938327393e+249, + 8.04792605747199e+251, + 1.17499720439091e+254, + 1.72724589045464e+256, + 2.55632391787286e+258, + 3.80892263763057e+260, + 5.71338395644585e+262, + 8.62720977423323e+264, + 1.31133588568345e+267, + 2.00634390509568e+269, + 3.08976961384735e+271, + 4.78914290146339e+273, + 7.47106292628289e+275, + 1.17295687942641e+278, + 1.85327186949373e+280, + 2.94670227249504e+282, + 4.71472363599206e+284, + 7.59070505394721e+286, + 1.22969421873945e+289, + 2.0044015765453e+291, + 3.28721858553429e+293, + 5.42391066613159e+295, + 9.00369170577843e+297, + 1.503616514865e+300, // nmaxfactorial = 167 +}; + diff --git a/src/compute_orientorder_atom.h b/src/compute_orientorder_atom.h index d5905df63b..643875ccd0 100644 --- a/src/compute_orientorder_atom.h +++ b/src/compute_orientorder_atom.h @@ -33,7 +33,7 @@ class ComputeOrientOrderAtom : public Compute { void compute_peratom(); double memory_usage(); double cutsq; - int iqlcomp, qlcomp, qlcompflag; + int iqlcomp, qlcomp, qlcompflag, wlflag, wlhatflag; int *qlist; int nqlist; @@ -55,6 +55,13 @@ class ComputeOrientOrderAtom : public Compute { double polar_prefactor(int, int, double); double associated_legendre(int, int, double); + + static const int nmaxfactorial = 167; + static const double nfac_table[]; + double factorial(int); + void init_clebsch_gordan(); + double *cglist; // Clebsch-Gordan coeffs + int idxcg_max; }; }