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Removed the bogus loop in numdiff and manually se the factors in numdiff.

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Germain Clavier
2022-02-10 11:51:03 +01:00
parent 4d6fcb3a8b
commit 4f36dad942
4 changed files with 62 additions and 32 deletions
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7
examples/cij_nvt/in.ljfcc
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@ -11,7 +11,7 @@
variable nsteps index 50 # length of run
variable nthermo index 10 # thermo output interval
variable nlat index 3 # size of box
variable nlat index 5 # size of box
variable delta index 1.0e-6 # strain size
variable temp index 0.3 # temperature
variable rho index 0.8442 # reduced density
@ -38,10 +38,9 @@ fix 1 all nvt temp ${temp} ${temp} 0.1
run 100
compute born all born/matrix
variable born vector c_born/vol
thermo ${nthermo}
thermo_style custom step temp pe press v_born[1] v_born[2] v_born[3] v_born[4] v_born[5] v_born[6] v_born[7] v_born[8] v_born[9] v_born[10] v_born[11] v_born[12] v_born[13] v_born[14] v_born[15] v_born[16] v_born[17] v_born[18] v_born[19] v_born[20] v_born[21]
thermo_modify line multi
thermo_style custom step temp pe press c_born[*]
thermo_modify line multi
run ${nsteps}

9
examples/cij_nvt/in.ljfcc_both
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@ -13,7 +13,7 @@
variable nsteps index 200 # length of run
variable nthermo index 10 # thermo output interval
variable nlat index 3 # size of box
variable nlat index 5 # size of box
variable delta index 1.0e-8 # strain size
variable temp index 0.3 # temperature
variable rho index 0.8442 # reduced density
@ -37,15 +37,14 @@ neigh_modify every 1 delay 0 check no
fix 1 all nvt temp ${temp} ${temp} 0.1
variable vol equal vol
compute myvirial all pressure NULL virial
compute bornnum all born/matrix numdiff ${delta} myvirial
compute born all born/matrix
variable bornrel vector 1.0-c_bornnum/c_born*v_vol
fix bornrel all ave/time 1 1 ${nthermo} v_bornrel mode vector ave running
variable bornrel vector 1.0-c_bornnum/c_born
fix bornrel all ave/time 1 1 ${nthermo} v_bornrel start 100 mode vector ave running
thermo ${nthermo}
thermo_style custom step temp pe press &
thermo_style custom step temp pe press c_born[10] c_bornnum[10] &
v_bornrel[1] v_bornrel[2] v_bornrel[3] v_bornrel[4] v_bornrel[5] v_bornrel[6] v_bornrel[7] v_bornrel[8] v_bornrel[9] v_bornrel[10] v_bornrel[11] v_bornrel[12] v_bornrel[13] v_bornrel[14] v_bornrel[15] v_bornrel[16] v_bornrel[17] v_bornrel[18] v_bornrel[19] v_bornrel[20] v_bornrel[21]
thermo_modify line multi

2
examples/cij_nvt/in.ljfcc_num
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@ -13,7 +13,7 @@
variable nsteps index 50 # length of run
variable nthermo index 10 # thermo output interval
variable nlat index 3 # size of box
variable nlat index 5 # size of box
variable delta index 1.0e-6 # strain size
variable temp index 0.3 # temperature
variable rho index 0.8442 # reduced density

76
src/EXTRA-COMPUTE/compute_born_matrix.cpp
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@ -633,8 +633,8 @@ void ComputeBornMatrix::displace_atoms(int nall, int idir, double magnitude)
// A.T.
// this works for vector indices 7, 8, 9, 12, 14, 18 and 15, 16, 17
// corresponding i,j indices 12, 13, 14, 23, 25, 36 and 26, 34, 35
int k = dirlist[idir][1];
int l = dirlist[idir][0];
// int k = dirlist[idir][1];
// int l = dirlist[idir][0];
// A.T.
// this works for vector indices 7, 8, 9, 12, 14, 18 and 10, 11, 13
@ -642,8 +642,8 @@ void ComputeBornMatrix::displace_atoms(int nall, int idir, double magnitude)
// G.C.:
// I see no difference with a 0 step simulation between both
// methods.
// int k = dirlist[idir][0];
// int l = dirlist[idir][1];
int k = dirlist[idir][0];
int l = dirlist[idir][1];
for (int i = 0; i < nall; i++)
x[i][k] = temp_x[i][k] + numdelta * magnitude * (temp_x[i][l] - fixedpoint[l]);
}
@ -715,29 +715,61 @@ void ComputeBornMatrix::virial_addon()
double* sigv = compute_virial->vector;
double modefactor[6] = {1.0, 1.0, 1.0, 0.5, 0.5, 0.5};
for (int idir = 0; idir < NDIR_VIRIAL; idir++) {
int ijvgt = idir; // this is it.
double addon;
// Back to the ugly way
// You can compute these factor by looking at
// every Dijkl terms and adding the proper virials
// Take into account the symmetries. For example:
// B2323 = s33+D2323; B3232= s22+D3232;
// but D3232=D2323 (computed in compute_numdiff)
// and Cijkl = (Bijkl+Bjikl+Bijlk+Bjilk)/4. = (Bijkl+Bjilk)/2.
// see Yoshimoto eq 15.and eq A3.
values_global[0] += 2.0*sigv[0];
values_global[1] += 2.0*sigv[1];
values_global[2] += 2.0*sigv[2];
values_global[3] += 0.5*(sigv[1]+sigv[2]);
values_global[4] += 0.5*(sigv[0]+sigv[2]);
values_global[5] += 0.5*(sigv[0]+sigv[1]);
values_global[6] += 0.0;
values_global[7] += 0.0;
values_global[8] += 0.0;
values_global[9] += sigv[4];
values_global[10] += sigv[3];
values_global[11] += 0.0;
values_global[12] += sigv[5];
values_global[13] += 0.0;
values_global[14] += sigv[3];
values_global[15] += sigv[5];
values_global[16] += sigv[4];
values_global[17] += 0.0;
values_global[18] += 0.0;
values_global[19] += sigv[4];
values_global[20] += sigv[5];
// extract the two indices composing the voigt representation
// This loop is actually bogus.
//
// for (int idir = 0; idir < NDIR_VIRIAL; idir++) {
// int ijvgt = idir; // this is it.
// double addon;
id = voigt3VtoM[ijvgt][0];
jd = voigt3VtoM[ijvgt][1];
// // extract the two indices composing the voigt representation
for (int knvgt=ijvgt; knvgt < NDIR_VIRIAL; knvgt++) {
kd = voigt3VtoM[knvgt][0];
nd = voigt3VtoM[knvgt][1];
addon = kronecker[id][nd]*sigv[virialMtoV[jd][kd]] +
kronecker[id][kd]*sigv[virialMtoV[jd][nd]];
if(id != jd)
addon += kronecker[jd][nd]*sigv[virialMtoV[id][kd]] +
kronecker[jd][kd]*sigv[virialMtoV[id][nd]];
// id = voigt3VtoM[ijvgt][0];
// jd = voigt3VtoM[ijvgt][1];
m = revalbe[ijvgt][knvgt];
// for (int knvgt=ijvgt; knvgt < NDIR_VIRIAL; knvgt++) {
// kd = voigt3VtoM[knvgt][0];
// nd = voigt3VtoM[knvgt][1];
// addon = kronecker[id][nd]*sigv[virialMtoV[jd][kd]] +
// kronecker[id][kd]*sigv[virialMtoV[jd][nd]];
// if(id != jd)
// addon += kronecker[jd][nd]*sigv[virialMtoV[id][kd]] +
// kronecker[jd][kd]*sigv[virialMtoV[id][nd]];
values_global[revalbe[ijvgt][knvgt]] += 0.5*modefactor[idir]*addon;
}
}
// m = revalbe[ijvgt][knvgt];
// values_global[revalbe[ijvgt][knvgt]] += 0.5*modefactor[idir]*addon;
// }
// }
}
/* ----------------------------------------------------------------------