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fix whitespace issues

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This commit is contained in:
Axel Kohlmeyer
2021-01-26 18:39:02 -05:00
parent d1be5d49ca
commit bca3164fc4
20 changed files with 102 additions and 102 deletions
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2
doc/src/Developer_notes.rst
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@ -57,7 +57,7 @@ value of 1 in their constructor:
* *energy_peratom_flag* to contribute to peratom energy, :doc:`fix cmap <fix_cmap>`
* *virial_global_flag* to contribute to global virial, example: :doc:`fix wall <fix_wall>`
* *virial_peratom_flag* to contribute to peratom virial, example: :doc:`fix wall <fix_wall>`
The fix must also do the following:
* For global energy, implement a compute_scalar() method that returns

2
doc/src/fix_modify.rst
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@ -86,7 +86,7 @@ appropriate fix.
For most fixes that suppport the *energy* keyword, the default
setting is *no*. For a few it is *yes*, when a user would expect
that to be the case. The doc page of each fix gives the default.
The *virial* keyword can be used with fixes that support it, which is
explained at the bottom of their doc page. *Virial yes* will add a
contribution to the virial of the system. More specifically, the

2
doc/src/thermo_style.rst
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@ -298,7 +298,7 @@ thermostatting or barostatting to their coupling reservoirs. I.e. it
is *pe* + *ke* + *econserve*\ . Ideally, for a simulation in the NVE,
NPH, or NPT ensembles, the *econserve* quantity should remain constant
over time.
The *fmax* and *fnorm* keywords are useful for monitoring the progress
of an :doc:`energy minimization <minimize>`. The *fmax* keyword
calculates the maximum force in any dimension on any atom in the

100
src/KSPACE/pppm_dipole.cpp
View File

@ -463,7 +463,7 @@ void PPPMDipole::compute(int eflag, int vflag)
if (evflag_atom)
gc_dipole->forward_comm_kspace(this,18,sizeof(FFT_SCALAR),FORWARD_MU_PERATOM,
gc_buf1,gc_buf2,MPI_FFT_SCALAR);
gc_buf1,gc_buf2,MPI_FFT_SCALAR);
// calculate the force on my particles
@ -1333,7 +1333,7 @@ void PPPMDipole::poisson_ik_dipole()
wimg = (work1[n+1]*fkx[i] + work2[n+1]*fky[j] + work3[n+1]*fkz[k]);
energy +=
s2 * greensfn[ii] * (wreal*wreal + wimg*wimg);
ii++;
ii++;
n += 2;
}
}
@ -1430,9 +1430,9 @@ void PPPMDipole::poisson_ik_dipole()
for (j = nylo_fft; j <= nyhi_fft; j++)
for (i = nxlo_fft; i <= nxhi_fft; i++) {
work4[n] = -fkx[i]*fkx[i]*(work1[n+1]*fkx[i] +
work2[n+1]*fky[j] + work3[n+1]*fkz[k]);
work2[n+1]*fky[j] + work3[n+1]*fkz[k]);
work4[n+1] = fkx[i]*fkx[i]*(work1[n]*fkx[i] +
work2[n]*fky[j] + work3[n]*fkz[k]);
work2[n]*fky[j] + work3[n]*fkz[k]);
n += 2;
}
@ -1453,9 +1453,9 @@ void PPPMDipole::poisson_ik_dipole()
for (j = nylo_fft; j <= nyhi_fft; j++)
for (i = nxlo_fft; i <= nxhi_fft; i++) {
work4[n] = -fky[j]*fky[j]*(work1[n+1]*fkx[i] +
work2[n+1]*fky[j] + work3[n+1]*fkz[k]);
work2[n+1]*fky[j] + work3[n+1]*fkz[k]);
work4[n+1] = fky[j]*fky[j]*(work1[n]*fkx[i] +
work2[n]*fky[j] + work3[n]*fkz[k]);
work2[n]*fky[j] + work3[n]*fkz[k]);
n += 2;
}
@ -1476,9 +1476,9 @@ void PPPMDipole::poisson_ik_dipole()
for (j = nylo_fft; j <= nyhi_fft; j++)
for (i = nxlo_fft; i <= nxhi_fft; i++) {
work4[n] = -fkz[k]*fkz[k]*(work1[n+1]*fkx[i] +
work2[n+1]*fky[j] + work3[n+1]*fkz[k]);
work2[n+1]*fky[j] + work3[n+1]*fkz[k]);
work4[n+1] = fkz[k]*fkz[k]*(work1[n]*fkx[i] +
work2[n]*fky[j] + work3[n]*fkz[k]);
work2[n]*fky[j] + work3[n]*fkz[k]);
n += 2;
}
@ -1499,9 +1499,9 @@ void PPPMDipole::poisson_ik_dipole()
for (j = nylo_fft; j <= nyhi_fft; j++)
for (i = nxlo_fft; i <= nxhi_fft; i++) {
work4[n] = -fkx[i]*fky[j]*(work1[n+1]*fkx[i] +
work2[n+1]*fky[j] + work3[n+1]*fkz[k]);
work2[n+1]*fky[j] + work3[n+1]*fkz[k]);
work4[n+1] = fkx[i]*fky[j]*(work1[n]*fkx[i] +
work2[n]*fky[j] + work3[n]*fkz[k]);
work2[n]*fky[j] + work3[n]*fkz[k]);
n += 2;
}
@ -1522,9 +1522,9 @@ void PPPMDipole::poisson_ik_dipole()
for (j = nylo_fft; j <= nyhi_fft; j++)
for (i = nxlo_fft; i <= nxhi_fft; i++) {
work4[n] = -fkx[i]*fkz[k]*(work1[n+1]*fkx[i] +
work2[n+1]*fky[j] + work3[n+1]*fkz[k]);
work2[n+1]*fky[j] + work3[n+1]*fkz[k]);
work4[n+1] = fkx[i]*fkz[k]*(work1[n]*fkx[i] +
work2[n]*fky[j] + work3[n]*fkz[k]);
work2[n]*fky[j] + work3[n]*fkz[k]);
n += 2;
}
@ -1545,9 +1545,9 @@ void PPPMDipole::poisson_ik_dipole()
for (j = nylo_fft; j <= nyhi_fft; j++)
for (i = nxlo_fft; i <= nxhi_fft; i++) {
work4[n] = -fky[j]*fkz[k]*(work1[n+1]*fkx[i] +
work2[n+1]*fky[j] + work3[n+1]*fkz[k]);
work2[n+1]*fky[j] + work3[n+1]*fkz[k]);
work4[n+1] = fky[j]*fkz[k]*(work1[n]*fkx[i] +
work2[n]*fky[j] + work3[n]*fkz[k]);
work2[n]*fky[j] + work3[n]*fkz[k]);
n += 2;
}
@ -1582,9 +1582,9 @@ void PPPMDipole::poisson_peratom_dipole()
for (j = nylo_fft; j <= nyhi_fft; j++)
for (i = nxlo_fft; i <= nxhi_fft; i++) {
work4[n] = fkx[i]*(vg[ii][0]*(work1[n]*fkx[i] + work2[n]*fky[j] +
work3[n]*fkz[k]) + 2.0*fkx[i]*work1[n]);
work3[n]*fkz[k]) + 2.0*fkx[i]*work1[n]);
work4[n+1] = fkx[i]*(vg[ii][0]*(work1[n+1]*fkx[i] + work2[n+1]*fky[j] +
work3[n+1]*fkz[k]) + 2.0*fkx[i]*work1[n+1]);
work3[n+1]*fkz[k]) + 2.0*fkx[i]*work1[n+1]);
n += 2;
ii++;
}
@ -1607,9 +1607,9 @@ void PPPMDipole::poisson_peratom_dipole()
for (j = nylo_fft; j <= nyhi_fft; j++)
for (i = nxlo_fft; i <= nxhi_fft; i++) {
work4[n] = fky[j]*(vg[ii][0]*(work1[n]*fkx[i] + work2[n]*fky[j] +
work3[n]*fkz[k]) + 2.0*fkx[i]*work1[n]);
work3[n]*fkz[k]) + 2.0*fkx[i]*work1[n]);
work4[n+1] = fky[j]*(vg[ii][0]*(work1[n+1]*fkx[i] + work2[n+1]*fky[j] +
work3[n+1]*fkz[k]) + 2.0*fkx[i]*work1[n+1]);
work3[n+1]*fkz[k]) + 2.0*fkx[i]*work1[n+1]);
n += 2;
ii++;
}
@ -1632,9 +1632,9 @@ void PPPMDipole::poisson_peratom_dipole()
for (j = nylo_fft; j <= nyhi_fft; j++)
for (i = nxlo_fft; i <= nxhi_fft; i++) {
work4[n] = fkz[k]*(vg[ii][0]*(work1[n]*fkx[i] + work2[n]*fky[j] +
work3[n]*fkz[k]) + 2.0*fkx[i]*work1[n]);
work3[n]*fkz[k]) + 2.0*fkx[i]*work1[n]);
work4[n+1] = fkz[k]*(vg[ii][0]*(work1[n+1]*fkx[i] + work2[n+1]*fky[j] +
work3[n+1]*fkz[k]) + 2.0*fkx[i]*work1[n+1]);
work3[n+1]*fkz[k]) + 2.0*fkx[i]*work1[n+1]);
n += 2;
ii++;
}
@ -1657,9 +1657,9 @@ void PPPMDipole::poisson_peratom_dipole()
for (j = nylo_fft; j <= nyhi_fft; j++)
for (i = nxlo_fft; i <= nxhi_fft; i++) {
work4[n] = fkx[i]*(vg[ii][1]*(work1[n]*fkx[i] + work2[n]*fky[j] +
work3[n]*fkz[k]) + 2.0*fky[j]*work2[n]);
work3[n]*fkz[k]) + 2.0*fky[j]*work2[n]);
work4[n+1] = fkx[i]*(vg[ii][1]*(work1[n+1]*fkx[i] + work2[n+1]*fky[j] +
work3[n+1]*fkz[k]) + 2.0*fky[j]*work2[n+1]);
work3[n+1]*fkz[k]) + 2.0*fky[j]*work2[n+1]);
n += 2;
ii++;
}
@ -1682,9 +1682,9 @@ void PPPMDipole::poisson_peratom_dipole()
for (j = nylo_fft; j <= nyhi_fft; j++)
for (i = nxlo_fft; i <= nxhi_fft; i++) {
work4[n] = fky[j]*(vg[ii][1]*(work1[n]*fkx[i] + work2[n]*fky[j] +
work3[n]*fkz[k]) + 2.0*fky[j]*work2[n]);
work3[n]*fkz[k]) + 2.0*fky[j]*work2[n]);
work4[n+1] = fky[j]*(vg[ii][1]*(work1[n+1]*fkx[i] + work2[n+1]*fky[j] +
work3[n+1]*fkz[k]) + 2.0*fky[j]*work2[n+1]);
work3[n+1]*fkz[k]) + 2.0*fky[j]*work2[n+1]);
n += 2;
ii++;
}
@ -1707,9 +1707,9 @@ void PPPMDipole::poisson_peratom_dipole()
for (j = nylo_fft; j <= nyhi_fft; j++)
for (i = nxlo_fft; i <= nxhi_fft; i++) {
work4[n] = fkz[k]*(vg[ii][1]*(work1[n]*fkx[i] + work2[n]*fky[j] +
work3[n]*fkz[k]) + 2.0*fky[j]*work2[n]);
work3[n]*fkz[k]) + 2.0*fky[j]*work2[n]);
work4[n+1] = fkz[k]*(vg[ii][1]*(work1[n+1]*fkx[i] + work2[n+1]*fky[j] +
work3[n+1]*fkz[k]) + 2.0*fky[j]*work2[n+1]);
work3[n+1]*fkz[k]) + 2.0*fky[j]*work2[n+1]);
n += 2;
ii++;
}
@ -1732,9 +1732,9 @@ void PPPMDipole::poisson_peratom_dipole()
for (j = nylo_fft; j <= nyhi_fft; j++)
for (i = nxlo_fft; i <= nxhi_fft; i++) {
work4[n] = fkx[i]*(vg[ii][2]*(work1[n]*fkx[i] + work2[n]*fky[j] +
work3[n]*fkz[k]) + 2.0*fkz[k]*work3[n]);
work3[n]*fkz[k]) + 2.0*fkz[k]*work3[n]);
work4[n+1] = fkx[i]*(vg[ii][2]*(work1[n+1]*fkx[i] + work2[n+1]*fky[j] +
work3[n+1]*fkz[k]) + 2.0*fkz[k]*work3[n+1]);
work3[n+1]*fkz[k]) + 2.0*fkz[k]*work3[n+1]);
n += 2;
ii++;
}
@ -1757,9 +1757,9 @@ void PPPMDipole::poisson_peratom_dipole()
for (j = nylo_fft; j <= nyhi_fft; j++)
for (i = nxlo_fft; i <= nxhi_fft; i++) {
work4[n] = fky[j]*(vg[ii][2]*(work1[n]*fkx[i] + work2[n]*fky[j] +
work3[n]*fkz[k]) + 2.0*fkz[k]*work3[n]);
work3[n]*fkz[k]) + 2.0*fkz[k]*work3[n]);
work4[n+1] = fky[j]*(vg[ii][2]*(work1[n+1]*fkx[i] + work2[n+1]*fky[j] +
work3[n+1]*fkz[k]) + 2.0*fkz[k]*work3[n+1]);
work3[n+1]*fkz[k]) + 2.0*fkz[k]*work3[n+1]);
n += 2;
ii++;
}
@ -1782,9 +1782,9 @@ void PPPMDipole::poisson_peratom_dipole()
for (j = nylo_fft; j <= nyhi_fft; j++)
for (i = nxlo_fft; i <= nxhi_fft; i++) {
work4[n] = fkz[k]*(vg[ii][2]*(work1[n]*fkx[i] + work2[n]*fky[j] +
work3[n]*fkz[k]) + 2.0*fkz[k]*work3[n]);
work3[n]*fkz[k]) + 2.0*fkz[k]*work3[n]);
work4[n+1] = fkz[k]*(vg[ii][2]*(work1[n+1]*fkx[i] + work2[n+1]*fky[j] +
work3[n+1]*fkz[k]) + 2.0*fkz[k]*work3[n+1]);
work3[n+1]*fkz[k]) + 2.0*fkz[k]*work3[n+1]);
n += 2;
ii++;
}
@ -1807,9 +1807,9 @@ void PPPMDipole::poisson_peratom_dipole()
for (j = nylo_fft; j <= nyhi_fft; j++)
for (i = nxlo_fft; i <= nxhi_fft; i++) {
work4[n] = fkx[i]*(vg[ii][3]*(work1[n]*fkx[i] + work2[n]*fky[j] +
work3[n]*fkz[k]) + 2.0*fky[j]*work1[n]);
work3[n]*fkz[k]) + 2.0*fky[j]*work1[n]);
work4[n+1] = fkx[i]*(vg[ii][3]*(work1[n+1]*fkx[i] + work2[n+1]*fky[j] +
work3[n+1]*fkz[k]) + 2.0*fky[j]*work1[n+1]);
work3[n+1]*fkz[k]) + 2.0*fky[j]*work1[n+1]);
n += 2;
ii++;
}
@ -1832,9 +1832,9 @@ void PPPMDipole::poisson_peratom_dipole()
for (j = nylo_fft; j <= nyhi_fft; j++)
for (i = nxlo_fft; i <= nxhi_fft; i++) {
work4[n] = fky[j]*(vg[ii][3]*(work1[n]*fkx[i] + work2[n]*fky[j] +
work3[n]*fkz[k]) + 2.0*fky[j]*work1[n]);
work3[n]*fkz[k]) + 2.0*fky[j]*work1[n]);
work4[n+1] = fky[j]*(vg[ii][3]*(work1[n+1]*fkx[i] + work2[n+1]*fky[j] +
work3[n+1]*fkz[k]) + 2.0*fky[j]*work1[n+1]);
work3[n+1]*fkz[k]) + 2.0*fky[j]*work1[n+1]);
n += 2;
ii++;
}
@ -1857,9 +1857,9 @@ void PPPMDipole::poisson_peratom_dipole()
for (j = nylo_fft; j <= nyhi_fft; j++)
for (i = nxlo_fft; i <= nxhi_fft; i++) {
work4[n] = fkz[k]*(vg[ii][3]*(work1[n]*fkx[i] + work2[n]*fky[j] +
work3[n]*fkz[k]) + 2.0*fky[j]*work1[n]);
work3[n]*fkz[k]) + 2.0*fky[j]*work1[n]);
work4[n+1] = fkz[k]*(vg[ii][3]*(work1[n+1]*fkx[i] + work2[n+1]*fky[j] +
work3[n+1]*fkz[k]) + 2.0*fky[j]*work1[n+1]);
work3[n+1]*fkz[k]) + 2.0*fky[j]*work1[n+1]);
n += 2;
ii++;
}
@ -1882,9 +1882,9 @@ void PPPMDipole::poisson_peratom_dipole()
for (j = nylo_fft; j <= nyhi_fft; j++)
for (i = nxlo_fft; i <= nxhi_fft; i++) {
work4[n] = fkx[i]*(vg[ii][4]*(work1[n]*fkx[i] + work2[n]*fky[j] +
work3[n]*fkz[k]) + 2.0*fkz[k]*work1[n]);
work3[n]*fkz[k]) + 2.0*fkz[k]*work1[n]);
work4[n+1] = fkx[i]*(vg[ii][4]*(work1[n+1]*fkx[i] + work2[n+1]*fky[j] +
work3[n+1]*fkz[k]) + 2.0*fkz[k]*work1[n+1]);
work3[n+1]*fkz[k]) + 2.0*fkz[k]*work1[n+1]);
n += 2;
ii++;
}
@ -1907,9 +1907,9 @@ void PPPMDipole::poisson_peratom_dipole()
for (j = nylo_fft; j <= nyhi_fft; j++)
for (i = nxlo_fft; i <= nxhi_fft; i++) {
work4[n] = fky[j]*(vg[ii][4]*(work1[n]*fkx[i] + work2[n]*fky[j] +
work3[n]*fkz[k]) + 2.0*fkz[k]*work1[n]);
work3[n]*fkz[k]) + 2.0*fkz[k]*work1[n]);
work4[n+1] = fky[j]*(vg[ii][4]*(work1[n+1]*fkx[i] + work2[n+1]*fky[j] +
work3[n+1]*fkz[k]) + 2.0*fkz[k]*work1[n+1]);
work3[n+1]*fkz[k]) + 2.0*fkz[k]*work1[n+1]);
n += 2;
ii++;
}
@ -1932,9 +1932,9 @@ void PPPMDipole::poisson_peratom_dipole()
for (j = nylo_fft; j <= nyhi_fft; j++)
for (i = nxlo_fft; i <= nxhi_fft; i++) {
work4[n] = fkz[k]*(vg[ii][4]*(work1[n]*fkx[i] + work2[n]*fky[j] +
work3[n]*fkz[k]) + 2.0*fkz[k]*work1[n]);
work3[n]*fkz[k]) + 2.0*fkz[k]*work1[n]);
work4[n+1] = fkz[k]*(vg[ii][4]*(work1[n+1]*fkx[i] + work2[n+1]*fky[j] +
work3[n+1]*fkz[k]) + 2.0*fkz[k]*work1[n+1]);
work3[n+1]*fkz[k]) + 2.0*fkz[k]*work1[n+1]);
n += 2;
ii++;
}
@ -1957,9 +1957,9 @@ void PPPMDipole::poisson_peratom_dipole()
for (j = nylo_fft; j <= nyhi_fft; j++)
for (i = nxlo_fft; i <= nxhi_fft; i++) {
work4[n] = fkx[i]*(vg[ii][5]*(work1[n]*fkx[i] + work2[n]*fky[j] +
work3[n]*fkz[k]) + 2.0*fkz[k]*work2[n]);
work3[n]*fkz[k]) + 2.0*fkz[k]*work2[n]);
work4[n+1] = fkx[i]*(vg[ii][5]*(work1[n+1]*fkx[i] + work2[n+1]*fky[j] +
work3[n+1]*fkz[k]) + 2.0*fkz[k]*work2[n+1]);
work3[n+1]*fkz[k]) + 2.0*fkz[k]*work2[n+1]);
n += 2;
ii++;
}
@ -1982,9 +1982,9 @@ void PPPMDipole::poisson_peratom_dipole()
for (j = nylo_fft; j <= nyhi_fft; j++)
for (i = nxlo_fft; i <= nxhi_fft; i++) {
work4[n] = fky[j]*(vg[ii][5]*(work1[n]*fkx[i] + work2[n]*fky[j] +
work3[n]*fkz[k]) + 2.0*fkz[k]*work2[n]);
work3[n]*fkz[k]) + 2.0*fkz[k]*work2[n]);
work4[n+1] = fky[j]*(vg[ii][5]*(work1[n+1]*fkx[i] + work2[n+1]*fky[j] +
work3[n+1]*fkz[k]) + 2.0*fkz[k]*work2[n+1]);
work3[n+1]*fkz[k]) + 2.0*fkz[k]*work2[n+1]);
n += 2;
ii++;
}
@ -2007,9 +2007,9 @@ void PPPMDipole::poisson_peratom_dipole()
for (j = nylo_fft; j <= nyhi_fft; j++)
for (i = nxlo_fft; i <= nxhi_fft; i++) {
work4[n] = fkz[k]*(vg[ii][5]*(work1[n]*fkx[i] + work2[n]*fky[j] +
work3[n]*fkz[k]) + 2.0*fkz[k]*work2[n]);
work3[n]*fkz[k]) + 2.0*fkz[k]*work2[n]);
work4[n+1] = fkz[k]*(vg[ii][5]*(work1[n+1]*fkx[i] + work2[n+1]*fky[j] +
work3[n+1]*fkz[k]) + 2.0*fkz[k]*work2[n+1]);
work3[n+1]*fkz[k]) + 2.0*fkz[k]*work2[n+1]);
n += 2;
ii++;
}

50
src/KSPACE/pppm_disp.cpp
View File

@ -689,9 +689,9 @@ void PPPMDisp::setup()
vg[n][3] = 0.0;
vg[n][4] = 0.0;
vg[n][5] = 0.0;
vg2[n][0] = 0.0;
vg2[n][1] = 0.0;
vg2[n][2] = 0.0;
vg2[n][0] = 0.0;
vg2[n][1] = 0.0;
vg2[n][2] = 0.0;
} else {
vterm = -2.0 * (1.0/sqk + 0.25*gew2inv);
vg[n][0] = 1.0 + vterm*fkx[i]*fkx[i];
@ -1048,7 +1048,7 @@ void PPPMDisp::compute(int eflag, int vflag)
make_rho_a();
gc6->reverse_comm_kspace(this,7,sizeof(FFT_SCALAR),REVERSE_RHO_ARITH,
gc6_buf1,gc6_buf2,MPI_FFT_SCALAR);
gc6_buf1,gc6_buf2,MPI_FFT_SCALAR);
brick2fft_a();
@ -1143,7 +1143,7 @@ void PPPMDisp::compute(int eflag, int vflag)
make_rho_none();
gc6->reverse_comm_kspace(this,nsplit_alloc,sizeof(FFT_SCALAR),REVERSE_RHO_NONE,
gc6_buf1,gc6_buf2,MPI_FFT_SCALAR);
gc6_buf1,gc6_buf2,MPI_FFT_SCALAR);
brick2fft_none();
@ -1158,14 +1158,14 @@ void PPPMDisp::compute(int eflag, int vflag)
}
gc6->forward_comm_kspace(this,1*nsplit_alloc,sizeof(FFT_SCALAR),
FORWARD_AD_NONE,
FORWARD_AD_NONE,
gc6_buf1,gc6_buf2,MPI_FFT_SCALAR);
fieldforce_none_ad();
if (vflag_atom)
gc6->forward_comm_kspace(this,6*nsplit_alloc,sizeof(FFT_SCALAR),
FORWARD_AD_PERATOM_NONE,
FORWARD_AD_PERATOM_NONE,
gc6_buf1,gc6_buf2,MPI_FFT_SCALAR);
} else {
@ -1180,14 +1180,14 @@ void PPPMDisp::compute(int eflag, int vflag)
}
gc6->forward_comm_kspace(this,3*nsplit_alloc,sizeof(FFT_SCALAR),
FORWARD_IK_NONE,
FORWARD_IK_NONE,
gc6_buf1,gc6_buf2,MPI_FFT_SCALAR);
fieldforce_none_ik();
if (evflag_atom)
gc6->forward_comm_kspace(this,7*nsplit_alloc,sizeof(FFT_SCALAR),
FORWARD_IK_PERATOM_NONE,
FORWARD_IK_PERATOM_NONE,
gc6_buf1,gc6_buf2,MPI_FFT_SCALAR);
}
@ -1321,7 +1321,7 @@ void PPPMDisp::init_coeffs()
converged = qr_alg(A,Q,n);
if (function[3] && !converged) {
error->all(FLERR,
"Matrix factorization to split dispersion coefficients failed");
"Matrix factorization to split dispersion coefficients failed");
}
// determine number of used eigenvalues
@ -1409,8 +1409,8 @@ void PPPMDisp::init_coeffs()
utils::logmesg(lmp,fmt::format(" Using {} structure factors\n",
nsplit));
if (nsplit > 9)
error->warning(FLERR,"Simulations might be very slow "
"because of large number of structure factors");
error->warning(FLERR,"Simulations might be very slow "
"because of large number of structure factors");
}
memory->destroy(A);
@ -4564,11 +4564,11 @@ void PPPMDisp::make_rho_none()
my = m+ny;
x0 = y0*rho1d_6[1][m];
for (l = nlower_6; l <= nupper_6; l++) {
mx = l+nx;
mx = l+nx;
w = x0*rho1d_6[0][l];
for (k = 0; k < nsplit; k++) {
density_brick_none[k][mz][my][mx] += w*B[nsplit*type + k];
}
}
}
}
}
@ -4813,13 +4813,13 @@ void PPPMDisp::poisson_ad(FFT_SCALAR* wk1, FFT_SCALAR* wk2,
------------------------------------------------------------------------- */
void PPPMDisp::poisson_peratom(FFT_SCALAR* wk1, FFT_SCALAR* wk2, LAMMPS_NS::FFT3d* ft2,
double** vcoeff, double** vcoeff2, int nft,
int nxlo_i, int nylo_i, int nzlo_i,
int nxhi_i, int nyhi_i, int nzhi_i,
FFT_SCALAR*** v0_pa, FFT_SCALAR*** v1_pa,
FFT_SCALAR*** v2_pa,
FFT_SCALAR*** v3_pa, FFT_SCALAR*** v4_pa,
FFT_SCALAR*** v5_pa)
double** vcoeff, double** vcoeff2, int nft,
int nxlo_i, int nylo_i, int nzlo_i,
int nxhi_i, int nyhi_i, int nzhi_i,
FFT_SCALAR*** v0_pa, FFT_SCALAR*** v1_pa,
FFT_SCALAR*** v2_pa,
FFT_SCALAR*** v3_pa, FFT_SCALAR*** v4_pa,
FFT_SCALAR*** v5_pa)
{
// v0 & v1 term
@ -5227,8 +5227,8 @@ poisson_none_ik(int n1, int n2,FFT_SCALAR* dfft_1, FFT_SCALAR* dfft_2,
if (vflag_atom)
poisson_none_peratom(n1,n2,
v0_pa[n1],v1_pa[n1],v2_pa[n1],v3_pa[n1],v4_pa[n1],v5_pa[n1],
v0_pa[n2],v1_pa[n2],v2_pa[n2],v3_pa[n2],v4_pa[n2],v5_pa[n2]);
v0_pa[n1],v1_pa[n1],v2_pa[n1],v3_pa[n1],v4_pa[n1],v5_pa[n1],
v0_pa[n2],v1_pa[n2],v2_pa[n2],v3_pa[n2],v4_pa[n2],v5_pa[n2]);
}
/* ----------------------------------------------------------------------
@ -5429,8 +5429,8 @@ poisson_none_ad(int n1, int n2, FFT_SCALAR* dfft_1, FFT_SCALAR* dfft_2,
if (vflag_atom)
poisson_none_peratom(n1,n2,
v0_pa[n1],v1_pa[n1],v2_pa[n1],v3_pa[n1],v4_pa[n1],v5_pa[n1],
v0_pa[n2],v1_pa[n2],v2_pa[n2],v3_pa[n2],v4_pa[n2],v5_pa[n2]);
v0_pa[n1],v1_pa[n1],v2_pa[n1],v3_pa[n1],v4_pa[n1],v5_pa[n1],
v0_pa[n2],v1_pa[n2],v2_pa[n2],v3_pa[n2],v4_pa[n2],v5_pa[n2]);
}
/* ----------------------------------------------------------------------

2
src/RIGID/fix_rigid_nh.cpp
View File

@ -50,7 +50,7 @@ FixRigidNH::FixRigidNH(LAMMPS *lmp, int narg, char **arg) :
id_press(nullptr), temperature(nullptr), pressure(nullptr)
{
if (tstat_flag || pstat_flag) ecouple_flag = 1;
// error checks: could be moved up to FixRigid
if ((p_flag[0] == 1 && p_period[0] <= 0.0) ||

8
src/USER-BOCS/compute_pressure_bocs.cpp
View File

@ -231,7 +231,7 @@ double ComputePressureBocs::find_index(double * grid, double value)
------------------------------------------------------------------------- */
double ComputePressureBocs::get_cg_p_corr(double ** grid, int basis_type,
double vCG)
double vCG)
{
int i = find_index(grid[0],vCG);
double correction, deltax = vCG - grid[0][i];
@ -259,8 +259,8 @@ double ComputePressureBocs::get_cg_p_corr(double ** grid, int basis_type,
------------------------------------------------------------------------- */
void ComputePressureBocs::send_cg_info(int basis_type, int sent_N_basis,
double *sent_phi_coeff, int sent_N_mol,
double sent_vavg)
double *sent_phi_coeff, int sent_N_mol,
double sent_vavg)
{
if (basis_type == BASIS_ANALYTIC) { p_basis_type = BASIS_ANALYTIC; }
else
@ -285,7 +285,7 @@ void ComputePressureBocs::send_cg_info(int basis_type, int sent_N_basis,
------------------------------------------------------------------------- */
void ComputePressureBocs::send_cg_info(int basis_type,
double ** in_splines, int gridsize)
double ** in_splines, int gridsize)
{
if (basis_type == BASIS_LINEAR_SPLINE) { p_basis_type = BASIS_LINEAR_SPLINE; }
else if (basis_type == BASIS_CUBIC_SPLINE) { p_basis_type = BASIS_CUBIC_SPLINE; }

2
src/USER-BOCS/fix_bocs.cpp
View File

@ -88,7 +88,7 @@ FixBocs::FixBocs(LAMMPS *lmp, int narg, char **arg) :
extscalar = 1;
extvector = 0;
ecouple_flag = 1;
// default values
pcouple = NONE;

2
src/USER-COLVARS/fix_colvars.cpp
View File

@ -299,7 +299,7 @@ FixColvars::FixColvars(LAMMPS *lmp, int narg, char **arg) :
extscalar = 1;
restart_global = 1;
energy_global_flag = 1;
me = comm->me;
root2root = MPI_COMM_NULL;

2
src/USER-DRUDE/fix_tgnh_drude.cpp
View File

@ -67,7 +67,7 @@ FixTGNHDrude::FixTGNHDrude(LAMMPS *lmp, int narg, char **arg) :
extscalar = 1;
extvector = 0;
ecouple_flag = 1;
// default values
pcouple = NONE;

6
src/USER-MISC/fix_flow_gauss.cpp
View File

@ -82,7 +82,7 @@ FixFlowGauss::FixFlowGauss(LAMMPS *lmp, int narg, char **arg) :
}
// by default, do not compute work done
workflag=0;
// process optional keyword
@ -137,11 +137,11 @@ void FixFlowGauss::init()
void FixFlowGauss::setup(int vflag)
{
// need to compute work done if fix_modify energy yes is set
if (thermo_energy) workflag = 1;
// get total mass of group
mTot=group->mass(igroup);
if (mTot <= 0.0)
error->all(FLERR,"Invalid group mass in fix flow/gauss");

2
src/USER-MISC/fix_ti_spring.cpp
View File

@ -65,7 +65,7 @@ FixTISpring::FixTISpring(LAMMPS *lmp, int narg, char **arg) :
extscalar = 1;
extvector = 1;
energy_global_flag = 1;
// disallow resetting the time step, while this fix is defined
time_depend = 1;

4
src/USER-MISC/fix_wall_region_ees.cpp
View File

@ -38,7 +38,7 @@ FixWallRegionEES::FixWallRegionEES(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg != 7) error->all(FLERR,"Illegal fix wall/region/ees command");
scalar_flag = 1;
vector_flag = 1;
size_vector = 3;
@ -46,7 +46,7 @@ FixWallRegionEES::FixWallRegionEES(LAMMPS *lmp, int narg, char **arg) :
extscalar = 1;
extvector = 1;
energy_global_flag = 1;
// parse args
iregion = domain->find_region(arg[3]);

2
src/USER-PLUMED/fix_plumed.cpp
View File

@ -213,7 +213,7 @@ FixPlumed::FixPlumed(LAMMPS *lmp, int narg, char **arg) :
scalar_flag = 1;
energy_global_flag = virial_global_flag = 1;
thermo_energy = thermo_virial = 1;
// This is the real initialization:
p->cmd("init");

6
src/USER-QTB/fix_qbmsst.cpp
View File

@ -63,7 +63,7 @@ FixQBMSST::FixQBMSST(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
error->all(FLERR,"Illegal fix qbmsst command");
// default parameters
global_freq = 1;
extscalar = 1;
extvector = 0;
@ -74,7 +74,7 @@ FixQBMSST::FixQBMSST(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
vector_flag = 1;
size_vector = 5;
ecouple_flag = 1;
qmass = 1.0e1;
mu = 0.0;
p0 = 0.0;
@ -95,7 +95,7 @@ FixQBMSST::FixQBMSST(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
qtb_set = 0;
// reading parameters
int iarg = 5;
while (iarg < narg) {
if (strcmp(arg[iarg],"q") == 0) {

2
src/USER-QTB/fix_qtb.cpp
View File

@ -46,7 +46,7 @@ FixQTB::FixQTB(LAMMPS *lmp, int narg, char **arg) :
if (narg < 3) error->all(FLERR,"Illegal fix qtb command");
// default parameters
t_target = 300.0;
t_period = 1.0;
fric_coef = 1/t_period;

4
src/fix.cpp
View File

@ -152,7 +152,7 @@ void Fix::modify_params(int narg, char **arg)
if (strcmp(arg[iarg+1],"no") == 0) thermo_energy = 0;
else if (strcmp(arg[iarg+1],"yes") == 0) {
if (energy_global_flag == 0 && energy_peratom_flag == 0)
error->all(FLERR,"Illegal fix_modify command");
error->all(FLERR,"Illegal fix_modify command");
thermo_energy = 1;
} else error->all(FLERR,"Illegal fix_modify command");
iarg += 2;
@ -161,7 +161,7 @@ void Fix::modify_params(int narg, char **arg)
if (strcmp(arg[iarg+1],"no") == 0) thermo_virial = 0;
else if (strcmp(arg[iarg+1],"yes") == 0) {
if (virial_global_flag == 0 && virial_peratom_flag == 0)
error->all(FLERR,"Illegal fix_modify command");
error->all(FLERR,"Illegal fix_modify command");
thermo_virial = 1;
} else error->all(FLERR,"Illegal fix_modify command");
iarg += 2;

2
src/fix.h
View File

@ -245,7 +245,7 @@ class Fix : protected Pointers {
void ev_init(int eflag, int vflag) {
if ((eflag && thermo_energy) || (vflag && thermo_virial)) ev_setup(eflag, vflag);
else evflag = eflag_either = eflag_global = eflag_atom =
vflag_either = vflag_global = vflag_atom = 0;
vflag_either = vflag_global = vflag_atom = 0;
}
void ev_setup(int, int);
void ev_tally(int, int *, double, double, double *);

2
src/fix_nh.cpp
View File

@ -786,7 +786,7 @@ void FixNH::setup(int /*vflag*/)
t0 = temperature->compute_scalar();
if (t0 < EPSILON)
error->all(FLERR,"Current temperature too close to zero, "
"consider using ptemp setting");
"consider using ptemp setting");
}
}
t_target = t0;

2
src/fix_wall.cpp
View File

@ -315,7 +315,7 @@ void FixWall::post_force(int vflag)
v_init(vflag);
// energy intialize
for (int m = 0; m <= nwall; m++) ewall[m] = 0.0;
// coord = current position of wall