diff --git a/doc/src/Developer_notes.rst b/doc/src/Developer_notes.rst index 81161fa348..d4fee7b9a0 100644 --- a/doc/src/Developer_notes.rst +++ b/doc/src/Developer_notes.rst @@ -57,7 +57,7 @@ value of 1 in their constructor: * *energy_peratom_flag* to contribute to peratom energy, :doc:`fix cmap ` * *virial_global_flag* to contribute to global virial, example: :doc:`fix wall ` * *virial_peratom_flag* to contribute to peratom virial, example: :doc:`fix wall ` - + The fix must also do the following: * For global energy, implement a compute_scalar() method that returns diff --git a/doc/src/fix_modify.rst b/doc/src/fix_modify.rst index d382d3ebe8..3f97b158e2 100644 --- a/doc/src/fix_modify.rst +++ b/doc/src/fix_modify.rst @@ -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 diff --git a/doc/src/thermo_style.rst b/doc/src/thermo_style.rst index c43bf9ed0d..ac53e575e5 100644 --- a/doc/src/thermo_style.rst +++ b/doc/src/thermo_style.rst @@ -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 `. The *fmax* keyword calculates the maximum force in any dimension on any atom in the diff --git a/src/KSPACE/pppm_dipole.cpp b/src/KSPACE/pppm_dipole.cpp index 7a472be818..54810158aa 100644 --- a/src/KSPACE/pppm_dipole.cpp +++ b/src/KSPACE/pppm_dipole.cpp @@ -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++; } diff --git a/src/KSPACE/pppm_disp.cpp b/src/KSPACE/pppm_disp.cpp index a9af0aff40..d982d57853 100644 --- a/src/KSPACE/pppm_disp.cpp +++ b/src/KSPACE/pppm_disp.cpp @@ -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]); } /* ---------------------------------------------------------------------- diff --git a/src/RIGID/fix_rigid_nh.cpp b/src/RIGID/fix_rigid_nh.cpp index 7fefdaebfe..a29c8d9863 100644 --- a/src/RIGID/fix_rigid_nh.cpp +++ b/src/RIGID/fix_rigid_nh.cpp @@ -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) || diff --git a/src/USER-BOCS/compute_pressure_bocs.cpp b/src/USER-BOCS/compute_pressure_bocs.cpp index 004a11d048..a84442e658 100644 --- a/src/USER-BOCS/compute_pressure_bocs.cpp +++ b/src/USER-BOCS/compute_pressure_bocs.cpp @@ -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; } diff --git a/src/USER-BOCS/fix_bocs.cpp b/src/USER-BOCS/fix_bocs.cpp index 3df1cc2bd3..28a0d6c01a 100644 --- a/src/USER-BOCS/fix_bocs.cpp +++ b/src/USER-BOCS/fix_bocs.cpp @@ -88,7 +88,7 @@ FixBocs::FixBocs(LAMMPS *lmp, int narg, char **arg) : extscalar = 1; extvector = 0; ecouple_flag = 1; - + // default values pcouple = NONE; diff --git a/src/USER-COLVARS/fix_colvars.cpp b/src/USER-COLVARS/fix_colvars.cpp index 4bcd68dae9..1a8338ccf6 100644 --- a/src/USER-COLVARS/fix_colvars.cpp +++ b/src/USER-COLVARS/fix_colvars.cpp @@ -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; diff --git a/src/USER-DRUDE/fix_tgnh_drude.cpp b/src/USER-DRUDE/fix_tgnh_drude.cpp index ee47d8a0d9..8185b9bcbb 100644 --- a/src/USER-DRUDE/fix_tgnh_drude.cpp +++ b/src/USER-DRUDE/fix_tgnh_drude.cpp @@ -67,7 +67,7 @@ FixTGNHDrude::FixTGNHDrude(LAMMPS *lmp, int narg, char **arg) : extscalar = 1; extvector = 0; ecouple_flag = 1; - + // default values pcouple = NONE; diff --git a/src/USER-MISC/fix_flow_gauss.cpp b/src/USER-MISC/fix_flow_gauss.cpp index f5cbeaeed5..3c913f8039 100644 --- a/src/USER-MISC/fix_flow_gauss.cpp +++ b/src/USER-MISC/fix_flow_gauss.cpp @@ -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"); diff --git a/src/USER-MISC/fix_ti_spring.cpp b/src/USER-MISC/fix_ti_spring.cpp index 9e6c1ce296..cb343fc9d6 100644 --- a/src/USER-MISC/fix_ti_spring.cpp +++ b/src/USER-MISC/fix_ti_spring.cpp @@ -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; diff --git a/src/USER-MISC/fix_wall_region_ees.cpp b/src/USER-MISC/fix_wall_region_ees.cpp index 7fe3ab24a3..44067b0742 100644 --- a/src/USER-MISC/fix_wall_region_ees.cpp +++ b/src/USER-MISC/fix_wall_region_ees.cpp @@ -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]); diff --git a/src/USER-PLUMED/fix_plumed.cpp b/src/USER-PLUMED/fix_plumed.cpp index cd6292d64e..5e85cc56de 100644 --- a/src/USER-PLUMED/fix_plumed.cpp +++ b/src/USER-PLUMED/fix_plumed.cpp @@ -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"); diff --git a/src/USER-QTB/fix_qbmsst.cpp b/src/USER-QTB/fix_qbmsst.cpp index 7e442aceba..fea549c07e 100644 --- a/src/USER-QTB/fix_qbmsst.cpp +++ b/src/USER-QTB/fix_qbmsst.cpp @@ -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) { diff --git a/src/USER-QTB/fix_qtb.cpp b/src/USER-QTB/fix_qtb.cpp index 761a0ed537..a344a5eaec 100644 --- a/src/USER-QTB/fix_qtb.cpp +++ b/src/USER-QTB/fix_qtb.cpp @@ -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; diff --git a/src/fix.cpp b/src/fix.cpp index 074040a4d8..8cf13f6f1d 100644 --- a/src/fix.cpp +++ b/src/fix.cpp @@ -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; diff --git a/src/fix.h b/src/fix.h index c8db215255..7092b56c8f 100644 --- a/src/fix.h +++ b/src/fix.h @@ -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 *); diff --git a/src/fix_nh.cpp b/src/fix_nh.cpp index f4de07a5ae..d1a2cb1463 100644 --- a/src/fix_nh.cpp +++ b/src/fix_nh.cpp @@ -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; diff --git a/src/fix_wall.cpp b/src/fix_wall.cpp index 942dd1f81a..56bc91e5f6 100644 --- a/src/fix_wall.cpp +++ b/src/fix_wall.cpp @@ -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