From 1d56981bb11e1efc6fc924345b7987e5c0908587 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 31 Jan 2025 15:15:10 -0500 Subject: [PATCH 001/113] reassign error URL numbers to match list in pull request --- doc/src/Errors_details.rst | 52 +++++++++++++++++++---------- src/INTEL/npair_bin_ghost_intel.cpp | 2 +- src/INTEL/npair_bin_intel.cpp | 6 ++-- src/INTEL/npair_full_bin_intel.cpp | 2 +- src/nbin_multi.cpp | 8 ++--- src/nbin_standard.cpp | 6 ++-- 6 files changed, 47 insertions(+), 29 deletions(-) diff --git a/doc/src/Errors_details.rst b/doc/src/Errors_details.rst index ab92d16ccb..6ae768326a 100644 --- a/doc/src/Errors_details.rst +++ b/doc/src/Errors_details.rst @@ -12,9 +12,12 @@ following are discussions of such cases. - :ref:`Incorrect format in ... section of data file ` - :ref:`Illegal variable command: expected X arguments but found Y ` - :ref:`Out of range atoms - cannot compute ... ` -- :ref:`Cannot use neighbor bins - box size \<\< cutoff ` -- :ref:`Too many neighbor bins ` -- :ref:`Domain too large for neighbor bins ` +- :ref:`Too many neighbor bins ` +- :ref:`Cannot use neighbor bins - box size \<\< cutoff ` +- :ref:`Domain too large for neighbor bins ` +- :ref:`Molecule topology/atom exceeds system topology/atom ` +- :ref:`Molecule topology type exceeds system topology type ` +- :ref:`Molecule attributes do not match system attributes ` ------ @@ -276,7 +279,19 @@ help to temporarily use a cutoff-Coulomb pair style and no kspace style until the system has somewhat equilibrated and then switch to the long-range solver. -.. _err0005: +.. _err0009: + +Too many neighbor bins +---------------------- + +The simulation box has become too large relative to the size of a +neighbor bin and LAMMPS is unable to store the needed number of +bins. This typically implies the simulation box has expanded too far. +This can happen when some atoms move rapidly apart with shrinkwrap +boundaries or when a fix (like fix deform or a barostat) excessively +grows the simulation box. + +.. _err0015: Cannot use neighbor bins - box size \<\< cutoff ----------------------------------------------- @@ -290,19 +305,7 @@ fill space. This error can be avoided using the generally slower :doc:`nsq neighbor style ` or by increasing the size of the smallest box lengths. -.. _err0006: - -Too many neighbor bins ----------------------- - -The simulation box has become too large relative to the size of a -neighbor bin and LAMMPS is unable to store the needed number of -bins. This typically implies the simulation box has expanded too far. -This can happen when some atoms move rapidly apart with shrinkwrap -boundaries or when a fix (like fix deform or a barostat) excessively -grows the simulation box. - -.. _err0007: +.. _err0017: Domain too large for neighbor bins ---------------------------------- @@ -312,3 +315,18 @@ be used. Too many neighbor bins would need to be created to fill space Most likely, one or more atoms have been blown out of the simulation box to a great distance or a fix (like fix deform or a barostat) has excessively grown the simulation box. + +.. _err0024: + +Molecule topology/atom exceeds system topology/atom +--------------------------------------------------- + +.. _err0025: + +Molecule topology type exceeds system topology type +--------------------------------------------------- + +.. _err0026: + +Molecule attributes do not match system attributes +-------------------------------------------------- diff --git a/src/INTEL/npair_bin_ghost_intel.cpp b/src/INTEL/npair_bin_ghost_intel.cpp index 1210f33b9a..6fc3e99df3 100644 --- a/src/INTEL/npair_bin_ghost_intel.cpp +++ b/src/INTEL/npair_bin_ghost_intel.cpp @@ -48,7 +48,7 @@ void NPairFullBinGhostIntel::build(NeighList *list) #endif if (nstencil > INTEL_MAX_STENCIL_CHECK) - error->all(FLERR, "Too many neighbor bins for INTEL package."); + error->all(FLERR, "Too many neighbor bins for INTEL package" + utils::errorurl(9)); #ifdef _LMP_INTEL_OFFLOAD if (exclude) diff --git a/src/INTEL/npair_bin_intel.cpp b/src/INTEL/npair_bin_intel.cpp index f4942022ec..314b539fa5 100644 --- a/src/INTEL/npair_bin_intel.cpp +++ b/src/INTEL/npair_bin_intel.cpp @@ -41,7 +41,7 @@ NPairHalfBinNewtonIntel::NPairHalfBinNewtonIntel(LAMMPS *lmp) : void NPairHalfBinNewtonIntel::build(NeighList *list) { if (nstencil / 2 > INTEL_MAX_STENCIL_CHECK) - error->all(FLERR, "Too many neighbor bins for INTEL package."); + error->all(FLERR, "Too many neighbor bins for INTEL package" + utils::errorurl(9)); #ifdef _LMP_INTEL_OFFLOAD if (exclude) @@ -123,7 +123,7 @@ NPairHalfBinNewtonTriIntel::NPairHalfBinNewtonTriIntel(LAMMPS *lmp) : void NPairHalfBinNewtonTriIntel::build(NeighList *list) { if (nstencil > INTEL_MAX_STENCIL) - error->all(FLERR, "Too many neighbor bins for INTEL package."); + error->all(FLERR, "Too many neighbor bins for INTEL package" + utils::errorurl(9)); #ifdef _LMP_INTEL_OFFLOAD if (exclude) @@ -202,7 +202,7 @@ NPairFullBinIntel::NPairFullBinIntel(LAMMPS *lmp) : NPairIntel(lmp) {} void NPairFullBinIntel::build(NeighList *list) { if (nstencil > INTEL_MAX_STENCIL_CHECK) - error->all(FLERR, "Too many neighbor bins for INTEL package."); + error->all(FLERR, "Too many neighbor bins for INTEL package" + utils::errorurl(9)); #ifdef _LMP_INTEL_OFFLOAD if (exclude) diff --git a/src/INTEL/npair_full_bin_intel.cpp b/src/INTEL/npair_full_bin_intel.cpp index 285ed35ec9..038e50ab0b 100644 --- a/src/INTEL/npair_full_bin_intel.cpp +++ b/src/INTEL/npair_full_bin_intel.cpp @@ -38,7 +38,7 @@ NPairFullBinIntel::NPairFullBinIntel(LAMMPS *lmp) : NPairIntel(lmp) {} void NPairFullBinIntel::build(NeighList *list) { if (nstencil > INTEL_MAX_STENCIL_CHECK) - error->all(FLERR, "Too many neighbor bins for INTEL package."); + error->all(FLERR, "Too many neighbor bins for INTEL package" + utils::errorurl(9)); #ifdef _LMP_INTEL_OFFLOAD if (exclude) diff --git a/src/nbin_multi.cpp b/src/nbin_multi.cpp index 85bf911808..2e01380121 100644 --- a/src/nbin_multi.cpp +++ b/src/nbin_multi.cpp @@ -205,7 +205,7 @@ void NBinMulti::setup_bins(int /*style*/) if (bbox[0]*binsizeinv > MAXSMALLINT || bbox[1]*binsizeinv > MAXSMALLINT || bbox[2]*binsizeinv > MAXSMALLINT) - error->all(FLERR,"Domain too large for neighbor bins{}", utils::errorurl(7)); + error->all(FLERR,"Domain too large for neighbor bins" + utils::errorurl(17)); // create actual bins // always have one bin even if cutoff > bbox @@ -236,9 +236,9 @@ void NBinMulti::setup_bins(int /*style*/) if (binsize_optimal*bininvx_multi[n] > CUT2BIN_RATIO || binsize_optimal*bininvy_multi[n] > CUT2BIN_RATIO) - error->all(FLERR,"Cannot use neighbor bins - box size << cutoff{}", utils::errorurl(5)); + error->all(FLERR,"Cannot use neighbor bins - box size << cutoff" + utils::errorurl(15)); if ((dimension == 3) && (binsize_optimal*bininvz_multi[n] > CUT2BIN_RATIO)) - error->all(FLERR,"Cannot use neighbor bins - box size << cutoff{}", utils::errorurl(5)); + error->all(FLERR,"Cannot use neighbor bins - box size << cutoff" + utils::errorurl(15)); // mbinlo/hi = lowest and highest global bins my ghost atoms could be in // coord = lowest and highest values of coords for my ghost atoms @@ -284,7 +284,7 @@ void NBinMulti::setup_bins(int /*style*/) bigint bbin = ((bigint) mbinx_multi[n]) * ((bigint) mbiny_multi[n]) * ((bigint) mbinz_multi[n]) + 1; - if (bbin > MAXSMALLINT) error->one(FLERR,"Too many neighbor bins{}", utils::errorurl(6)); + if (bbin > MAXSMALLINT) error->one(FLERR,"Too many neighbor bins" + utils::errorurl(9)); mbins_multi[n] = bbin; } diff --git a/src/nbin_standard.cpp b/src/nbin_standard.cpp index 2ce07ecac2..bf4ae29096 100644 --- a/src/nbin_standard.cpp +++ b/src/nbin_standard.cpp @@ -130,7 +130,7 @@ void NBinStandard::setup_bins(int style) if (bbox[0]*binsizeinv > MAXSMALLINT || bbox[1]*binsizeinv > MAXSMALLINT || bbox[2]*binsizeinv > MAXSMALLINT) - error->all(FLERR,"Domain too large for neighbor bins{}", utils::errorurl(7)); + error->all(FLERR,"Domain too large for neighbor bins" + utils::errorurl(17)); // create actual bins // always have one bin even if cutoff > bbox @@ -162,7 +162,7 @@ void NBinStandard::setup_bins(int style) if (binsize_optimal*bininvx > CUT2BIN_RATIO || binsize_optimal*bininvy > CUT2BIN_RATIO || binsize_optimal*bininvz > CUT2BIN_RATIO) - error->all(FLERR,"Cannot use neighbor bins - box size << cutoff{}", utils::errorurl(5)); + error->all(FLERR,"Cannot use neighbor bins - box size << cutoff" + utils::errorurl(15)); // mbinlo/hi = lowest and highest global bins my ghost atoms could be in // coord = lowest and highest values of coords for my ghost atoms @@ -210,7 +210,7 @@ void NBinStandard::setup_bins(int style) mbinz = mbinzhi - mbinzlo + 1; bigint bbin = ((bigint) mbinx) * ((bigint) mbiny) * ((bigint) mbinz) + 1; - if (bbin > MAXSMALLINT) error->one(FLERR,"Too many neighbor bins{}", utils::errorurl(6)); + if (bbin > MAXSMALLINT) error->one(FLERR,"Too many neighbor bins" + utils::errorurl(9)); mbins = bbin; } From 8c2bbc1608cfbf506ad4804a215f6c4fdf2bfbf3 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 31 Jan 2025 15:57:53 -0500 Subject: [PATCH 002/113] add error URLs for molecule files --- doc/src/Errors_details.rst | 37 +++++++++++++++++++++++++++++++++++++ src/molecule.cpp | 8 +++++--- 2 files changed, 42 insertions(+), 3 deletions(-) diff --git a/doc/src/Errors_details.rst b/doc/src/Errors_details.rst index 6ae768326a..b285818e0e 100644 --- a/doc/src/Errors_details.rst +++ b/doc/src/Errors_details.rst @@ -321,12 +321,49 @@ excessively grown the simulation box. Molecule topology/atom exceeds system topology/atom --------------------------------------------------- +LAMMPS uses :doc:`domain decomposition ` to +distribute data (i.e. atoms) across the MPI processes in parallel runs. +This includes topology data, that is data about bonds, angles, +dihedrals, impropers and :doc:`"special" neighbors `. +This information is stored with either one or all atoms involved in such +a topology entry (which of the two option applies depends on the +:doc:`newton ` setting for bonds. When reading a data file, +LAMMPS analyzes the requirements for this file and then the values +are "locked in" and cannot be extended. + +So loading a molecule file that requires more of the topology per atom +storage or adding a data file with such needs will lead to an error. To +avoid the error, one or more of the `extra/XXX/per/atom` keywords are +required to extend the corresponding storage. It is no problem to +choose those numbers generously and have more storage reserved than +actually needed, but having these numbers set too small will lead to an +error. + .. _err0025: Molecule topology type exceeds system topology type --------------------------------------------------- +The total number of atom, bond, angle, dihedral, and improper types is +"locked in" when LAMMPS creates the simulation box. This can happen +through either the :doc:`create_box `, the :doc:`read_data +`, or the :doc:`read_restart ` command. After +this it is not possible to refer to an additional type. So loading a +molecule file that uses additional types or adding a data file that +would require additional types will lead to an error. To avoid the +error, one or more of the `extra/XXX/types` keywords are required to +extend the maximum number of the individual types. + .. _err0026: Molecule attributes do not match system attributes -------------------------------------------------- + +Choosing an :doc:`atom_style ` in LAMMPS determines which +per-atom properties are available. In a :doc:`molecule file +`, however, it is possible to add sections (for example Masses +or Charges) that are not supported by the atom style. Masses for +example, are usually not a per-atom property, but defined through the +atom type. Thus it would not be required to have a Masses section and +the included data would be ignored. LAMMPS prints this warning to +inform about this case. diff --git a/src/molecule.cpp b/src/molecule.cpp index 2a9b8a944d..8530f6c990 100644 --- a/src/molecule.cpp +++ b/src/molecule.cpp @@ -1876,7 +1876,7 @@ void Molecule::check_attributes() if (rmassflag && !atom->rmass_flag) mismatch = 1; if (mismatch && me == 0) - error->warning(FLERR, "Molecule attributes do not match system attributes"); + error->warning(FLERR, "Molecule attributes do not match system attributes" + utils::errorurl(26)); // for all atom styles, check nbondtype,etc @@ -1886,7 +1886,8 @@ void Molecule::check_attributes() if (atom->ndihedraltypes < ndihedraltypes) mismatch = 1; if (atom->nimpropertypes < nimpropertypes) mismatch = 1; - if (mismatch) error->all(FLERR, "Molecule topology type exceeds system topology type"); + if (mismatch) + error->all(FLERR, "Molecule topology type exceeds system topology type" + utils::errorurl(25)); // for molecular atom styles, check bond_per_atom,etc + maxspecial // do not check for atom style template, since nothing stored per atom @@ -1898,7 +1899,8 @@ void Molecule::check_attributes() if (atom->avec->impropers_allow && atom->improper_per_atom < improper_per_atom) mismatch = 1; if (atom->maxspecial < maxspecial) mismatch = 1; - if (mismatch) error->all(FLERR, "Molecule topology/atom exceeds system topology/atom"); + if (mismatch) + error->all(FLERR, "Molecule topology/atom exceeds system topology/atom" + utils::errorurl(24)); } // warn if molecule topology defined but no special settings From 4e582993c4782a35b7b9bba54c01eff4216d0c8f Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 31 Jan 2025 16:07:39 -0500 Subject: [PATCH 003/113] use simpler std::string concatenation instead of implicit fmt::format() processing --- src/GPU/pppm_gpu.cpp | 2 +- src/INTEL/pppm_disp_intel.cpp | 2 +- src/INTEL/pppm_intel.cpp | 2 +- src/KOKKOS/pppm_kokkos.cpp | 2 +- src/KSPACE/msm_cg.cpp | 2 +- src/KSPACE/pppm.cpp | 2 +- src/KSPACE/pppm_cg.cpp | 2 +- src/KSPACE/pppm_disp.cpp | 2 +- src/KSPACE/pppm_disp_tip4p.cpp | 2 +- src/KSPACE/pppm_stagger.cpp | 2 +- src/KSPACE/pppm_tip4p.cpp | 2 +- src/OPENMP/pppm_disp_omp.cpp | 2 +- src/OPENMP/pppm_disp_tip4p_omp.cpp | 2 +- src/OPENMP/pppm_tip4p_omp.cpp | 2 +- 14 files changed, 14 insertions(+), 14 deletions(-) diff --git a/src/GPU/pppm_gpu.cpp b/src/GPU/pppm_gpu.cpp index 9bfa01b846..593aed827c 100644 --- a/src/GPU/pppm_gpu.cpp +++ b/src/GPU/pppm_gpu.cpp @@ -197,7 +197,7 @@ void PPPMGPU::compute(int eflag, int vflag) if (!success) error->one(FLERR,"Insufficient memory on accelerator"); if (flag != 0) - error->one(FLERR,"Out of range atoms - cannot compute PPPM{}", utils::errorurl(4)); + error->one(FLERR,"Out of range atoms - cannot compute PPPM" + utils::errorurl(4)); } // convert atoms from box to lamda coords diff --git a/src/INTEL/pppm_disp_intel.cpp b/src/INTEL/pppm_disp_intel.cpp index 97d4cfc451..8053036112 100644 --- a/src/INTEL/pppm_disp_intel.cpp +++ b/src/INTEL/pppm_disp_intel.cpp @@ -777,7 +777,7 @@ void PPPMDispIntel::particle_map_intel(double delx, double dely, double delz, } } - if (flag) error->one(FLERR,"Out of range atoms - cannot compute PPPMDisp{}", utils::errorurl(4)); + if (flag) error->one(FLERR,"Out of range atoms - cannot compute PPPMDisp" + utils::errorurl(4)); } /* ---------------------------------------------------------------------- diff --git a/src/INTEL/pppm_intel.cpp b/src/INTEL/pppm_intel.cpp index d1596ec757..8d46cc28e9 100644 --- a/src/INTEL/pppm_intel.cpp +++ b/src/INTEL/pppm_intel.cpp @@ -404,7 +404,7 @@ void PPPMIntel::particle_map(IntelBuffers *buffers) } } - if (flag) error->one(FLERR,"Out of range atoms - cannot compute PPPM{}", utils::errorurl(4)); + if (flag) error->one(FLERR,"Out of range atoms - cannot compute PPPM" + utils::errorurl(4)); } diff --git a/src/KOKKOS/pppm_kokkos.cpp b/src/KOKKOS/pppm_kokkos.cpp index d30170c33d..34c3d7579e 100644 --- a/src/KOKKOS/pppm_kokkos.cpp +++ b/src/KOKKOS/pppm_kokkos.cpp @@ -1147,7 +1147,7 @@ void PPPMKokkos::particle_map() k_flag.template modify(); k_flag.template sync(); if (k_flag.h_view()) - error->one(FLERR,"Out of range atoms - cannot compute PPPM{}", utils::errorurl(4)); + error->one(FLERR,"Out of range atoms - cannot compute PPPM" + utils::errorurl(4)); } template diff --git a/src/KSPACE/msm_cg.cpp b/src/KSPACE/msm_cg.cpp index c643d86a89..60aebc0f60 100644 --- a/src/KSPACE/msm_cg.cpp +++ b/src/KSPACE/msm_cg.cpp @@ -335,7 +335,7 @@ void MSMCG::particle_map() flag = 1; } - if (flag) error->one(FLERR,"Out of range atoms - cannot compute MSM{}", utils::errorurl(4)); + if (flag) error->one(FLERR,"Out of range atoms - cannot compute MSM" + utils::errorurl(4)); } /* ---------------------------------------------------------------------- diff --git a/src/KSPACE/pppm.cpp b/src/KSPACE/pppm.cpp index 3cd743cd0c..611e29360b 100644 --- a/src/KSPACE/pppm.cpp +++ b/src/KSPACE/pppm.cpp @@ -1830,7 +1830,7 @@ void PPPM::particle_map() flag = 1; } - if (flag) error->one(FLERR,"Out of range atoms - cannot compute PPPM{}", utils::errorurl(4)); + if (flag) error->one(FLERR,"Out of range atoms - cannot compute PPPM" + utils::errorurl(4)); } /* ---------------------------------------------------------------------- diff --git a/src/KSPACE/pppm_cg.cpp b/src/KSPACE/pppm_cg.cpp index de5d26d17f..5e244c8a37 100644 --- a/src/KSPACE/pppm_cg.cpp +++ b/src/KSPACE/pppm_cg.cpp @@ -304,7 +304,7 @@ void PPPMCG::particle_map() flag = 1; } - if (flag) error->one(FLERR,"Out of range atoms - cannot compute PPPM{}", utils::errorurl(4)); + if (flag) error->one(FLERR,"Out of range atoms - cannot compute PPPM" + utils::errorurl(4)); } /* ---------------------------------------------------------------------- diff --git a/src/KSPACE/pppm_disp.cpp b/src/KSPACE/pppm_disp.cpp index ff61c61ab9..8ff2ae2635 100644 --- a/src/KSPACE/pppm_disp.cpp +++ b/src/KSPACE/pppm_disp.cpp @@ -4252,7 +4252,7 @@ void PPPMDisp::particle_map(double delx, double dely, double delz, flag = 1; } - if (flag) error->one(FLERR,"Out of range atoms - cannot compute PPPMDisp{}", utils::errorurl(4)); + if (flag) error->one(FLERR,"Out of range atoms - cannot compute PPPMDisp" + utils::errorurl(4)); } /* ---------------------------------------------------------------------- diff --git a/src/KSPACE/pppm_disp_tip4p.cpp b/src/KSPACE/pppm_disp_tip4p.cpp index 9f66807781..a07387443b 100644 --- a/src/KSPACE/pppm_disp_tip4p.cpp +++ b/src/KSPACE/pppm_disp_tip4p.cpp @@ -100,7 +100,7 @@ void PPPMDispTIP4P::particle_map_c(double delx, double dely, double delz, flag = 1; } - if (flag) error->one(FLERR,"Out of range atoms - cannot compute PPPM{}", utils::errorurl(4)); + if (flag) error->one(FLERR,"Out of range atoms - cannot compute PPPM" + utils::errorurl(4)); } /* ---------------------------------------------------------------------- diff --git a/src/KSPACE/pppm_stagger.cpp b/src/KSPACE/pppm_stagger.cpp index 117b6d840e..4d0fb7f20a 100644 --- a/src/KSPACE/pppm_stagger.cpp +++ b/src/KSPACE/pppm_stagger.cpp @@ -699,7 +699,7 @@ void PPPMStagger::particle_map() flag = 1; } - if (flag) error->one(FLERR,"Out of range atoms - cannot compute PPPM{}", utils::errorurl(4)); + if (flag) error->one(FLERR,"Out of range atoms - cannot compute PPPM" + utils::errorurl(4)); } /* ---------------------------------------------------------------------- diff --git a/src/KSPACE/pppm_tip4p.cpp b/src/KSPACE/pppm_tip4p.cpp index bf86a00cdc..0ece29768e 100644 --- a/src/KSPACE/pppm_tip4p.cpp +++ b/src/KSPACE/pppm_tip4p.cpp @@ -98,7 +98,7 @@ void PPPMTIP4P::particle_map() int flag_all; MPI_Allreduce(&flag,&flag_all,1,MPI_INT,MPI_SUM,world); - if (flag_all) error->all(FLERR,"Out of range atoms - cannot compute PPPM{}", utils::errorurl(4)); + if (flag_all) error->all(FLERR,"Out of range atoms - cannot compute PPPM" + utils::errorurl(4)); } /* ---------------------------------------------------------------------- diff --git a/src/OPENMP/pppm_disp_omp.cpp b/src/OPENMP/pppm_disp_omp.cpp index 56d4715891..6fceca6a14 100644 --- a/src/OPENMP/pppm_disp_omp.cpp +++ b/src/OPENMP/pppm_disp_omp.cpp @@ -388,7 +388,7 @@ void PPPMDispOMP::particle_map(double dxinv, double dyinv, int flag_all; MPI_Allreduce(&flag,&flag_all,1,MPI_INT,MPI_SUM,world); - if (flag_all) error->all(FLERR,"Out of range atoms - cannot compute PPPM{}", utils::errorurl(4)); + if (flag_all) error->all(FLERR,"Out of range atoms - cannot compute PPPM" + utils::errorurl(4)); } /* ---------------------------------------------------------------------- diff --git a/src/OPENMP/pppm_disp_tip4p_omp.cpp b/src/OPENMP/pppm_disp_tip4p_omp.cpp index a4db1c197f..d3a9c9528c 100644 --- a/src/OPENMP/pppm_disp_tip4p_omp.cpp +++ b/src/OPENMP/pppm_disp_tip4p_omp.cpp @@ -392,7 +392,7 @@ void PPPMDispTIP4POMP::particle_map_c(double dxinv, double dyinv, int flag_all; MPI_Allreduce(&flag,&flag_all,1,MPI_INT,MPI_SUM,world); - if (flag_all) error->all(FLERR,"Out of range atoms - cannot compute PPPM{}", utils::errorurl(4)); + if (flag_all) error->all(FLERR,"Out of range atoms - cannot compute PPPM" + utils::errorurl(4)); } /* ---------------------------------------------------------------------- diff --git a/src/OPENMP/pppm_tip4p_omp.cpp b/src/OPENMP/pppm_tip4p_omp.cpp index 0bdadec77d..640b7d4d35 100644 --- a/src/OPENMP/pppm_tip4p_omp.cpp +++ b/src/OPENMP/pppm_tip4p_omp.cpp @@ -388,7 +388,7 @@ void PPPMTIP4POMP::particle_map() int flag_all; MPI_Allreduce(&flag,&flag_all,1,MPI_INT,MPI_SUM,world); - if (flag_all) error->all(FLERR,"Out of range atoms - cannot compute PPPM{}", utils::errorurl(4)); + if (flag_all) error->all(FLERR,"Out of range atoms - cannot compute PPPM" + utils::errorurl(4)); } /* ---------------------------------------------------------------------- From 504e747f3d8bf675c88034f715a61be8bfb5d0f7 Mon Sep 17 00:00:00 2001 From: megmcca Date: Mon, 3 Feb 2025 11:56:39 -0700 Subject: [PATCH 004/113] add initial error URL and test --- doc/src/Errors_details.rst | 9 +++++++++ src/ML-SNAP/pair_snap.cpp | 2 +- 2 files changed, 10 insertions(+), 1 deletion(-) diff --git a/doc/src/Errors_details.rst b/doc/src/Errors_details.rst index b285818e0e..2211333cd6 100644 --- a/doc/src/Errors_details.rst +++ b/doc/src/Errors_details.rst @@ -15,6 +15,7 @@ following are discussions of such cases. - :ref:`Too many neighbor bins ` - :ref:`Cannot use neighbor bins - box size \<\< cutoff ` - :ref:`Domain too large for neighbor bins ` +- :ref:`Incorrect args for pair coefficients ` - :ref:`Molecule topology/atom exceeds system topology/atom ` - :ref:`Molecule topology type exceeds system topology type ` - :ref:`Molecule attributes do not match system attributes ` @@ -316,6 +317,14 @@ Most likely, one or more atoms have been blown out of the simulation box to a great distance or a fix (like fix deform or a barostat) has excessively grown the simulation box. +.. _err0021: + +Incorrect args for pair coefficients +------------------------------------ + +The parameters in the :doc:`pair_coeff `, command for a specified :doc:`pair_style ` +have a missing or erroneous argument. Outside of normal typos, this error can have several sources. In all cases, the first step is to compare one's code to the expected format relevant :doc:`pair_style ` page. This can uncover cases where a pair style was changed, but the pair coefficients were not updated. This can happen especially with pair style variants such as :doc:`pair_style eam ` vs. :doc:`pair_style eam/alloy ` that are very similar but accept different numbers of coefficients. Note also that using multiple pair styles with commands such as :doc:`pair_style hybrid `. Using hybrid pair styles requires adding an extra "label" argument in the :doc:`pair_coeff ` commands that designates which pair style the command line refers to. Other errors might require a close look at files that are read in by the input script, such as data files or restart files. + .. _err0024: Molecule topology/atom exceeds system topology/atom diff --git a/src/ML-SNAP/pair_snap.cpp b/src/ML-SNAP/pair_snap.cpp index ff6409095d..5011256dd2 100644 --- a/src/ML-SNAP/pair_snap.cpp +++ b/src/ML-SNAP/pair_snap.cpp @@ -383,7 +383,7 @@ void PairSNAP::settings(int narg, char ** /* arg */) void PairSNAP::coeff(int narg, char **arg) { if (!allocated) allocate(); - if (narg != 4 + atom->ntypes) error->all(FLERR,"Incorrect args for pair coefficients"); + if (narg != 4 + atom->ntypes) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); map_element2type(narg-4,arg+4); From 32d0bf1bee0573f1f341e50f87c65d9cf36672a1 Mon Sep 17 00:00:00 2001 From: megmcca Date: Mon, 3 Feb 2025 12:13:52 -0700 Subject: [PATCH 005/113] update all simple coeff messages --- src/AMOEBA/pair_amoeba.cpp | 2 +- src/ASPHERE/pair_gayberne.cpp | 4 ++-- src/ASPHERE/pair_line_lj.cpp | 4 ++-- src/ASPHERE/pair_resquared.cpp | 4 ++-- src/ASPHERE/pair_tri_lj.cpp | 4 ++-- src/ASPHERE/pair_ylz.cpp | 4 ++-- src/AWPMD/pair_awpmd_cut.cpp | 4 ++-- src/BODY/pair_body_nparticle.cpp | 4 ++-- src/BODY/pair_body_rounded_polygon.cpp | 4 ++-- src/BODY/pair_body_rounded_polyhedron.cpp | 4 ++-- src/BPM/pair_bpm_spring.cpp | 6 +++--- src/CG-SPICA/pair_lj_spica.cpp | 4 ++-- src/CG-SPICA/pair_lj_spica_coul_long.cpp | 4 ++-- src/CLASS2/pair_lj_class2.cpp | 4 ++-- src/CLASS2/pair_lj_class2_coul_cut.cpp | 4 ++-- src/CLASS2/pair_lj_class2_coul_long.cpp | 4 ++-- src/COLLOID/pair_brownian.cpp | 4 ++-- src/COLLOID/pair_colloid.cpp | 4 ++-- src/COLLOID/pair_lubricate.cpp | 4 ++-- src/COLLOID/pair_lubricateU.cpp | 4 ++-- src/DIPOLE/pair_lj_cut_dipole_cut.cpp | 4 ++-- src/DIPOLE/pair_lj_cut_dipole_long.cpp | 4 ++-- src/DIPOLE/pair_lj_long_dipole_long.cpp | 6 +++--- src/DIPOLE/pair_lj_sf_dipole_sf.cpp | 8 ++++---- src/DPD-BASIC/pair_dpd.cpp | 4 ++-- src/DPD-BASIC/pair_dpd_coul_slater_long.cpp | 4 ++-- src/DPD-BASIC/pair_dpd_ext.cpp | 4 ++-- src/DPD-BASIC/pair_dpd_ext_tstat.cpp | 4 ++-- src/DPD-BASIC/pair_dpd_tstat.cpp | 4 ++-- src/DPD-MESO/pair_edpd.cpp | 10 +++++----- src/DPD-MESO/pair_mdpd.cpp | 2 +- src/DPD-MESO/pair_mdpd_rhosum.cpp | 4 ++-- src/DPD-MESO/pair_tdpd.cpp | 4 ++-- src/DPD-REACT/pair_dpd_fdt.cpp | 4 ++-- src/DPD-REACT/pair_dpd_fdt_energy.cpp | 4 ++-- src/DPD-REACT/pair_exp6_rx.cpp | 18 +++++++++--------- .../pair_sdpd_taitwater_isothermal.cpp | 4 ++-- src/DRUDE/pair_coul_tt.cpp | 4 ++-- src/DRUDE/pair_lj_cut_thole_long.cpp | 4 ++-- src/DRUDE/pair_thole.cpp | 4 ++-- src/EFF/pair_eff_cut.cpp | 2 +- .../pair_hbond_dreiding_lj_angleoffset.cpp | 6 +++--- .../pair_hbond_dreiding_morse_angleoffset.cpp | 6 +++--- src/EXTRA-PAIR/pair_beck.cpp | 4 ++-- src/EXTRA-PAIR/pair_born_coul_dsf.cpp | 6 +++--- src/EXTRA-PAIR/pair_born_coul_wolf.cpp | 6 +++--- src/EXTRA-PAIR/pair_born_gauss.cpp | 4 ++-- src/EXTRA-PAIR/pair_buck_mdf.cpp | 6 +++--- src/EXTRA-PAIR/pair_coul_cut_global.cpp | 2 +- src/EXTRA-PAIR/pair_coul_diel.cpp | 4 ++-- src/EXTRA-PAIR/pair_coul_exclude.cpp | 4 ++-- src/EXTRA-PAIR/pair_coul_slater_long.cpp | 4 ++-- src/EXTRA-PAIR/pair_dispersion_d3.cpp | 2 +- src/EXTRA-PAIR/pair_gauss.cpp | 4 ++-- src/EXTRA-PAIR/pair_gauss_cut.cpp | 6 +++--- src/EXTRA-PAIR/pair_harmonic_cut.cpp | 4 ++-- src/EXTRA-PAIR/pair_lennard_mdf.cpp | 4 ++-- src/EXTRA-PAIR/pair_lj96_cut.cpp | 4 ++-- src/EXTRA-PAIR/pair_lj_cubic.cpp | 4 ++-- src/EXTRA-PAIR/pair_lj_cut_coul_dsf.cpp | 4 ++-- src/EXTRA-PAIR/pair_lj_cut_coul_wolf.cpp | 4 ++-- src/EXTRA-PAIR/pair_lj_cut_sphere.cpp | 4 ++-- src/EXTRA-PAIR/pair_lj_expand_coul_long.cpp | 4 ++-- src/EXTRA-PAIR/pair_lj_expand_sphere.cpp | 4 ++-- src/EXTRA-PAIR/pair_lj_gromacs.cpp | 6 +++--- .../pair_lj_gromacs_coul_gromacs.cpp | 4 ++-- src/EXTRA-PAIR/pair_lj_mdf.cpp | 4 ++-- src/EXTRA-PAIR/pair_lj_relres.cpp | 10 +++++----- src/EXTRA-PAIR/pair_lj_smooth.cpp | 6 +++--- src/EXTRA-PAIR/pair_lj_smooth_linear.cpp | 4 ++-- src/EXTRA-PAIR/pair_mie_cut.cpp | 4 ++-- src/EXTRA-PAIR/pair_momb.cpp | 4 ++-- src/EXTRA-PAIR/pair_morse_smooth_linear.cpp | 4 ++-- src/EXTRA-PAIR/pair_nm_cut.cpp | 4 ++-- src/EXTRA-PAIR/pair_nm_cut_coul_cut.cpp | 4 ++-- src/EXTRA-PAIR/pair_nm_cut_coul_long.cpp | 4 ++-- src/EXTRA-PAIR/pair_pedone.cpp | 4 ++-- src/EXTRA-PAIR/pair_ufm.cpp | 4 ++-- src/EXTRA-PAIR/pair_wf_cut.cpp | 4 ++-- src/FEP/pair_coul_cut_soft.cpp | 4 ++-- src/FEP/pair_coul_long_soft.cpp | 4 ++-- src/FEP/pair_lj_charmm_coul_long_soft.cpp | 2 +- src/FEP/pair_lj_class2_coul_cut_soft.cpp | 6 +++--- src/FEP/pair_lj_class2_coul_long_soft.cpp | 6 +++--- src/FEP/pair_lj_class2_soft.cpp | 6 +++--- src/FEP/pair_lj_cut_coul_cut_soft.cpp | 6 +++--- src/FEP/pair_lj_cut_coul_long_soft.cpp | 6 +++--- src/FEP/pair_lj_cut_soft.cpp | 6 +++--- src/FEP/pair_morse_soft.cpp | 4 ++-- src/GPU/pair_eam_alloy_gpu.cpp | 2 +- src/GPU/pair_eam_fs_gpu.cpp | 2 +- src/GRANULAR/pair_gran_hooke_history.cpp | 4 ++-- src/GRANULAR/pair_granular.cpp | 4 ++-- src/INTEL/pair_eam_alloy_intel.cpp | 2 +- src/INTEL/pair_eam_fs_intel.cpp | 2 +- src/INTEL/pair_snap_intel.cpp | 2 +- src/INTERLAYER/pair_coul_shield.cpp | 4 ++-- src/INTERLAYER/pair_kolmogorov_crespi_z.cpp | 2 +- src/INTERLAYER/pair_lebedeva_z.cpp | 2 +- src/KIM/pair_kim.cpp | 4 ++-- src/KOKKOS/pair_eam_alloy_kokkos.cpp | 2 +- src/KOKKOS/pair_eam_fs_kokkos.cpp | 2 +- src/KOKKOS/pair_hybrid_overlay_kokkos.cpp | 8 ++++---- src/KOKKOS/pair_mliap_kokkos.cpp | 8 ++++---- src/KSPACE/pair_born_coul_long.cpp | 6 +++--- src/KSPACE/pair_buck_coul_long.cpp | 6 +++--- src/KSPACE/pair_buck_long_coul_long.cpp | 4 ++-- src/KSPACE/pair_coul_long.cpp | 4 ++-- src/KSPACE/pair_lj_charmm_coul_long.cpp | 2 +- src/KSPACE/pair_lj_charmmfsw_coul_long.cpp | 2 +- src/KSPACE/pair_lj_cut_coul_long.cpp | 4 ++-- src/KSPACE/pair_lj_long_coul_long.cpp | 4 ++-- src/LEPTON/pair_lepton.cpp | 4 ++-- src/MACHDYN/pair_smd_hertz.cpp | 4 ++-- src/MACHDYN/pair_smd_triangulated_surface.cpp | 4 ++-- src/MANYBODY/pair_adp.cpp | 6 +++--- src/MANYBODY/pair_airebo.cpp | 2 +- src/MANYBODY/pair_atm.cpp | 4 ++-- src/MANYBODY/pair_eam.cpp | 4 ++-- src/MANYBODY/pair_eam_alloy.cpp | 2 +- src/MANYBODY/pair_eam_fs.cpp | 2 +- src/MANYBODY/pair_eim.cpp | 4 ++-- src/MANYBODY/pair_lcbop.cpp | 2 +- src/MANYBODY/pair_local_density.cpp | 6 +++--- src/MANYBODY/pair_meam_spline.cpp | 4 ++-- src/MANYBODY/pair_rebomos.cpp | 8 ++++---- src/MANYBODY/pair_sw.cpp | 2 +- src/MC/pair_dsmc.cpp | 4 ++-- src/MEAM/pair_meam.cpp | 6 +++--- src/MGPT/pair_mgpt.cpp | 8 ++++---- src/MISC/pair_list.cpp | 2 +- src/MISC/pair_tracker.cpp | 6 +++--- src/ML-HDNNP/pair_hdnnp.cpp | 6 +++--- src/ML-IAP/pair_mliap.cpp | 6 +++--- src/ML-QUIP/pair_quip.cpp | 2 +- src/ML-RANN/pair_rann.cpp | 6 +++--- src/MOFFF/pair_buck6d_coul_gauss_dsf.cpp | 4 ++-- src/MOFFF/pair_buck6d_coul_gauss_long.cpp | 4 ++-- src/MOLECULE/pair_hbond_dreiding_lj.cpp | 6 +++--- src/MOLECULE/pair_hbond_dreiding_morse.cpp | 6 +++--- src/MOLECULE/pair_lj_charmm_coul_charmm.cpp | 4 ++-- .../pair_lj_charmmfsw_coul_charmmfsh.cpp | 4 ++-- src/MOLECULE/pair_lj_cut_tip4p_cut.cpp | 4 ++-- src/MOLECULE/pair_tip4p_cut.cpp | 4 ++-- src/OPENMP/pair_coul_cut_global_omp.cpp | 2 +- src/OPENMP/pair_eam_alloy_omp.cpp | 2 +- src/OPENMP/pair_eam_fs_omp.cpp | 2 +- .../pair_hbond_dreiding_lj_angleoffset_omp.cpp | 6 +++--- ...ir_hbond_dreiding_morse_angleoffset_omp.cpp | 6 +++--- src/PERI/pair_peri_eps.cpp | 4 ++-- src/PERI/pair_peri_lps.cpp | 4 ++-- src/PERI/pair_peri_pmb.cpp | 4 ++-- src/PERI/pair_peri_ves.cpp | 4 ++-- src/PYTHON/pair_python.cpp | 4 ++-- src/REAXFF/pair_reaxff.cpp | 4 ++-- src/RHEO/pair_rheo_solid.cpp | 6 +++--- src/SMTBQ/pair_smatb.cpp | 2 +- src/SMTBQ/pair_smatb_single.cpp | 2 +- src/SPH/pair_sph_heatconduction.cpp | 4 ++-- src/SPH/pair_sph_lj.cpp | 4 ++-- src/SPH/pair_sph_rhosum.cpp | 4 ++-- src/SPH/pair_sph_taitwater.cpp | 4 ++-- src/SPH/pair_sph_taitwater_morris.cpp | 4 ++-- src/SPIN/pair_spin_dipole_cut.cpp | 2 +- src/SPIN/pair_spin_dipole_long.cpp | 2 +- src/SPIN/pair_spin_exchange.cpp | 6 +++--- src/SPIN/pair_spin_exchange_biquadratic.cpp | 6 +++--- src/YAFF/pair_lj_switch3_coulgauss_long.cpp | 4 ++-- src/YAFF/pair_mm3_switch3_coulgauss_long.cpp | 4 ++-- src/pair.cpp | 2 +- src/pair_born.cpp | 6 +++--- src/pair_buck.cpp | 6 +++--- src/pair_buck_coul_cut.cpp | 6 +++--- src/pair_coul_cut.cpp | 4 ++-- src/pair_coul_dsf.cpp | 4 ++-- src/pair_coul_wolf.cpp | 4 ++-- src/pair_hybrid.cpp | 2 +- src/pair_hybrid_overlay.cpp | 8 ++++---- src/pair_hybrid_scaled.cpp | 8 ++++---- src/pair_lj_cut.cpp | 4 ++-- src/pair_lj_cut_coul_cut.cpp | 4 ++-- src/pair_lj_expand.cpp | 4 ++-- src/pair_morse.cpp | 4 ++-- src/pair_soft.cpp | 4 ++-- src/pair_yukawa.cpp | 4 ++-- src/pair_zbl.cpp | 6 +++--- src/pair_zero.cpp | 4 ++-- 187 files changed, 404 insertions(+), 404 deletions(-) diff --git a/src/AMOEBA/pair_amoeba.cpp b/src/AMOEBA/pair_amoeba.cpp index 1bdd36dd94..673b511d7b 100644 --- a/src/AMOEBA/pair_amoeba.cpp +++ b/src/AMOEBA/pair_amoeba.cpp @@ -723,7 +723,7 @@ void PairAmoeba::coeff(int narg, char **arg) if (!allocated) allocate(); - if ((narg < 3) || (narg > 4)) error->all(FLERR,"Incorrect args for pair coefficients"); + if ((narg < 3) || (narg > 4)) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); // set setflag since coeff() is only called once with I,J = * * diff --git a/src/ASPHERE/pair_gayberne.cpp b/src/ASPHERE/pair_gayberne.cpp index 600889e0d1..92dbb932f3 100644 --- a/src/ASPHERE/pair_gayberne.cpp +++ b/src/ASPHERE/pair_gayberne.cpp @@ -292,7 +292,7 @@ void PairGayBerne::settings(int narg, char **arg) void PairGayBerne::coeff(int narg, char **arg) { if (narg < 10 || narg > 11) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -336,7 +336,7 @@ void PairGayBerne::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } diff --git a/src/ASPHERE/pair_line_lj.cpp b/src/ASPHERE/pair_line_lj.cpp index 3bfc10758c..a9db2a21ca 100644 --- a/src/ASPHERE/pair_line_lj.cpp +++ b/src/ASPHERE/pair_line_lj.cpp @@ -363,7 +363,7 @@ void PairLineLJ::settings(int narg, char **arg) void PairLineLJ::coeff(int narg, char **arg) { if (narg < 7 || narg > 8) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -393,7 +393,7 @@ void PairLineLJ::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/ASPHERE/pair_resquared.cpp b/src/ASPHERE/pair_resquared.cpp index 2044b83325..744ff863a1 100644 --- a/src/ASPHERE/pair_resquared.cpp +++ b/src/ASPHERE/pair_resquared.cpp @@ -260,7 +260,7 @@ void PairRESquared::settings(int narg, char **arg) void PairRESquared::coeff(int narg, char **arg) { - if (narg < 10 || narg > 11) error->all(FLERR, "Incorrect args for pair coefficients"); + if (narg < 10 || narg > 11) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo, ihi, jlo, jhi; @@ -308,7 +308,7 @@ void PairRESquared::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/ASPHERE/pair_tri_lj.cpp b/src/ASPHERE/pair_tri_lj.cpp index b9cb2528ca..738f39c4cc 100644 --- a/src/ASPHERE/pair_tri_lj.cpp +++ b/src/ASPHERE/pair_tri_lj.cpp @@ -434,7 +434,7 @@ void PairTriLJ::settings(int narg, char **arg) void PairTriLJ::coeff(int narg, char **arg) { if (narg < 4 || narg > 5) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -458,7 +458,7 @@ void PairTriLJ::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/ASPHERE/pair_ylz.cpp b/src/ASPHERE/pair_ylz.cpp index 833dc8e3e4..78692c833c 100644 --- a/src/ASPHERE/pair_ylz.cpp +++ b/src/ASPHERE/pair_ylz.cpp @@ -239,7 +239,7 @@ void PairYLZ::settings(int narg, char **arg) void PairYLZ::coeff(int narg, char **arg) { - if (narg < 8 || narg > 8) error->all(FLERR, "Incorrect args for pair coefficients"); + if (narg < 8 || narg > 8) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo, ihi, jlo, jhi; @@ -268,7 +268,7 @@ void PairYLZ::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/AWPMD/pair_awpmd_cut.cpp b/src/AWPMD/pair_awpmd_cut.cpp index e0ce319ebd..eb779e90be 100644 --- a/src/AWPMD/pair_awpmd_cut.cpp +++ b/src/AWPMD/pair_awpmd_cut.cpp @@ -459,7 +459,7 @@ void PairAWPMDCut::settings(int narg, char **arg) { // pair settings are as usual void PairAWPMDCut::coeff(int narg, char **arg) { - if (narg < 2 || narg > 3) error->all(FLERR,"Incorrect args for pair coefficients"); + if (narg < 2 || narg > 3) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); /*if(domain->xperiodic == 1 || domain->yperiodic == 1 || domain->zperiodic == 1) {*/ @@ -496,7 +496,7 @@ void PairAWPMDCut::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/BODY/pair_body_nparticle.cpp b/src/BODY/pair_body_nparticle.cpp index 29ee06dbef..a6611c4e09 100644 --- a/src/BODY/pair_body_nparticle.cpp +++ b/src/BODY/pair_body_nparticle.cpp @@ -383,7 +383,7 @@ void PairBodyNparticle::settings(int narg, char **arg) void PairBodyNparticle::coeff(int narg, char **arg) { if (narg < 4 || narg > 5) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -407,7 +407,7 @@ void PairBodyNparticle::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/BODY/pair_body_rounded_polygon.cpp b/src/BODY/pair_body_rounded_polygon.cpp index 2293f56a98..d07c47c6ef 100644 --- a/src/BODY/pair_body_rounded_polygon.cpp +++ b/src/BODY/pair_body_rounded_polygon.cpp @@ -382,7 +382,7 @@ void PairBodyRoundedPolygon::settings(int narg, char **arg) void PairBodyRoundedPolygon::coeff(int narg, char **arg) { if (narg < 4 || narg > 5) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -402,7 +402,7 @@ void PairBodyRoundedPolygon::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/BODY/pair_body_rounded_polyhedron.cpp b/src/BODY/pair_body_rounded_polyhedron.cpp index ed83dc49e2..321f00f5db 100644 --- a/src/BODY/pair_body_rounded_polyhedron.cpp +++ b/src/BODY/pair_body_rounded_polyhedron.cpp @@ -360,7 +360,7 @@ void PairBodyRoundedPolyhedron::settings(int narg, char **arg) void PairBodyRoundedPolyhedron::coeff(int narg, char **arg) { if (narg < 4 || narg > 5) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -380,7 +380,7 @@ void PairBodyRoundedPolyhedron::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/BPM/pair_bpm_spring.cpp b/src/BPM/pair_bpm_spring.cpp index bf58b9e515..d01264a2dc 100644 --- a/src/BPM/pair_bpm_spring.cpp +++ b/src/BPM/pair_bpm_spring.cpp @@ -191,7 +191,7 @@ void PairBPMSpring::settings(int narg, char ** arg) void PairBPMSpring::coeff(int narg, char **arg) { if ((!anharmonic_flag && narg != 5) || (anharmonic_flag && narg != 6)) - error->all(FLERR, "Incorrect args for pair coefficients"); + error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo, ihi, jlo, jhi; @@ -206,7 +206,7 @@ void PairBPMSpring::coeff(int narg, char **arg) if (anharmonic_flag) ka_one = utils::numeric(FLERR, arg[5], false, lmp); - if (cut_one <= 0.0) error->all(FLERR, "Incorrect args for pair coefficients"); + if (cut_one <= 0.0) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); int count = 0; for (int i = ilo; i <= ihi; i++) { @@ -221,7 +221,7 @@ void PairBPMSpring::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/CG-SPICA/pair_lj_spica.cpp b/src/CG-SPICA/pair_lj_spica.cpp index 03fab85954..9fc31e821e 100644 --- a/src/CG-SPICA/pair_lj_spica.cpp +++ b/src/CG-SPICA/pair_lj_spica.cpp @@ -267,7 +267,7 @@ void PairLJSPICA::settings(int narg, char **arg) void PairLJSPICA::coeff(int narg, char **arg) { - if (narg < 5 || narg > 6) error->all(FLERR,"Incorrect args for pair coefficients"); + if (narg < 5 || narg > 6) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -296,7 +296,7 @@ void PairLJSPICA::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/CG-SPICA/pair_lj_spica_coul_long.cpp b/src/CG-SPICA/pair_lj_spica_coul_long.cpp index 176c076da9..020025bbac 100644 --- a/src/CG-SPICA/pair_lj_spica_coul_long.cpp +++ b/src/CG-SPICA/pair_lj_spica_coul_long.cpp @@ -321,7 +321,7 @@ void PairLJSPICACoulLong::settings(int narg, char **arg) void PairLJSPICACoulLong::coeff(int narg, char **arg) { - if (narg < 5 || narg > 6) error->all(FLERR, "Incorrect args for pair coefficients"); + if (narg < 5 || narg > 6) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo, ihi, jlo, jhi; @@ -349,7 +349,7 @@ void PairLJSPICACoulLong::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/CLASS2/pair_lj_class2.cpp b/src/CLASS2/pair_lj_class2.cpp index 1208fedfca..75651e31df 100644 --- a/src/CLASS2/pair_lj_class2.cpp +++ b/src/CLASS2/pair_lj_class2.cpp @@ -447,7 +447,7 @@ void PairLJClass2::settings(int narg, char **arg) void PairLJClass2::coeff(int narg, char **arg) { - if (narg < 4 || narg > 5) error->all(FLERR, "Incorrect args for pair coefficients"); + if (narg < 4 || narg > 5) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo, ihi, jlo, jhi; @@ -471,7 +471,7 @@ void PairLJClass2::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/CLASS2/pair_lj_class2_coul_cut.cpp b/src/CLASS2/pair_lj_class2_coul_cut.cpp index 3f66f1550f..5834b29f61 100644 --- a/src/CLASS2/pair_lj_class2_coul_cut.cpp +++ b/src/CLASS2/pair_lj_class2_coul_cut.cpp @@ -221,7 +221,7 @@ void PairLJClass2CoulCut::settings(int narg, char **arg) void PairLJClass2CoulCut::coeff(int narg, char **arg) { - if (narg < 4 || narg > 6) error->all(FLERR, "Incorrect args for pair coefficients"); + if (narg < 4 || narg > 6) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); @@ -249,7 +249,7 @@ void PairLJClass2CoulCut::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/CLASS2/pair_lj_class2_coul_long.cpp b/src/CLASS2/pair_lj_class2_coul_long.cpp index 965810c8f7..2482edc0a4 100644 --- a/src/CLASS2/pair_lj_class2_coul_long.cpp +++ b/src/CLASS2/pair_lj_class2_coul_long.cpp @@ -625,7 +625,7 @@ void PairLJClass2CoulLong::settings(int narg, char **arg) void PairLJClass2CoulLong::coeff(int narg, char **arg) { - if (narg < 4 || narg > 5) error->all(FLERR, "Incorrect args for pair coefficients"); + if (narg < 4 || narg > 5) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); @@ -650,7 +650,7 @@ void PairLJClass2CoulLong::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/COLLOID/pair_brownian.cpp b/src/COLLOID/pair_brownian.cpp index 6773900e44..fec29acc85 100644 --- a/src/COLLOID/pair_brownian.cpp +++ b/src/COLLOID/pair_brownian.cpp @@ -403,7 +403,7 @@ void PairBrownian::settings(int narg, char **arg) void PairBrownian::coeff(int narg, char **arg) { - if (narg != 2 && narg != 4) error->all(FLERR, "Incorrect args for pair coefficients"); + if (narg != 2 && narg != 4) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); @@ -428,7 +428,7 @@ void PairBrownian::coeff(int narg, char **arg) count++; } - if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/COLLOID/pair_colloid.cpp b/src/COLLOID/pair_colloid.cpp index 55424fa398..ce4228fa3f 100644 --- a/src/COLLOID/pair_colloid.cpp +++ b/src/COLLOID/pair_colloid.cpp @@ -266,7 +266,7 @@ void PairColloid::settings(int narg, char **arg) void PairColloid::coeff(int narg, char **arg) { if (narg < 6 || narg > 7) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -300,7 +300,7 @@ void PairColloid::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/COLLOID/pair_lubricate.cpp b/src/COLLOID/pair_lubricate.cpp index 14e587e5f8..ec92f97121 100644 --- a/src/COLLOID/pair_lubricate.cpp +++ b/src/COLLOID/pair_lubricate.cpp @@ -493,7 +493,7 @@ void PairLubricate::settings(int narg, char **arg) void PairLubricate::coeff(int narg, char **arg) { if (narg != 2 && narg != 4) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); @@ -518,7 +518,7 @@ void PairLubricate::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/COLLOID/pair_lubricateU.cpp b/src/COLLOID/pair_lubricateU.cpp index 7a240c3bb9..7cb00f738c 100644 --- a/src/COLLOID/pair_lubricateU.cpp +++ b/src/COLLOID/pair_lubricateU.cpp @@ -1726,7 +1726,7 @@ void PairLubricateU::settings(int narg, char **arg) void PairLubricateU::coeff(int narg, char **arg) { if (narg != 2 && narg != 4) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); @@ -1751,7 +1751,7 @@ void PairLubricateU::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/DIPOLE/pair_lj_cut_dipole_cut.cpp b/src/DIPOLE/pair_lj_cut_dipole_cut.cpp index 237eaa183e..94bd5aa9f5 100644 --- a/src/DIPOLE/pair_lj_cut_dipole_cut.cpp +++ b/src/DIPOLE/pair_lj_cut_dipole_cut.cpp @@ -325,7 +325,7 @@ void PairLJCutDipoleCut::settings(int narg, char **arg) void PairLJCutDipoleCut::coeff(int narg, char **arg) { if (narg < 4 || narg > 6) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -352,7 +352,7 @@ void PairLJCutDipoleCut::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/DIPOLE/pair_lj_cut_dipole_long.cpp b/src/DIPOLE/pair_lj_cut_dipole_long.cpp index 5d71842d54..eb342cd335 100644 --- a/src/DIPOLE/pair_lj_cut_dipole_long.cpp +++ b/src/DIPOLE/pair_lj_cut_dipole_long.cpp @@ -364,7 +364,7 @@ void PairLJCutDipoleLong::settings(int narg, char **arg) void PairLJCutDipoleLong::coeff(int narg, char **arg) { if (narg < 4 || narg > 5) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -388,7 +388,7 @@ void PairLJCutDipoleLong::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/DIPOLE/pair_lj_long_dipole_long.cpp b/src/DIPOLE/pair_lj_long_dipole_long.cpp index 2e1a9c4db0..2e8703e3e8 100644 --- a/src/DIPOLE/pair_lj_long_dipole_long.cpp +++ b/src/DIPOLE/pair_lj_long_dipole_long.cpp @@ -79,7 +79,7 @@ void PairLJLongDipoleLong::settings(int narg, char **arg) options(arg, 1); if (!comm->me && ewald_order&(1<<6)) - error->warning(FLERR,"Geometric mixing assumed for 1/r^6 coefficients"); + error->warning(FLERR,"Geometric mixing assumed for 1/r^6 coefficients" + utils::errorurl(21)); if (!comm->me && ewald_order==((1<<3)|(1<<6))) error->warning(FLERR,"Using largest cut-off for lj/long/dipole/long long long"); if (!*(++arg)) @@ -185,7 +185,7 @@ void *PairLJLongDipoleLong::extract(const char *id, int &dim) void PairLJLongDipoleLong::coeff(int narg, char **arg) { if (narg < 4 || narg > 5) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -209,7 +209,7 @@ void PairLJLongDipoleLong::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/DIPOLE/pair_lj_sf_dipole_sf.cpp b/src/DIPOLE/pair_lj_sf_dipole_sf.cpp index 1cd84ed490..f17e167031 100644 --- a/src/DIPOLE/pair_lj_sf_dipole_sf.cpp +++ b/src/DIPOLE/pair_lj_sf_dipole_sf.cpp @@ -355,7 +355,7 @@ void PairLJSFDipoleSF::settings(int narg, char **arg) void PairLJSFDipoleSF::coeff(int narg, char **arg) { if (narg < 4 || narg > 8) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -382,10 +382,10 @@ void PairLJSFDipoleSF::coeff(int narg, char **arg) if (strcmp(arg[iarg],"scale") == 0) { scale_one = utils::numeric(FLERR,arg[iarg+1],false,lmp); iarg += 2; - } else error->all(FLERR,"Incorrect args for pair coefficients"); + } else error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } if (iarg != narg) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); int count = 0; for (int i = ilo; i <= ihi; i++) { @@ -400,7 +400,7 @@ void PairLJSFDipoleSF::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/DPD-BASIC/pair_dpd.cpp b/src/DPD-BASIC/pair_dpd.cpp index 1f60074280..b8b3d78327 100644 --- a/src/DPD-BASIC/pair_dpd.cpp +++ b/src/DPD-BASIC/pair_dpd.cpp @@ -223,7 +223,7 @@ void PairDPD::settings(int narg, char **arg) void PairDPD::coeff(int narg, char **arg) { if (narg < 4 || narg > 5) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -247,7 +247,7 @@ void PairDPD::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/DPD-BASIC/pair_dpd_coul_slater_long.cpp b/src/DPD-BASIC/pair_dpd_coul_slater_long.cpp index 665249b0ba..ca9f601811 100644 --- a/src/DPD-BASIC/pair_dpd_coul_slater_long.cpp +++ b/src/DPD-BASIC/pair_dpd_coul_slater_long.cpp @@ -279,7 +279,7 @@ void PairDPDCoulSlaterLong::settings(int narg, char **arg) void PairDPDCoulSlaterLong::coeff(int narg, char **arg) { if (narg < 4 || narg > 6) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -312,7 +312,7 @@ void PairDPDCoulSlaterLong::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/DPD-BASIC/pair_dpd_ext.cpp b/src/DPD-BASIC/pair_dpd_ext.cpp index e87ba893d8..a9c0779edd 100644 --- a/src/DPD-BASIC/pair_dpd_ext.cpp +++ b/src/DPD-BASIC/pair_dpd_ext.cpp @@ -275,7 +275,7 @@ void PairDPDExt::settings(int narg, char **arg) void PairDPDExt::coeff(int narg, char **arg) { if (narg < 7 || narg > 8) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -306,7 +306,7 @@ void PairDPDExt::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/DPD-BASIC/pair_dpd_ext_tstat.cpp b/src/DPD-BASIC/pair_dpd_ext_tstat.cpp index 86a862604a..19fb6d0330 100644 --- a/src/DPD-BASIC/pair_dpd_ext_tstat.cpp +++ b/src/DPD-BASIC/pair_dpd_ext_tstat.cpp @@ -219,7 +219,7 @@ void PairDPDExtTstat::settings(int narg, char **arg) void PairDPDExtTstat::coeff(int narg, char **arg) { if (narg < 6 || narg > 7) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -249,7 +249,7 @@ void PairDPDExtTstat::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/DPD-BASIC/pair_dpd_tstat.cpp b/src/DPD-BASIC/pair_dpd_tstat.cpp index 108177ed69..dd2d79657b 100644 --- a/src/DPD-BASIC/pair_dpd_tstat.cpp +++ b/src/DPD-BASIC/pair_dpd_tstat.cpp @@ -174,7 +174,7 @@ void PairDPDTstat::settings(int narg, char **arg) void PairDPDTstat::coeff(int narg, char **arg) { if (narg < 3 || narg > 4) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -198,7 +198,7 @@ void PairDPDTstat::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/DPD-MESO/pair_edpd.cpp b/src/DPD-MESO/pair_edpd.cpp index b575956f71..84c1f92534 100644 --- a/src/DPD-MESO/pair_edpd.cpp +++ b/src/DPD-MESO/pair_edpd.cpp @@ -300,7 +300,7 @@ void PairEDPD::settings(int narg, char **arg) void PairEDPD::coeff(int narg, char **arg) { if (narg < 9) - error->all(FLERR,"Incorrect args for pair edpd coefficients"); + error->all(FLERR,"Incorrect args for pair edpd coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -321,20 +321,20 @@ void PairEDPD::coeff(int narg, char **arg) int n = atom->ntypes; while (iarg < narg) { if (strcmp(arg[iarg],"power") == 0) { - if (iarg+5 > narg) error->all(FLERR,"Illegal pair edpd coefficients"); + if (iarg+5 > narg) error->all(FLERR,"Illegal pair edpd coefficients" + utils::errorurl(21)); for (int i = 0; i < 4; i++) sc_one[i] = utils::numeric(FLERR,arg[iarg+i+1],false,lmp); iarg += 5; power_flag = 1; memory->create(sc,n+1,n+1,4,"pair:sc"); } else if (strcmp(arg[iarg],"kappa") == 0) { - if (iarg+5 > narg) error->all(FLERR,"Illegal pair edpd coefficients"); + if (iarg+5 > narg) error->all(FLERR,"Illegal pair edpd coefficients" + utils::errorurl(21)); for (int i = 0; i < 4; i++) kc_one[i] = utils::numeric(FLERR,arg[iarg+i+1],false,lmp); iarg += 5; kappa_flag = 1; memory->create(kc,n+1,n+1,4,"pair:kc"); - } else error->all(FLERR,"Illegal pair edpd coefficients"); + } else error->all(FLERR,"Illegal pair edpd coefficients" + utils::errorurl(21)); } int count = 0; @@ -360,7 +360,7 @@ void PairEDPD::coeff(int narg, char **arg) count++; } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/DPD-MESO/pair_mdpd.cpp b/src/DPD-MESO/pair_mdpd.cpp index de148189e0..dbc78101ac 100644 --- a/src/DPD-MESO/pair_mdpd.cpp +++ b/src/DPD-MESO/pair_mdpd.cpp @@ -270,7 +270,7 @@ void PairMDPD::coeff(int narg, char **arg) count++; } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/DPD-MESO/pair_mdpd_rhosum.cpp b/src/DPD-MESO/pair_mdpd_rhosum.cpp index 6dbeaf2125..0e25b16352 100644 --- a/src/DPD-MESO/pair_mdpd_rhosum.cpp +++ b/src/DPD-MESO/pair_mdpd_rhosum.cpp @@ -190,7 +190,7 @@ void PairMDPDRhoSum::settings(int narg, char **/*arg*/) { void PairMDPDRhoSum::coeff(int narg, char **arg) { if (narg != 3) - error->all(FLERR,"Incorrect number of args for mdpd/rhosum coefficients"); + error->all(FLERR,"Incorrect number of args for mdpd/rhosum coefficients" + utils::errorurl(21)); if (!allocated) allocate(); @@ -210,7 +210,7 @@ void PairMDPDRhoSum::coeff(int narg, char **arg) { } if (count == 0) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/DPD-MESO/pair_tdpd.cpp b/src/DPD-MESO/pair_tdpd.cpp index 038b3c3cdc..cd74c2f501 100644 --- a/src/DPD-MESO/pair_tdpd.cpp +++ b/src/DPD-MESO/pair_tdpd.cpp @@ -268,7 +268,7 @@ void PairTDPD::settings(int narg, char **arg) void PairTDPD::coeff(int narg, char **arg) { if (narg != 7 + 3*cc_species) - error->all(FLERR,"Incorrect args for pair tdpd coefficients"); + error->all(FLERR,"Incorrect args for pair tdpd coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -310,7 +310,7 @@ void PairTDPD::coeff(int narg, char **arg) delete[] epsilon_one; delete[] powercc_one; - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/DPD-REACT/pair_dpd_fdt.cpp b/src/DPD-REACT/pair_dpd_fdt.cpp index 44920a6bda..24b54cf69d 100644 --- a/src/DPD-REACT/pair_dpd_fdt.cpp +++ b/src/DPD-REACT/pair_dpd_fdt.cpp @@ -275,7 +275,7 @@ void PairDPDfdt::settings(int narg, char **arg) void PairDPDfdt::coeff(int narg, char **arg) { - if (narg < 4 || narg > 5) error->all(FLERR,"Incorrect args for pair coefficients"); + if (narg < 4 || narg > 5) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -301,7 +301,7 @@ void PairDPDfdt::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/DPD-REACT/pair_dpd_fdt_energy.cpp b/src/DPD-REACT/pair_dpd_fdt_energy.cpp index 12d6dc5fb7..3bb6d57ec3 100644 --- a/src/DPD-REACT/pair_dpd_fdt_energy.cpp +++ b/src/DPD-REACT/pair_dpd_fdt_energy.cpp @@ -363,7 +363,7 @@ void PairDPDfdtEnergy::settings(int narg, char **arg) void PairDPDfdtEnergy::coeff(int narg, char **arg) { - if (narg < 5 || narg > 6) error->all(FLERR,"Incorrect args for pair coefficients"); + if (narg < 5 || narg > 6) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -394,7 +394,7 @@ void PairDPDfdtEnergy::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/DPD-REACT/pair_exp6_rx.cpp b/src/DPD-REACT/pair_exp6_rx.cpp index 0cd9dd3a05..d914b0592d 100644 --- a/src/DPD-REACT/pair_exp6_rx.cpp +++ b/src/DPD-REACT/pair_exp6_rx.cpp @@ -578,7 +578,7 @@ void PairExp6rx::settings(int narg, char **arg) void PairExp6rx::coeff(int narg, char **arg) { - if (narg < 6 || narg > 9) error->all(FLERR,"Incorrect args for pair coefficients"); + if (narg < 6 || narg > 9) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); bool rx_flag = false; for (int i = 0; i < modify->nfix; i++) @@ -602,7 +602,7 @@ void PairExp6rx::coeff(int narg, char **arg) if (strcmp(site1,&atom->dvname[ispecies][0]) == 0) break; } if (ispecies == nspecies && strcmp(site1,"1fluid") != 0) - error->all(FLERR,"Site1 name not recognized in pair coefficients"); + error->all(FLERR,"Site1 name not recognized in pair coefficients" + utils::errorurl(21)); site2 = utils::strdup(arg[4]); @@ -610,7 +610,7 @@ void PairExp6rx::coeff(int narg, char **arg) if (strcmp(site2,&atom->dvname[ispecies][0]) == 0) break; } if (ispecies == nspecies && strcmp(site2,"1fluid") != 0) - error->all(FLERR,"Site2 name not recognized in pair coefficients"); + error->all(FLERR,"Site2 name not recognized in pair coefficients" + utils::errorurl(21)); { // Set isite1 and isite2 parameters based on site1 and site2 strings. @@ -623,7 +623,7 @@ void PairExp6rx::coeff(int narg, char **arg) if (strcmp(site1, &atom->dvname[isp][0]) == 0) break; if (isp == nspecies) - error->all(FLERR,"Site1 name not recognized in pair coefficients"); + error->all(FLERR,"Site1 name not recognized in pair coefficients" + utils::errorurl(21)); else isite1 = isp; } @@ -636,7 +636,7 @@ void PairExp6rx::coeff(int narg, char **arg) if (strcmp(site2, &atom->dvname[isp][0]) == 0) break; if (isp == nspecies) - error->all(FLERR,"Site2 name not recognized in pair coefficients"); + error->all(FLERR,"Site2 name not recognized in pair coefficients" + utils::errorurl(21)); else isite2 = isp; } @@ -667,14 +667,14 @@ void PairExp6rx::coeff(int narg, char **arg) memory->create(coeffEps,6,"pair:coeffEps"); memory->create(coeffRm,6,"pair:coeffRm"); read_file2(arg[6]); - if (narg > 8) error->all(FLERR,"Incorrect args for pair coefficients"); + if (narg > 8) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (narg == 8) cut_one = utils::numeric(FLERR,arg[7],false,lmp); } else if (strcmp(arg[5],"none") == 0) { scalingFlag = NONE; - if (narg > 7) error->all(FLERR,"Incorrect args for pair coefficients"); + if (narg > 7) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (narg == 7) cut_one = utils::numeric(FLERR,arg[6],false,lmp); } else { - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } int count = 0; @@ -686,7 +686,7 @@ void PairExp6rx::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/DPD-SMOOTH/pair_sdpd_taitwater_isothermal.cpp b/src/DPD-SMOOTH/pair_sdpd_taitwater_isothermal.cpp index 2deeefe90e..8a81d24b9e 100644 --- a/src/DPD-SMOOTH/pair_sdpd_taitwater_isothermal.cpp +++ b/src/DPD-SMOOTH/pair_sdpd_taitwater_isothermal.cpp @@ -269,7 +269,7 @@ void PairSDPDTaitwaterIsothermal::settings (int narg, char **arg) { void PairSDPDTaitwaterIsothermal::coeff (int narg, char **arg) { if (narg != 5) error->all (FLERR, "Incorrect args for pair_style " - "sph/taitwater/morris coefficients"); + "sph/taitwater/morris coefficients" + utils::errorurl(21)); if (!allocated) allocate(); @@ -300,7 +300,7 @@ void PairSDPDTaitwaterIsothermal::coeff (int narg, char **arg) { } if (count == 0) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/DRUDE/pair_coul_tt.cpp b/src/DRUDE/pair_coul_tt.cpp index b8814265b6..8b305d6e8a 100644 --- a/src/DRUDE/pair_coul_tt.cpp +++ b/src/DRUDE/pair_coul_tt.cpp @@ -242,7 +242,7 @@ void PairCoulTT::settings(int narg, char **arg) void PairCoulTT::coeff(int narg, char **arg) { if (narg < 3 || narg > 6) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -273,7 +273,7 @@ void PairCoulTT::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } diff --git a/src/DRUDE/pair_lj_cut_thole_long.cpp b/src/DRUDE/pair_lj_cut_thole_long.cpp index b7f1ce9be9..77f79fb220 100644 --- a/src/DRUDE/pair_lj_cut_thole_long.cpp +++ b/src/DRUDE/pair_lj_cut_thole_long.cpp @@ -317,7 +317,7 @@ void PairLJCutTholeLong::settings(int narg, char **arg) void PairLJCutTholeLong::coeff(int narg, char **arg) { if (narg < 5 || narg > 7) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -348,7 +348,7 @@ void PairLJCutTholeLong::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/DRUDE/pair_thole.cpp b/src/DRUDE/pair_thole.cpp index 4039fd72fa..65cb0c3b9b 100644 --- a/src/DRUDE/pair_thole.cpp +++ b/src/DRUDE/pair_thole.cpp @@ -216,7 +216,7 @@ void PairThole::settings(int narg, char **arg) void PairThole::coeff(int narg, char **arg) { if (narg < 3 || narg > 5) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -242,7 +242,7 @@ void PairThole::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } diff --git a/src/EFF/pair_eff_cut.cpp b/src/EFF/pair_eff_cut.cpp index 5f32de9912..bea1387409 100644 --- a/src/EFF/pair_eff_cut.cpp +++ b/src/EFF/pair_eff_cut.cpp @@ -917,7 +917,7 @@ void PairEffCut::coeff(int narg, char **arg) count++; } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } else { int ecp; ecp = utils::inumeric(FLERR,arg[0],false,lmp); diff --git a/src/EXTRA-MOLECULE/pair_hbond_dreiding_lj_angleoffset.cpp b/src/EXTRA-MOLECULE/pair_hbond_dreiding_lj_angleoffset.cpp index 02ac009773..d33c502ebe 100644 --- a/src/EXTRA-MOLECULE/pair_hbond_dreiding_lj_angleoffset.cpp +++ b/src/EXTRA-MOLECULE/pair_hbond_dreiding_lj_angleoffset.cpp @@ -55,7 +55,7 @@ PairHbondDreidingLJAngleoffset::PairHbondDreidingLJAngleoffset(LAMMPS *lmp) void PairHbondDreidingLJAngleoffset::coeff(int narg, char **arg) { if (narg < 6 || narg > 11) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi,klo,khi; @@ -66,7 +66,7 @@ void PairHbondDreidingLJAngleoffset::coeff(int narg, char **arg) int donor_flag; if (strcmp(arg[3],"i") == 0) donor_flag = 0; else if (strcmp(arg[3],"j") == 0) donor_flag = 1; - else error->all(FLERR,"Incorrect args for pair coefficients"); + else error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); double epsilon_one = utils::numeric(FLERR, arg[4], false, lmp); double sigma_one = utils::numeric(FLERR, arg[5], false, lmp); @@ -127,5 +127,5 @@ void PairHbondDreidingLJAngleoffset::coeff(int narg, char **arg) } nparams++; - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } diff --git a/src/EXTRA-MOLECULE/pair_hbond_dreiding_morse_angleoffset.cpp b/src/EXTRA-MOLECULE/pair_hbond_dreiding_morse_angleoffset.cpp index 21f26ea8d1..8842b45d53 100644 --- a/src/EXTRA-MOLECULE/pair_hbond_dreiding_morse_angleoffset.cpp +++ b/src/EXTRA-MOLECULE/pair_hbond_dreiding_morse_angleoffset.cpp @@ -53,7 +53,7 @@ PairHbondDreidingMorseAngleoffset::PairHbondDreidingMorseAngleoffset(LAMMPS *lmp void PairHbondDreidingMorseAngleoffset::coeff(int narg, char **arg) { if (narg < 7 || narg > 12) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi,klo,khi; @@ -64,7 +64,7 @@ void PairHbondDreidingMorseAngleoffset::coeff(int narg, char **arg) int donor_flag; if (strcmp(arg[3],"i") == 0) donor_flag = 0; else if (strcmp(arg[3],"j") == 0) donor_flag = 1; - else error->all(FLERR,"Incorrect args for pair coefficients"); + else error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); double d0_one = utils::numeric(FLERR, arg[4], false, lmp); double alpha_one = utils::numeric(FLERR, arg[5], false, lmp); @@ -125,5 +125,5 @@ void PairHbondDreidingMorseAngleoffset::coeff(int narg, char **arg) } nparams++; - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } diff --git a/src/EXTRA-PAIR/pair_beck.cpp b/src/EXTRA-PAIR/pair_beck.cpp index f0dffed7fe..cd24609216 100644 --- a/src/EXTRA-PAIR/pair_beck.cpp +++ b/src/EXTRA-PAIR/pair_beck.cpp @@ -190,7 +190,7 @@ void PairBeck::settings(int narg, char **arg) void PairBeck::coeff(int narg, char **arg) { - if (narg != 7 && narg != 8) error->all(FLERR, "Incorrect args for pair coefficients"); + if (narg != 7 && narg != 8) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo, ihi, jlo, jhi; @@ -220,7 +220,7 @@ void PairBeck::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/EXTRA-PAIR/pair_born_coul_dsf.cpp b/src/EXTRA-PAIR/pair_born_coul_dsf.cpp index c1be749d7b..6cd19ec54f 100644 --- a/src/EXTRA-PAIR/pair_born_coul_dsf.cpp +++ b/src/EXTRA-PAIR/pair_born_coul_dsf.cpp @@ -237,7 +237,7 @@ void PairBornCoulDSF::settings(int narg, char **arg) void PairBornCoulDSF::coeff(int narg, char **arg) { if (narg < 7 || narg > 8) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -247,7 +247,7 @@ void PairBornCoulDSF::coeff(int narg, char **arg) double a_one = utils::numeric(FLERR,arg[2],false,lmp); double rho_one = utils::numeric(FLERR,arg[3],false,lmp); double sigma_one = utils::numeric(FLERR,arg[4],false,lmp); - if (rho_one <= 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (rho_one <= 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); double c_one = utils::numeric(FLERR,arg[5],false,lmp); double d_one = utils::numeric(FLERR,arg[6],false,lmp); @@ -268,7 +268,7 @@ void PairBornCoulDSF::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/EXTRA-PAIR/pair_born_coul_wolf.cpp b/src/EXTRA-PAIR/pair_born_coul_wolf.cpp index e3ebe884e2..8dce32ad21 100644 --- a/src/EXTRA-PAIR/pair_born_coul_wolf.cpp +++ b/src/EXTRA-PAIR/pair_born_coul_wolf.cpp @@ -240,7 +240,7 @@ void PairBornCoulWolf::settings(int narg, char **arg) void PairBornCoulWolf::coeff(int narg, char **arg) { if (narg < 7 || narg > 8) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -250,7 +250,7 @@ void PairBornCoulWolf::coeff(int narg, char **arg) double a_one = utils::numeric(FLERR,arg[2],false,lmp); double rho_one = utils::numeric(FLERR,arg[3],false,lmp); double sigma_one = utils::numeric(FLERR,arg[4],false,lmp); - if (rho_one <= 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (rho_one <= 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); double c_one = utils::numeric(FLERR,arg[5],false,lmp); double d_one = utils::numeric(FLERR,arg[6],false,lmp); @@ -271,7 +271,7 @@ void PairBornCoulWolf::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/EXTRA-PAIR/pair_born_gauss.cpp b/src/EXTRA-PAIR/pair_born_gauss.cpp index 4b1390889d..0cd2102c58 100644 --- a/src/EXTRA-PAIR/pair_born_gauss.cpp +++ b/src/EXTRA-PAIR/pair_born_gauss.cpp @@ -177,7 +177,7 @@ void PairBornGauss::settings(int narg, char **arg) void PairBornGauss::coeff(int narg, char **arg) { - if (narg < 7 || narg > 8) error->all(FLERR, "Incorrect args for pair coefficients"); + if (narg < 7 || narg > 8) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo, ihi, jlo, jhi; @@ -206,7 +206,7 @@ void PairBornGauss::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/EXTRA-PAIR/pair_buck_mdf.cpp b/src/EXTRA-PAIR/pair_buck_mdf.cpp index 30485ec71d..3c93c0f5b3 100644 --- a/src/EXTRA-PAIR/pair_buck_mdf.cpp +++ b/src/EXTRA-PAIR/pair_buck_mdf.cpp @@ -205,7 +205,7 @@ void PairBuckMDF::settings(int narg, char **arg) void PairBuckMDF::coeff(int narg, char **arg) { if (narg != 5 && narg != 7) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -214,7 +214,7 @@ void PairBuckMDF::coeff(int narg, char **arg) double a_one = utils::numeric(FLERR,arg[2],false,lmp); double rho_one = utils::numeric(FLERR,arg[3],false,lmp); - if (rho_one <= 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (rho_one <= 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); double c_one = utils::numeric(FLERR,arg[4],false,lmp); double cut_inner_one = cut_inner_global; @@ -241,7 +241,7 @@ void PairBuckMDF::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/EXTRA-PAIR/pair_coul_cut_global.cpp b/src/EXTRA-PAIR/pair_coul_cut_global.cpp index e724a48959..401b0cee23 100644 --- a/src/EXTRA-PAIR/pair_coul_cut_global.cpp +++ b/src/EXTRA-PAIR/pair_coul_cut_global.cpp @@ -27,7 +27,7 @@ using namespace LAMMPS_NS; void PairCoulCutGlobal::coeff(int narg, char **arg) { if (narg != 2) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); PairCoulCut::coeff(narg,arg); } diff --git a/src/EXTRA-PAIR/pair_coul_diel.cpp b/src/EXTRA-PAIR/pair_coul_diel.cpp index 9d7904ba07..0b89f8bd28 100644 --- a/src/EXTRA-PAIR/pair_coul_diel.cpp +++ b/src/EXTRA-PAIR/pair_coul_diel.cpp @@ -178,7 +178,7 @@ void PairCoulDiel::settings(int narg, char **arg) void PairCoulDiel::coeff(int narg, char **arg) { - if (narg < 5 || narg > 6) error->all(FLERR,"Incorrect args for pair coefficients"); + if (narg < 5 || narg > 6) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -205,7 +205,7 @@ void PairCoulDiel::coeff(int narg, char **arg) a_eps = 0.5*(5.2+eps_s); b_eps = 0.5*(eps_s-5.2); - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } diff --git a/src/EXTRA-PAIR/pair_coul_exclude.cpp b/src/EXTRA-PAIR/pair_coul_exclude.cpp index 8781f6abf0..6ddbd62f99 100644 --- a/src/EXTRA-PAIR/pair_coul_exclude.cpp +++ b/src/EXTRA-PAIR/pair_coul_exclude.cpp @@ -154,7 +154,7 @@ void PairCoulExclude::settings(int narg, char **arg) void PairCoulExclude::coeff(int narg, char **arg) { if (narg != 2) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -169,7 +169,7 @@ void PairCoulExclude::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } diff --git a/src/EXTRA-PAIR/pair_coul_slater_long.cpp b/src/EXTRA-PAIR/pair_coul_slater_long.cpp index 09926f6533..c2cc9efdc6 100644 --- a/src/EXTRA-PAIR/pair_coul_slater_long.cpp +++ b/src/EXTRA-PAIR/pair_coul_slater_long.cpp @@ -181,7 +181,7 @@ void PairCoulSlaterLong::settings(int narg, char **arg) void PairCoulSlaterLong::coeff(int narg, char **arg) { - if (narg != 2) error->all(FLERR,"Incorrect args for pair coefficients"); + if (narg != 2) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -197,7 +197,7 @@ void PairCoulSlaterLong::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/EXTRA-PAIR/pair_dispersion_d3.cpp b/src/EXTRA-PAIR/pair_dispersion_d3.cpp index ae1ec4dc25..bd630545d1 100644 --- a/src/EXTRA-PAIR/pair_dispersion_d3.cpp +++ b/src/EXTRA-PAIR/pair_dispersion_d3.cpp @@ -293,7 +293,7 @@ void PairDispersionD3::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); for (int i = 1; i <= ntypes; i++) { r2r4[i] = r2r4_ref[atomic_numbers[i - 1]]; diff --git a/src/EXTRA-PAIR/pair_gauss.cpp b/src/EXTRA-PAIR/pair_gauss.cpp index a9c146999b..70665cb31a 100644 --- a/src/EXTRA-PAIR/pair_gauss.cpp +++ b/src/EXTRA-PAIR/pair_gauss.cpp @@ -179,7 +179,7 @@ void PairGauss::settings(int narg, char **arg) void PairGauss::coeff(int narg, char **arg) { - if (narg < 4 || narg > 5) error->all(FLERR, "Incorrect args for pair coefficients"); + if (narg < 4 || narg > 5) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo, ihi, jlo, jhi; @@ -203,7 +203,7 @@ void PairGauss::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/EXTRA-PAIR/pair_gauss_cut.cpp b/src/EXTRA-PAIR/pair_gauss_cut.cpp index 7e445d728e..a5590906ab 100644 --- a/src/EXTRA-PAIR/pair_gauss_cut.cpp +++ b/src/EXTRA-PAIR/pair_gauss_cut.cpp @@ -182,7 +182,7 @@ void PairGaussCut::settings(int narg, char **arg) void PairGaussCut::coeff(int narg, char **arg) { - if (narg < 5 || narg > 6) error->all(FLERR,"Incorrect args for pair coefficients"); + if (narg < 5 || narg > 6) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -193,7 +193,7 @@ void PairGaussCut::coeff(int narg, char **arg) double rmh_one = utils::numeric(FLERR,arg[3],false,lmp); double sigmah_one = utils::numeric(FLERR,arg[4],false,lmp); if (sigmah_one <= 0.0) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); double cut_one = cut_global; @@ -211,7 +211,7 @@ void PairGaussCut::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/EXTRA-PAIR/pair_harmonic_cut.cpp b/src/EXTRA-PAIR/pair_harmonic_cut.cpp index 8b588f2a22..08084fa0ec 100644 --- a/src/EXTRA-PAIR/pair_harmonic_cut.cpp +++ b/src/EXTRA-PAIR/pair_harmonic_cut.cpp @@ -159,7 +159,7 @@ void PairHarmonicCut::settings(int narg, char ** /*arg*/) void PairHarmonicCut::coeff(int narg, char **arg) { - if (narg != 4) error->all(FLERR, "Incorrect args for pair coefficients"); + if (narg != 4) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo, ihi, jlo, jhi; @@ -179,7 +179,7 @@ void PairHarmonicCut::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/EXTRA-PAIR/pair_lennard_mdf.cpp b/src/EXTRA-PAIR/pair_lennard_mdf.cpp index b97f0ba342..b56b7407f3 100644 --- a/src/EXTRA-PAIR/pair_lennard_mdf.cpp +++ b/src/EXTRA-PAIR/pair_lennard_mdf.cpp @@ -211,7 +211,7 @@ void PairLennardMDF::settings(int narg, char **arg) void PairLennardMDF::coeff(int narg, char **arg) { if (narg != 4 && narg != 6) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -242,7 +242,7 @@ void PairLennardMDF::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/EXTRA-PAIR/pair_lj96_cut.cpp b/src/EXTRA-PAIR/pair_lj96_cut.cpp index e89f76bd4c..dcb8dd1293 100644 --- a/src/EXTRA-PAIR/pair_lj96_cut.cpp +++ b/src/EXTRA-PAIR/pair_lj96_cut.cpp @@ -450,7 +450,7 @@ void PairLJ96Cut::settings(int narg, char **arg) void PairLJ96Cut::coeff(int narg, char **arg) { if (narg < 4 || narg > 5) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -474,7 +474,7 @@ void PairLJ96Cut::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/EXTRA-PAIR/pair_lj_cubic.cpp b/src/EXTRA-PAIR/pair_lj_cubic.cpp index e5d45786ac..a20c45928c 100644 --- a/src/EXTRA-PAIR/pair_lj_cubic.cpp +++ b/src/EXTRA-PAIR/pair_lj_cubic.cpp @@ -184,7 +184,7 @@ void PairLJCubic::settings(int narg, char ** /*arg*/) void PairLJCubic::coeff(int narg, char **arg) { - if (narg != 4) error->all(FLERR, "Incorrect args for pair coefficients"); + if (narg != 4) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo, ihi, jlo, jhi; @@ -207,7 +207,7 @@ void PairLJCubic::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/EXTRA-PAIR/pair_lj_cut_coul_dsf.cpp b/src/EXTRA-PAIR/pair_lj_cut_coul_dsf.cpp index 6ac0c1cdae..36ffcf3982 100644 --- a/src/EXTRA-PAIR/pair_lj_cut_coul_dsf.cpp +++ b/src/EXTRA-PAIR/pair_lj_cut_coul_dsf.cpp @@ -231,7 +231,7 @@ void PairLJCutCoulDSF::settings(int narg, char **arg) void PairLJCutCoulDSF::coeff(int narg, char **arg) { if (narg < 4 || narg > 5) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -255,7 +255,7 @@ void PairLJCutCoulDSF::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/EXTRA-PAIR/pair_lj_cut_coul_wolf.cpp b/src/EXTRA-PAIR/pair_lj_cut_coul_wolf.cpp index 20f38891ad..ef5dbe1e84 100644 --- a/src/EXTRA-PAIR/pair_lj_cut_coul_wolf.cpp +++ b/src/EXTRA-PAIR/pair_lj_cut_coul_wolf.cpp @@ -232,7 +232,7 @@ void PairLJCutCoulWolf::settings(int narg, char **arg) void PairLJCutCoulWolf::coeff(int narg, char **arg) { if (narg < 4 || narg > 5) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -256,7 +256,7 @@ void PairLJCutCoulWolf::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/EXTRA-PAIR/pair_lj_cut_sphere.cpp b/src/EXTRA-PAIR/pair_lj_cut_sphere.cpp index 852b2eea1d..f36ec89cb7 100644 --- a/src/EXTRA-PAIR/pair_lj_cut_sphere.cpp +++ b/src/EXTRA-PAIR/pair_lj_cut_sphere.cpp @@ -185,7 +185,7 @@ void PairLJCutSphere::settings(int narg, char **arg) void PairLJCutSphere::coeff(int narg, char **arg) { - if (narg < 3 || narg > 4) error->all(FLERR, "Incorrect args for pair coefficients"); + if (narg < 3 || narg > 4) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo, ihi, jlo, jhi; @@ -206,7 +206,7 @@ void PairLJCutSphere::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/EXTRA-PAIR/pair_lj_expand_coul_long.cpp b/src/EXTRA-PAIR/pair_lj_expand_coul_long.cpp index 428b105621..b6b0300cac 100644 --- a/src/EXTRA-PAIR/pair_lj_expand_coul_long.cpp +++ b/src/EXTRA-PAIR/pair_lj_expand_coul_long.cpp @@ -641,7 +641,7 @@ void PairLJExpandCoulLong::settings(int narg, char **arg) void PairLJExpandCoulLong::coeff(int narg, char **arg) { if (narg < 5 || narg > 6) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -667,7 +667,7 @@ void PairLJExpandCoulLong::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/EXTRA-PAIR/pair_lj_expand_sphere.cpp b/src/EXTRA-PAIR/pair_lj_expand_sphere.cpp index c275a9f9ee..b6520dcbc2 100644 --- a/src/EXTRA-PAIR/pair_lj_expand_sphere.cpp +++ b/src/EXTRA-PAIR/pair_lj_expand_sphere.cpp @@ -199,7 +199,7 @@ void PairLJExpandSphere::settings(int narg, char **arg) void PairLJExpandSphere::coeff(int narg, char **arg) { - if (narg < 4 || narg > 5) error->all(FLERR, "Incorrect args for pair coefficients"); + if (narg < 4 || narg > 5) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo, ihi, jlo, jhi; @@ -222,7 +222,7 @@ void PairLJExpandSphere::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/EXTRA-PAIR/pair_lj_gromacs.cpp b/src/EXTRA-PAIR/pair_lj_gromacs.cpp index 4f728b2fbb..8142203a6e 100644 --- a/src/EXTRA-PAIR/pair_lj_gromacs.cpp +++ b/src/EXTRA-PAIR/pair_lj_gromacs.cpp @@ -213,7 +213,7 @@ void PairLJGromacs::settings(int narg, char **arg) void PairLJGromacs::coeff(int narg, char **arg) { - if (narg != 4 && narg != 6) error->all(FLERR, "Incorrect args for pair coefficients"); + if (narg != 4 && narg != 6) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo, ihi, jlo, jhi; @@ -231,7 +231,7 @@ void PairLJGromacs::coeff(int narg, char **arg) } if (cut_inner_one <= 0.0 || cut_inner_one > cut_one) - error->all(FLERR, "Incorrect args for pair coefficients"); + error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); int count = 0; for (int i = ilo; i <= ihi; i++) { @@ -245,7 +245,7 @@ void PairLJGromacs::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/EXTRA-PAIR/pair_lj_gromacs_coul_gromacs.cpp b/src/EXTRA-PAIR/pair_lj_gromacs_coul_gromacs.cpp index e20af2b81f..db07466407 100644 --- a/src/EXTRA-PAIR/pair_lj_gromacs_coul_gromacs.cpp +++ b/src/EXTRA-PAIR/pair_lj_gromacs_coul_gromacs.cpp @@ -239,7 +239,7 @@ void PairLJGromacsCoulGromacs::settings(int narg, char **arg) void PairLJGromacsCoulGromacs::coeff(int narg, char **arg) { - if (narg != 4) error->all(FLERR, "Incorrect args for pair coefficients"); + if (narg != 4) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo, ihi, jlo, jhi; @@ -259,7 +259,7 @@ void PairLJGromacsCoulGromacs::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/EXTRA-PAIR/pair_lj_mdf.cpp b/src/EXTRA-PAIR/pair_lj_mdf.cpp index 091c49152c..39ecd13f70 100644 --- a/src/EXTRA-PAIR/pair_lj_mdf.cpp +++ b/src/EXTRA-PAIR/pair_lj_mdf.cpp @@ -213,7 +213,7 @@ void PairLJMDF::settings(int narg, char **arg) void PairLJMDF::coeff(int narg, char **arg) { if (narg != 4 && narg != 6) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -244,7 +244,7 @@ void PairLJMDF::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/EXTRA-PAIR/pair_lj_relres.cpp b/src/EXTRA-PAIR/pair_lj_relres.cpp index 1826f3f1db..189af60272 100644 --- a/src/EXTRA-PAIR/pair_lj_relres.cpp +++ b/src/EXTRA-PAIR/pair_lj_relres.cpp @@ -297,7 +297,7 @@ void PairLJRelRes::settings(int narg, char **arg) void PairLJRelRes::coeff(int narg, char **arg) { if (narg != 6 && narg != 10) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -322,11 +322,11 @@ void PairLJRelRes::coeff(int narg, char **arg) } if (cut_inner_one <= 0.0 || cut_inner_one > cut_one) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (cutf_inner_one <= 0.0 || cutf_inner_one > cutf_one) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (cutf_one > cut_inner_one) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (epsilon_one == 0.0) { //set cutoff for fg interactions cut_inner_one = cutf_one; cut_one = cutf_one; @@ -348,7 +348,7 @@ void PairLJRelRes::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/EXTRA-PAIR/pair_lj_smooth.cpp b/src/EXTRA-PAIR/pair_lj_smooth.cpp index 5092951dd3..309ca02b30 100644 --- a/src/EXTRA-PAIR/pair_lj_smooth.cpp +++ b/src/EXTRA-PAIR/pair_lj_smooth.cpp @@ -219,7 +219,7 @@ void PairLJSmooth::settings(int narg, char **arg) void PairLJSmooth::coeff(int narg, char **arg) { if (narg != 4 && narg != 6) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -237,7 +237,7 @@ void PairLJSmooth::coeff(int narg, char **arg) } if (cut_inner_one <= 0.0 || cut_inner_one > cut_one) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); int count = 0; for (int i = ilo; i <= ihi; i++) { @@ -251,7 +251,7 @@ void PairLJSmooth::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/EXTRA-PAIR/pair_lj_smooth_linear.cpp b/src/EXTRA-PAIR/pair_lj_smooth_linear.cpp index a1b847340f..cde36291a2 100644 --- a/src/EXTRA-PAIR/pair_lj_smooth_linear.cpp +++ b/src/EXTRA-PAIR/pair_lj_smooth_linear.cpp @@ -189,7 +189,7 @@ void PairLJSmoothLinear::settings(int narg, char **arg) void PairLJSmoothLinear::coeff(int narg, char **arg) { if (narg != 4 && narg != 5) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -215,7 +215,7 @@ void PairLJSmoothLinear::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/EXTRA-PAIR/pair_mie_cut.cpp b/src/EXTRA-PAIR/pair_mie_cut.cpp index 01e0104ae4..79b0ccd1f7 100644 --- a/src/EXTRA-PAIR/pair_mie_cut.cpp +++ b/src/EXTRA-PAIR/pair_mie_cut.cpp @@ -457,7 +457,7 @@ void PairMIECut::settings(int narg, char **arg) void PairMIECut::coeff(int narg, char **arg) { if (narg < 6 || narg > 7) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -485,7 +485,7 @@ void PairMIECut::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/EXTRA-PAIR/pair_momb.cpp b/src/EXTRA-PAIR/pair_momb.cpp index e6b03d623d..def4037157 100644 --- a/src/EXTRA-PAIR/pair_momb.cpp +++ b/src/EXTRA-PAIR/pair_momb.cpp @@ -211,7 +211,7 @@ void PairMomb::settings(int narg, char **arg) void PairMomb::coeff(int narg, char **arg) { if (narg < 7 || narg > 8) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); @@ -242,7 +242,7 @@ void PairMomb::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } diff --git a/src/EXTRA-PAIR/pair_morse_smooth_linear.cpp b/src/EXTRA-PAIR/pair_morse_smooth_linear.cpp index 2cbcf29a66..9d3b3d4dc5 100644 --- a/src/EXTRA-PAIR/pair_morse_smooth_linear.cpp +++ b/src/EXTRA-PAIR/pair_morse_smooth_linear.cpp @@ -181,7 +181,7 @@ void PairMorseSmoothLinear::settings(int narg, char **arg) void PairMorseSmoothLinear::coeff(int narg, char **arg) { - if (narg < 5 || narg > 6) error->all(FLERR,"Incorrect args for pair coefficients"); + if (narg < 5 || narg > 6) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -207,7 +207,7 @@ void PairMorseSmoothLinear::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } diff --git a/src/EXTRA-PAIR/pair_nm_cut.cpp b/src/EXTRA-PAIR/pair_nm_cut.cpp index 3156ec224d..d3c7dca54d 100644 --- a/src/EXTRA-PAIR/pair_nm_cut.cpp +++ b/src/EXTRA-PAIR/pair_nm_cut.cpp @@ -200,7 +200,7 @@ void PairNMCut::settings(int narg, char **arg) void PairNMCut::coeff(int narg, char **arg) { if (narg < 6 || narg > 7) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -228,7 +228,7 @@ void PairNMCut::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/EXTRA-PAIR/pair_nm_cut_coul_cut.cpp b/src/EXTRA-PAIR/pair_nm_cut_coul_cut.cpp index 531f0e615f..1fb98e3f4b 100644 --- a/src/EXTRA-PAIR/pair_nm_cut_coul_cut.cpp +++ b/src/EXTRA-PAIR/pair_nm_cut_coul_cut.cpp @@ -224,7 +224,7 @@ void PairNMCutCoulCut::settings(int narg, char **arg) void PairNMCutCoulCut::coeff(int narg, char **arg) { - if (narg < 6 || narg > 8) error->all(FLERR,"Incorrect args for pair coefficients"); + if (narg < 6 || narg > 8) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -255,7 +255,7 @@ void PairNMCutCoulCut::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/EXTRA-PAIR/pair_nm_cut_coul_long.cpp b/src/EXTRA-PAIR/pair_nm_cut_coul_long.cpp index 2d4d048e26..cd36d4a262 100644 --- a/src/EXTRA-PAIR/pair_nm_cut_coul_long.cpp +++ b/src/EXTRA-PAIR/pair_nm_cut_coul_long.cpp @@ -258,7 +258,7 @@ void PairNMCutCoulLong::settings(int narg, char **arg) void PairNMCutCoulLong::coeff(int narg, char **arg) { if (narg < 6 || narg > 7) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -286,7 +286,7 @@ void PairNMCutCoulLong::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/EXTRA-PAIR/pair_pedone.cpp b/src/EXTRA-PAIR/pair_pedone.cpp index 9b8ce451d9..3f97c76a7d 100644 --- a/src/EXTRA-PAIR/pair_pedone.cpp +++ b/src/EXTRA-PAIR/pair_pedone.cpp @@ -189,7 +189,7 @@ void PairPedone::settings(int narg, char **arg) void PairPedone::coeff(int narg, char **arg) { - if (narg < 6 || narg > 7) error->all(FLERR, "Incorrect args for pair coefficients"); + if (narg < 6 || narg > 7) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo, ihi, jlo, jhi; @@ -217,7 +217,7 @@ void PairPedone::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/EXTRA-PAIR/pair_ufm.cpp b/src/EXTRA-PAIR/pair_ufm.cpp index e45b0814b3..157e597227 100644 --- a/src/EXTRA-PAIR/pair_ufm.cpp +++ b/src/EXTRA-PAIR/pair_ufm.cpp @@ -182,7 +182,7 @@ void PairUFM::settings(int narg, char **arg) void PairUFM::coeff(int narg, char **arg) { if (narg < 4 || narg > 5) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -208,7 +208,7 @@ void PairUFM::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/EXTRA-PAIR/pair_wf_cut.cpp b/src/EXTRA-PAIR/pair_wf_cut.cpp index d572521d90..bb1978ff8c 100644 --- a/src/EXTRA-PAIR/pair_wf_cut.cpp +++ b/src/EXTRA-PAIR/pair_wf_cut.cpp @@ -193,7 +193,7 @@ void PairWFCut::settings(int narg, char **arg) void PairWFCut::coeff(int narg, char **arg) { if (narg < 6 || narg > 7) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -221,7 +221,7 @@ void PairWFCut::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/FEP/pair_coul_cut_soft.cpp b/src/FEP/pair_coul_cut_soft.cpp index df4d19fc41..a1dd247dde 100644 --- a/src/FEP/pair_coul_cut_soft.cpp +++ b/src/FEP/pair_coul_cut_soft.cpp @@ -182,7 +182,7 @@ void PairCoulCutSoft::settings(int narg, char **arg) void PairCoulCutSoft::coeff(int narg, char **arg) { if (narg < 3 || narg > 4) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -204,7 +204,7 @@ void PairCoulCutSoft::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } diff --git a/src/FEP/pair_coul_long_soft.cpp b/src/FEP/pair_coul_long_soft.cpp index bc3774fd1c..fd113e80c4 100644 --- a/src/FEP/pair_coul_long_soft.cpp +++ b/src/FEP/pair_coul_long_soft.cpp @@ -194,7 +194,7 @@ void PairCoulLongSoft::settings(int narg, char **arg) void PairCoulLongSoft::coeff(int narg, char **arg) { if (narg != 3) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -213,7 +213,7 @@ void PairCoulLongSoft::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/FEP/pair_lj_charmm_coul_long_soft.cpp b/src/FEP/pair_lj_charmm_coul_long_soft.cpp index 1fa2ff6ea6..759e3c3ac6 100644 --- a/src/FEP/pair_lj_charmm_coul_long_soft.cpp +++ b/src/FEP/pair_lj_charmm_coul_long_soft.cpp @@ -669,7 +669,7 @@ void PairLJCharmmCoulLongSoft::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/FEP/pair_lj_class2_coul_cut_soft.cpp b/src/FEP/pair_lj_class2_coul_cut_soft.cpp index 5dc8141190..c1ac05fddd 100644 --- a/src/FEP/pair_lj_class2_coul_cut_soft.cpp +++ b/src/FEP/pair_lj_class2_coul_cut_soft.cpp @@ -226,7 +226,7 @@ void PairLJClass2CoulCutSoft::settings(int narg, char **arg) void PairLJClass2CoulCutSoft::coeff(int narg, char **arg) { - if (narg < 5 || narg > 7) error->all(FLERR,"Incorrect args for pair coefficients"); + if (narg < 5 || narg > 7) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -237,7 +237,7 @@ void PairLJClass2CoulCutSoft::coeff(int narg, char **arg) double sigma_one = utils::numeric(FLERR,arg[3],false,lmp); double lambda_one = utils::numeric(FLERR,arg[4],false,lmp); if (sigma_one <= 0.0) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); double cut_lj_one = cut_lj_global; double cut_coul_one = cut_coul_global; @@ -257,7 +257,7 @@ void PairLJClass2CoulCutSoft::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/FEP/pair_lj_class2_coul_long_soft.cpp b/src/FEP/pair_lj_class2_coul_long_soft.cpp index 43801ef5c6..a1d36d31be 100644 --- a/src/FEP/pair_lj_class2_coul_long_soft.cpp +++ b/src/FEP/pair_lj_class2_coul_long_soft.cpp @@ -233,7 +233,7 @@ void PairLJClass2CoulLongSoft::settings(int narg, char **arg) void PairLJClass2CoulLongSoft::coeff(int narg, char **arg) { if (narg < 5 || narg > 6) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -244,7 +244,7 @@ void PairLJClass2CoulLongSoft::coeff(int narg, char **arg) double sigma_one = utils::numeric(FLERR,arg[3],false,lmp); double lambda_one = utils::numeric(FLERR,arg[4],false,lmp); if (sigma_one <= 0.0) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); double cut_lj_one = cut_lj_global; if (narg == 6) cut_lj_one = utils::numeric(FLERR,arg[5],false,lmp); @@ -261,7 +261,7 @@ void PairLJClass2CoulLongSoft::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/FEP/pair_lj_class2_soft.cpp b/src/FEP/pair_lj_class2_soft.cpp index 79d2f19da6..6fbe0e7566 100644 --- a/src/FEP/pair_lj_class2_soft.cpp +++ b/src/FEP/pair_lj_class2_soft.cpp @@ -191,7 +191,7 @@ void PairLJClass2Soft::settings(int narg, char **arg) void PairLJClass2Soft::coeff(int narg, char **arg) { - if (narg < 5 || narg > 6) error->all(FLERR,"Incorrect args for pair coefficients"); + if (narg < 5 || narg > 6) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -201,7 +201,7 @@ void PairLJClass2Soft::coeff(int narg, char **arg) double epsilon_one = utils::numeric(FLERR,arg[2],false,lmp); double sigma_one = utils::numeric(FLERR,arg[3],false,lmp); double lambda_one = utils::numeric(FLERR,arg[4],false,lmp); - if (sigma_one <= 0.0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (sigma_one <= 0.0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); double cut_one = cut_global; if (narg == 6) cut_one = utils::numeric(FLERR,arg[5],false,lmp); @@ -218,7 +218,7 @@ void PairLJClass2Soft::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/FEP/pair_lj_cut_coul_cut_soft.cpp b/src/FEP/pair_lj_cut_coul_cut_soft.cpp index 1405a18cf1..844d4fc1e7 100644 --- a/src/FEP/pair_lj_cut_coul_cut_soft.cpp +++ b/src/FEP/pair_lj_cut_coul_cut_soft.cpp @@ -227,7 +227,7 @@ void PairLJCutCoulCutSoft::settings(int narg, char **arg) void PairLJCutCoulCutSoft::coeff(int narg, char **arg) { if (narg < 5 || narg > 7) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -238,7 +238,7 @@ void PairLJCutCoulCutSoft::coeff(int narg, char **arg) double sigma_one = utils::numeric(FLERR,arg[3],false,lmp); double lambda_one = utils::numeric(FLERR,arg[4],false,lmp); if (sigma_one <= 0.0) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); double cut_lj_one = cut_lj_global; double cut_coul_one = cut_coul_global; @@ -258,7 +258,7 @@ void PairLJCutCoulCutSoft::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/FEP/pair_lj_cut_coul_long_soft.cpp b/src/FEP/pair_lj_cut_coul_long_soft.cpp index a5f9f03d12..e7251e44bd 100644 --- a/src/FEP/pair_lj_cut_coul_long_soft.cpp +++ b/src/FEP/pair_lj_cut_coul_long_soft.cpp @@ -584,7 +584,7 @@ void PairLJCutCoulLongSoft::settings(int narg, char **arg) void PairLJCutCoulLongSoft::coeff(int narg, char **arg) { if (narg < 5 || narg > 6) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -595,7 +595,7 @@ void PairLJCutCoulLongSoft::coeff(int narg, char **arg) double sigma_one = utils::numeric(FLERR,arg[3],false,lmp); double lambda_one = utils::numeric(FLERR,arg[4],false,lmp); if (sigma_one <= 0.0) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); double cut_lj_one = cut_lj_global; if (narg == 6) cut_lj_one = utils::numeric(FLERR,arg[5],false,lmp); @@ -612,7 +612,7 @@ void PairLJCutCoulLongSoft::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/FEP/pair_lj_cut_soft.cpp b/src/FEP/pair_lj_cut_soft.cpp index 95c88132a0..bbbd23f8b7 100644 --- a/src/FEP/pair_lj_cut_soft.cpp +++ b/src/FEP/pair_lj_cut_soft.cpp @@ -471,7 +471,7 @@ void PairLJCutSoft::settings(int narg, char **arg) void PairLJCutSoft::coeff(int narg, char **arg) { if (narg < 5 || narg > 6) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -482,7 +482,7 @@ void PairLJCutSoft::coeff(int narg, char **arg) double sigma_one = utils::numeric(FLERR,arg[3],false,lmp); double lambda_one = utils::numeric(FLERR,arg[4],false,lmp); if (sigma_one <= 0.0) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); double cut_one = cut_global; if (narg == 6) cut_one = utils::numeric(FLERR,arg[5],false,lmp); @@ -499,7 +499,7 @@ void PairLJCutSoft::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/FEP/pair_morse_soft.cpp b/src/FEP/pair_morse_soft.cpp index e2cb92e303..e13defefa6 100644 --- a/src/FEP/pair_morse_soft.cpp +++ b/src/FEP/pair_morse_soft.cpp @@ -166,7 +166,7 @@ void PairMorseSoft::allocate() void PairMorseSoft::coeff(int narg, char **arg) { - if (narg < 6 || narg > 7) error->all(FLERR, "Incorrect args for pair coefficients"); + if (narg < 6 || narg > 7) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo, ihi, jlo, jhi; @@ -194,7 +194,7 @@ void PairMorseSoft::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/GPU/pair_eam_alloy_gpu.cpp b/src/GPU/pair_eam_alloy_gpu.cpp index 971014296d..cc1b88d5e9 100644 --- a/src/GPU/pair_eam_alloy_gpu.cpp +++ b/src/GPU/pair_eam_alloy_gpu.cpp @@ -335,7 +335,7 @@ void PairEAMAlloyGPU::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/GPU/pair_eam_fs_gpu.cpp b/src/GPU/pair_eam_fs_gpu.cpp index 58dcc9c868..7b6d3164c4 100644 --- a/src/GPU/pair_eam_fs_gpu.cpp +++ b/src/GPU/pair_eam_fs_gpu.cpp @@ -335,7 +335,7 @@ void PairEAMFSGPU::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/GRANULAR/pair_gran_hooke_history.cpp b/src/GRANULAR/pair_gran_hooke_history.cpp index 79bf2b87aa..57f9d2510f 100644 --- a/src/GRANULAR/pair_gran_hooke_history.cpp +++ b/src/GRANULAR/pair_gran_hooke_history.cpp @@ -407,7 +407,7 @@ void PairGranHookeHistory::settings(int narg, char **arg) void PairGranHookeHistory::coeff(int narg, char **arg) { - if (narg > 2) error->all(FLERR, "Incorrect args for pair coefficients"); + if (narg > 2) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo, ihi, jlo, jhi; @@ -422,7 +422,7 @@ void PairGranHookeHistory::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/GRANULAR/pair_granular.cpp b/src/GRANULAR/pair_granular.cpp index bae3371ebc..05bc911689 100644 --- a/src/GRANULAR/pair_granular.cpp +++ b/src/GRANULAR/pair_granular.cpp @@ -334,7 +334,7 @@ void PairGranular::coeff(int narg, char **arg) double cutoff_one = -1; if (narg < 3) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); @@ -394,7 +394,7 @@ void PairGranular::coeff(int narg, char **arg) // If there are > ntype^2 models, delete unused models if (nmodels == maxmodels) prune_models(); - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/INTEL/pair_eam_alloy_intel.cpp b/src/INTEL/pair_eam_alloy_intel.cpp index 1f2b4cd257..93ef071fd8 100644 --- a/src/INTEL/pair_eam_alloy_intel.cpp +++ b/src/INTEL/pair_eam_alloy_intel.cpp @@ -100,7 +100,7 @@ void PairEAMAlloyIntel::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/INTEL/pair_eam_fs_intel.cpp b/src/INTEL/pair_eam_fs_intel.cpp index 7b62378310..5f0fe2c418 100644 --- a/src/INTEL/pair_eam_fs_intel.cpp +++ b/src/INTEL/pair_eam_fs_intel.cpp @@ -100,7 +100,7 @@ void PairEAMFSIntel::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/INTEL/pair_snap_intel.cpp b/src/INTEL/pair_snap_intel.cpp index c9a4ed3d5a..7b388206b4 100644 --- a/src/INTEL/pair_snap_intel.cpp +++ b/src/INTEL/pair_snap_intel.cpp @@ -347,7 +347,7 @@ void PairSNAPIntel::settings(int narg, char ** /* arg */) void PairSNAPIntel::coeff(int narg, char **arg) { if (!allocated) allocate(); - if (narg != 4 + atom->ntypes) error->all(FLERR,"Incorrect args for pair coefficients"); + if (narg != 4 + atom->ntypes) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); map_element2type(narg-4,arg+4); diff --git a/src/INTERLAYER/pair_coul_shield.cpp b/src/INTERLAYER/pair_coul_shield.cpp index a5e3e63442..203bef9d92 100644 --- a/src/INTERLAYER/pair_coul_shield.cpp +++ b/src/INTERLAYER/pair_coul_shield.cpp @@ -201,7 +201,7 @@ void PairCoulShield::settings(int narg, char **arg) void PairCoulShield::coeff(int narg, char **arg) { - if (narg < 3 || narg > 4) error->all(FLERR, "Incorrect args for pair coefficients"); + if (narg < 3 || narg > 4) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo, ihi, jlo, jhi; @@ -223,7 +223,7 @@ void PairCoulShield::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/INTERLAYER/pair_kolmogorov_crespi_z.cpp b/src/INTERLAYER/pair_kolmogorov_crespi_z.cpp index dc1b82647a..fa0fe9cad1 100644 --- a/src/INTERLAYER/pair_kolmogorov_crespi_z.cpp +++ b/src/INTERLAYER/pair_kolmogorov_crespi_z.cpp @@ -235,7 +235,7 @@ void PairKolmogorovCrespiZ::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/INTERLAYER/pair_lebedeva_z.cpp b/src/INTERLAYER/pair_lebedeva_z.cpp index b68db0184f..ff9f9dedaa 100644 --- a/src/INTERLAYER/pair_lebedeva_z.cpp +++ b/src/INTERLAYER/pair_lebedeva_z.cpp @@ -232,7 +232,7 @@ void PairLebedevaZ::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/KIM/pair_kim.cpp b/src/KIM/pair_kim.cpp index 024b5ccf40..93ba759de4 100644 --- a/src/KIM/pair_kim.cpp +++ b/src/KIM/pair_kim.cpp @@ -364,7 +364,7 @@ void PairKIM::coeff(int narg, char **arg) if (!allocated) allocate(); if (narg < 2 + atom->ntypes) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); // read args that map atom species to KIM elements // lmps_map_species_to_unique[i] = @@ -407,7 +407,7 @@ void PairKIM::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); // setup mapping between LAMMPS unique elements and KIM species codes if (kim_particle_codes_ok) { diff --git a/src/KOKKOS/pair_eam_alloy_kokkos.cpp b/src/KOKKOS/pair_eam_alloy_kokkos.cpp index 90a82616a6..5d9f4f3f8b 100644 --- a/src/KOKKOS/pair_eam_alloy_kokkos.cpp +++ b/src/KOKKOS/pair_eam_alloy_kokkos.cpp @@ -1229,7 +1229,7 @@ void PairEAMAlloyKokkos::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/KOKKOS/pair_eam_fs_kokkos.cpp b/src/KOKKOS/pair_eam_fs_kokkos.cpp index 11719a8979..a2bd7651cb 100644 --- a/src/KOKKOS/pair_eam_fs_kokkos.cpp +++ b/src/KOKKOS/pair_eam_fs_kokkos.cpp @@ -1229,7 +1229,7 @@ void PairEAMFSKokkos::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/KOKKOS/pair_hybrid_overlay_kokkos.cpp b/src/KOKKOS/pair_hybrid_overlay_kokkos.cpp index 387212f383..9f1d61516f 100644 --- a/src/KOKKOS/pair_hybrid_overlay_kokkos.cpp +++ b/src/KOKKOS/pair_hybrid_overlay_kokkos.cpp @@ -31,7 +31,7 @@ PairHybridOverlayKokkos::PairHybridOverlayKokkos(LAMMPS *lmp) : PairHybridKokkos void PairHybridOverlayKokkos::coeff(int narg, char **arg) { - if (narg < 3) error->all(FLERR,"Incorrect args for pair coefficients"); + if (narg < 3) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -50,7 +50,7 @@ void PairHybridOverlayKokkos::coeff(int narg, char **arg) if (strcmp(arg[2],keywords[m]) == 0) { if (multiple[m]) { multflag = 1; - if (narg < 4) error->all(FLERR,"Incorrect args for pair coefficients"); + if (narg < 4) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (multiple[m] == utils::inumeric(FLERR,arg[3],false,lmp)) break; else continue; } else break; @@ -74,7 +74,7 @@ void PairHybridOverlayKokkos::coeff(int narg, char **arg) if (!none && styles[m]->one_coeff) if ((strcmp(arg[0],"*") != 0) || (strcmp(arg[1],"*") != 0)) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); // invoke sub-style coeff() starting with 1st remaining arg @@ -104,7 +104,7 @@ void PairHybridOverlayKokkos::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } diff --git a/src/KOKKOS/pair_mliap_kokkos.cpp b/src/KOKKOS/pair_mliap_kokkos.cpp index 599c49f523..a57ef44c39 100644 --- a/src/KOKKOS/pair_mliap_kokkos.cpp +++ b/src/KOKKOS/pair_mliap_kokkos.cpp @@ -214,7 +214,7 @@ void PairMLIAPKokkos::settings(int narg, char ** arg) template void PairMLIAPKokkos::coeff(int narg, char **arg) { - if (narg < 3) error->all(FLERR,"Incorrect args for pair coefficients"); + if (narg < 3) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) { PairMLIAP::allocate(); allocate(); @@ -227,7 +227,7 @@ void PairMLIAPKokkos::coeff(int narg, char **arg) { // ensure I,J args are * * if (strcmp(type1,"*") != 0 || strcmp(type2,"*") != 0) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); // read args that map atom types to elements // map[i] = which element the Ith atom type is, -1 if not mapped @@ -244,7 +244,7 @@ void PairMLIAPKokkos::coeff(int narg, char **arg) { if (jelem < descriptor->nelements) map[i] = jelem; else if (strcmp(elemname,"NULL") == 0) map[i] = -1; - else error->all(FLERR,"Incorrect args for pair coefficients"); + else error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } k_map.modify(); k_map.sync(); @@ -268,7 +268,7 @@ void PairMLIAPKokkos::coeff(int narg, char **arg) { k_setflag.modify(); k_setflag.sync(); - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); // set up model, descriptor, and mliap data structures model->init(); diff --git a/src/KSPACE/pair_born_coul_long.cpp b/src/KSPACE/pair_born_coul_long.cpp index 0165beba0d..e9abe539c1 100644 --- a/src/KSPACE/pair_born_coul_long.cpp +++ b/src/KSPACE/pair_born_coul_long.cpp @@ -256,7 +256,7 @@ void PairBornCoulLong::settings(int narg, char **arg) void PairBornCoulLong::coeff(int narg, char **arg) { - if (narg < 7 || narg > 8) error->all(FLERR,"Incorrect args for pair coefficients"); + if (narg < 7 || narg > 8) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -266,7 +266,7 @@ void PairBornCoulLong::coeff(int narg, char **arg) double a_one = utils::numeric(FLERR,arg[2],false,lmp); double rho_one = utils::numeric(FLERR,arg[3],false,lmp); double sigma_one = utils::numeric(FLERR,arg[4],false,lmp); - if (rho_one <= 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (rho_one <= 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); double c_one = utils::numeric(FLERR,arg[5],false,lmp); double d_one = utils::numeric(FLERR,arg[6],false,lmp); @@ -287,7 +287,7 @@ void PairBornCoulLong::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/KSPACE/pair_buck_coul_long.cpp b/src/KSPACE/pair_buck_coul_long.cpp index a6a86f3d45..f3b7a91c0e 100644 --- a/src/KSPACE/pair_buck_coul_long.cpp +++ b/src/KSPACE/pair_buck_coul_long.cpp @@ -256,7 +256,7 @@ void PairBuckCoulLong::settings(int narg, char **arg) void PairBuckCoulLong::coeff(int narg, char **arg) { if (narg < 5 || narg > 6) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -265,7 +265,7 @@ void PairBuckCoulLong::coeff(int narg, char **arg) double a_one = utils::numeric(FLERR,arg[2],false,lmp); double rho_one = utils::numeric(FLERR,arg[3],false,lmp); - if (rho_one <= 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (rho_one <= 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); double c_one = utils::numeric(FLERR,arg[4],false,lmp); double cut_lj_one = cut_lj_global; @@ -283,7 +283,7 @@ void PairBuckCoulLong::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/KSPACE/pair_buck_long_coul_long.cpp b/src/KSPACE/pair_buck_long_coul_long.cpp index e7cce1071a..e1dac0a61b 100644 --- a/src/KSPACE/pair_buck_long_coul_long.cpp +++ b/src/KSPACE/pair_buck_long_coul_long.cpp @@ -191,7 +191,7 @@ void *PairBuckLongCoulLong::extract(const char *id, int &dim) void PairBuckLongCoulLong::coeff(int narg, char **arg) { if (narg < 5 || narg > 6) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -217,7 +217,7 @@ void PairBuckLongCoulLong::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/KSPACE/pair_coul_long.cpp b/src/KSPACE/pair_coul_long.cpp index ef1b60ac56..65ec9875cf 100644 --- a/src/KSPACE/pair_coul_long.cpp +++ b/src/KSPACE/pair_coul_long.cpp @@ -200,7 +200,7 @@ void PairCoulLong::settings(int narg, char **arg) void PairCoulLong::coeff(int narg, char **arg) { - if (narg != 2) error->all(FLERR, "Incorrect args for pair coefficients"); + if (narg != 2) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo, ihi, jlo, jhi; @@ -216,7 +216,7 @@ void PairCoulLong::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/KSPACE/pair_lj_charmm_coul_long.cpp b/src/KSPACE/pair_lj_charmm_coul_long.cpp index ef367f8742..ceee04f811 100644 --- a/src/KSPACE/pair_lj_charmm_coul_long.cpp +++ b/src/KSPACE/pair_lj_charmm_coul_long.cpp @@ -666,7 +666,7 @@ void PairLJCharmmCoulLong::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp b/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp index a0889d92ea..e0074da0ae 100644 --- a/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp +++ b/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp @@ -717,7 +717,7 @@ void PairLJCharmmfswCoulLong::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/KSPACE/pair_lj_cut_coul_long.cpp b/src/KSPACE/pair_lj_cut_coul_long.cpp index 969f235c55..a6b268e901 100644 --- a/src/KSPACE/pair_lj_cut_coul_long.cpp +++ b/src/KSPACE/pair_lj_cut_coul_long.cpp @@ -611,7 +611,7 @@ void PairLJCutCoulLong::settings(int narg, char **arg) void PairLJCutCoulLong::coeff(int narg, char **arg) { if (narg < 4 || narg > 5) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -635,7 +635,7 @@ void PairLJCutCoulLong::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/KSPACE/pair_lj_long_coul_long.cpp b/src/KSPACE/pair_lj_long_coul_long.cpp index 2955b24fe8..ab80e992b2 100644 --- a/src/KSPACE/pair_lj_long_coul_long.cpp +++ b/src/KSPACE/pair_lj_long_coul_long.cpp @@ -187,7 +187,7 @@ void *PairLJLongCoulLong::extract(const char *id, int &dim) void PairLJLongCoulLong::coeff(int narg, char **arg) { - if (narg < 4 || narg > 5) error->all(FLERR,"Incorrect args for pair coefficients"); + if (narg < 4 || narg > 5) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -211,7 +211,7 @@ void PairLJLongCoulLong::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/LEPTON/pair_lepton.cpp b/src/LEPTON/pair_lepton.cpp index 90003e9091..e55a77a583 100644 --- a/src/LEPTON/pair_lepton.cpp +++ b/src/LEPTON/pair_lepton.cpp @@ -216,7 +216,7 @@ void PairLepton::settings(int narg, char **arg) void PairLepton::coeff(int narg, char **arg) { - if (narg < 3 || narg > 4) error->all(FLERR, "Incorrect number of args for pair coefficients"); + if (narg < 3 || narg > 4) error->all(FLERR, "Incorrect number of args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo, ihi, jlo, jhi; @@ -270,7 +270,7 @@ void PairLepton::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- */ diff --git a/src/MACHDYN/pair_smd_hertz.cpp b/src/MACHDYN/pair_smd_hertz.cpp index 99e8ae6426..32b488ef03 100644 --- a/src/MACHDYN/pair_smd_hertz.cpp +++ b/src/MACHDYN/pair_smd_hertz.cpp @@ -253,7 +253,7 @@ void PairHertz::settings(int narg, char **arg) { void PairHertz::coeff(int narg, char **arg) { if (narg != 3) - error->all(FLERR, "Incorrect args for pair coefficients"); + error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); @@ -282,7 +282,7 @@ void PairHertz::coeff(int narg, char **arg) { } if (count == 0) - error->all(FLERR, "Incorrect args for pair coefficients"); + error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/MACHDYN/pair_smd_triangulated_surface.cpp b/src/MACHDYN/pair_smd_triangulated_surface.cpp index dc777cc66f..da9d5faa12 100644 --- a/src/MACHDYN/pair_smd_triangulated_surface.cpp +++ b/src/MACHDYN/pair_smd_triangulated_surface.cpp @@ -335,7 +335,7 @@ void PairTriSurf::settings(int narg, char **arg) { void PairTriSurf::coeff(int narg, char **arg) { if (narg != 3) - error->all(FLERR, "Incorrect args for pair coefficients"); + error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); @@ -364,7 +364,7 @@ void PairTriSurf::coeff(int narg, char **arg) { } if (count == 0) - error->all(FLERR, "Incorrect args for pair coefficients"); + error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/MANYBODY/pair_adp.cpp b/src/MANYBODY/pair_adp.cpp index 6a9cfd201b..6e7f5a7b82 100644 --- a/src/MANYBODY/pair_adp.cpp +++ b/src/MANYBODY/pair_adp.cpp @@ -441,12 +441,12 @@ void PairADP::coeff(int narg, char **arg) if (!allocated) allocate(); if (narg != 3 + atom->ntypes) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); // ensure I,J args are * * if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); // read ADP parameter file @@ -499,7 +499,7 @@ void PairADP::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } diff --git a/src/MANYBODY/pair_airebo.cpp b/src/MANYBODY/pair_airebo.cpp index 3d5334a471..4a3c3351ba 100644 --- a/src/MANYBODY/pair_airebo.cpp +++ b/src/MANYBODY/pair_airebo.cpp @@ -215,7 +215,7 @@ void PairAIREBO::coeff(int narg, char **arg) count++; } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/MANYBODY/pair_atm.cpp b/src/MANYBODY/pair_atm.cpp index 671b77b206..3d7e5e2600 100644 --- a/src/MANYBODY/pair_atm.cpp +++ b/src/MANYBODY/pair_atm.cpp @@ -222,7 +222,7 @@ void PairATM::settings(int narg, char **arg) void PairATM::coeff(int narg, char **arg) { - if (narg != 4) error->all(FLERR,"Incorrect args for pair coefficients"); + if (narg != 4) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi,klo,khi; @@ -259,7 +259,7 @@ void PairATM::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/MANYBODY/pair_eam.cpp b/src/MANYBODY/pair_eam.cpp index e4a0155ab9..b5a0ca0f77 100644 --- a/src/MANYBODY/pair_eam.cpp +++ b/src/MANYBODY/pair_eam.cpp @@ -384,7 +384,7 @@ void PairEAM::coeff(int narg, char **arg) { if (!allocated) allocate(); - if (narg != 3) error->all(FLERR,"Incorrect args for pair coefficients"); + if (narg != 3) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); // parse pair of atom types @@ -423,7 +423,7 @@ void PairEAM::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/MANYBODY/pair_eam_alloy.cpp b/src/MANYBODY/pair_eam_alloy.cpp index 0163cb6ed5..974c258a75 100644 --- a/src/MANYBODY/pair_eam_alloy.cpp +++ b/src/MANYBODY/pair_eam_alloy.cpp @@ -100,7 +100,7 @@ void PairEAMAlloy::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/MANYBODY/pair_eam_fs.cpp b/src/MANYBODY/pair_eam_fs.cpp index da4e2882b0..529b422288 100644 --- a/src/MANYBODY/pair_eam_fs.cpp +++ b/src/MANYBODY/pair_eam_fs.cpp @@ -101,7 +101,7 @@ void PairEAMFS::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/MANYBODY/pair_eim.cpp b/src/MANYBODY/pair_eim.cpp index 8a296b9133..6cb7ea674a 100644 --- a/src/MANYBODY/pair_eim.cpp +++ b/src/MANYBODY/pair_eim.cpp @@ -347,12 +347,12 @@ void PairEIM::coeff(int narg, char **arg) { if (!allocated) allocate(); - if (narg < 5) error->all(FLERR,"Incorrect args for pair coefficients"); + if (narg < 5) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); // ensure I,J args are * * if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); const int ntypes = atom->ntypes; map_element2type(ntypes,arg+(narg-ntypes)); diff --git a/src/MANYBODY/pair_lcbop.cpp b/src/MANYBODY/pair_lcbop.cpp index d4f8cd4ec4..75fd0f441e 100644 --- a/src/MANYBODY/pair_lcbop.cpp +++ b/src/MANYBODY/pair_lcbop.cpp @@ -131,7 +131,7 @@ void PairLCBOP::coeff(int narg, char **arg) // only element "C" is allowed if ((nelements != 1) || (strcmp(elements[0],"C") != 0)) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); // read potential file and initialize fitting splines diff --git a/src/MANYBODY/pair_local_density.cpp b/src/MANYBODY/pair_local_density.cpp index da405e9118..86d3ad6de4 100644 --- a/src/MANYBODY/pair_local_density.cpp +++ b/src/MANYBODY/pair_local_density.cpp @@ -382,12 +382,12 @@ void PairLocalDensity::coeff(int narg, char **arg) int i, j; if (!allocated) allocate(); - if (narg != 3) error->all(FLERR,"Incorrect args for pair coefficients"); + if (narg != 3) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); // ensure I,J args are * * if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); // parse LD file @@ -409,7 +409,7 @@ void PairLocalDensity::coeff(int narg, char **arg) count++; } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/MANYBODY/pair_meam_spline.cpp b/src/MANYBODY/pair_meam_spline.cpp index e3d17f6fae..160bde5916 100644 --- a/src/MANYBODY/pair_meam_spline.cpp +++ b/src/MANYBODY/pair_meam_spline.cpp @@ -382,7 +382,7 @@ void PairMEAMSpline::coeff(int narg, char **arg) int i,j,n; if (narg != 3 + atom->ntypes) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); // read potential file: also sets the number of elements. read_file(arg[2]); @@ -428,7 +428,7 @@ void PairMEAMSpline::coeff(int narg, char **arg) setflag[i][j] = 1; count++; } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); // check that each element is mapped to exactly one atom type diff --git a/src/MANYBODY/pair_rebomos.cpp b/src/MANYBODY/pair_rebomos.cpp index 0941ca0a3a..b8f3c6fde5 100644 --- a/src/MANYBODY/pair_rebomos.cpp +++ b/src/MANYBODY/pair_rebomos.cpp @@ -154,12 +154,12 @@ void PairREBOMoS::coeff(int narg, char **arg) if (!allocated) allocate(); if (narg != 3 + atom->ntypes) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); // insure I,J args are * * if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); // read args that map atom types to Mo and S // map[i] = which element (0,1) the Ith atom type is, -1 if NULL @@ -174,7 +174,7 @@ void PairREBOMoS::coeff(int narg, char **arg) map[i-2] = 0; } else if (strcmp(arg[i],"S") == 0) { map[i-2] = 1; - } else error->all(FLERR,"Incorrect args for pair coefficients"); + } else error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } // read potential file and initialize fitting splines @@ -198,7 +198,7 @@ void PairREBOMoS::coeff(int narg, char **arg) count++; } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/MANYBODY/pair_sw.cpp b/src/MANYBODY/pair_sw.cpp index 74d1ae1871..a28e523831 100644 --- a/src/MANYBODY/pair_sw.cpp +++ b/src/MANYBODY/pair_sw.cpp @@ -305,7 +305,7 @@ void PairSW::coeff(int narg, char **arg) count++; } } - if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); } } diff --git a/src/MC/pair_dsmc.cpp b/src/MC/pair_dsmc.cpp index 1c152906b3..a570113d07 100644 --- a/src/MC/pair_dsmc.cpp +++ b/src/MC/pair_dsmc.cpp @@ -240,7 +240,7 @@ void PairDSMC::settings(int narg, char **arg) void PairDSMC::coeff(int narg, char **arg) { - if (narg < 3 || narg > 4) error->all(FLERR,"Incorrect args for pair coefficients"); + if (narg < 3 || narg > 4) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -262,7 +262,7 @@ void PairDSMC::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/MEAM/pair_meam.cpp b/src/MEAM/pair_meam.cpp index 4138e9c31b..001d753512 100644 --- a/src/MEAM/pair_meam.cpp +++ b/src/MEAM/pair_meam.cpp @@ -234,9 +234,9 @@ void PairMEAM::coeff(int narg, char **arg) } if (paridx < 0) { if (msmeamflag) - error->all(FLERR, Error::NOPOINTER, "No MS-MEAM parameter file in pair coefficients"); + error->all(FLERR, Error::NOPOINTER, "No MS-MEAM parameter file in pair coefficients" + utils::errorurl(21)); else - error->all(FLERR, Error::NOPOINTER, "No MEAM parameter file in pair coefficients"); + error->all(FLERR, Error::NOPOINTER, "No MEAM parameter file in pair coefficients" + utils::errorurl(21)); } if ((narg - paridx - 1) != atom->ntypes) error->all(FLERR, Error::NOPOINTER, "Expected {} but found {} args for pair style {} " @@ -252,7 +252,7 @@ void PairMEAM::coeff(int narg, char **arg) } nlibelements = paridx - 3; - if (nlibelements < 1) error->all(FLERR, "Incorrect args for pair coefficients"); + if (nlibelements < 1) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); if (nlibelements > MAXELT) error->all(FLERR, "Too many elements extracted from MEAM library (current limit: {}). " diff --git a/src/MGPT/pair_mgpt.cpp b/src/MGPT/pair_mgpt.cpp index 986c3e4aef..c5cb1d1325 100644 --- a/src/MGPT/pair_mgpt.cpp +++ b/src/MGPT/pair_mgpt.cpp @@ -1846,7 +1846,7 @@ void PairMGPT::coeff(int narg, char **arg) // Make sure I,J args are * * if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); double vol; if (sscanf(arg[4], "%lg", &vol) != 1 || vol <= 0.0) @@ -1862,7 +1862,7 @@ void PairMGPT::coeff(int narg, char **arg) while (iarg < narg) { if (strcmp(arg[iarg],"volpress") == 0) { /* Volumetric pressure flag */ if (iarg+2 > narg) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (strcmp(arg[iarg+1],"yes") == 0) volpres_flag = 1; else if (strcmp(arg[iarg+1],"no") == 0) volpres_flag = 0; else { @@ -1876,7 +1876,7 @@ void PairMGPT::coeff(int narg, char **arg) if (comm->me == 0) printf("* volpress: volpres_flag = %d [%s %s]\n",volpres_flag,arg[iarg-2],arg[iarg-1]); } else if (strcmp(arg[iarg],"nbody") == 0) { if (iarg+2 > narg) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (strspn(arg[iarg+1],"1234") == strlen(arg[iarg+1])) { nbody_flag = 0; for (int i = 0; i<4; i++) @@ -1897,7 +1897,7 @@ void PairMGPT::coeff(int narg, char **arg) iarg += 2; } else if (strcmp(arg[iarg],"precision") == 0) { if (iarg+2 > narg) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (strcmp(arg[iarg+1],"single") == 0) single_precision = 1; else if (strcmp(arg[iarg+1],"double") == 0) single_precision = 0; else { diff --git a/src/MISC/pair_list.cpp b/src/MISC/pair_list.cpp index 25e53149f6..0a92821a33 100644 --- a/src/MISC/pair_list.cpp +++ b/src/MISC/pair_list.cpp @@ -361,7 +361,7 @@ void PairList::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/MISC/pair_tracker.cpp b/src/MISC/pair_tracker.cpp index 72463d84e9..43a576d963 100644 --- a/src/MISC/pair_tracker.cpp +++ b/src/MISC/pair_tracker.cpp @@ -309,8 +309,8 @@ void PairTracker::settings(int narg, char **arg) void PairTracker::coeff(int narg, char **arg) { - if (narg > 2 && finitecutflag) error->all(FLERR, "Incorrect args for pair coefficients"); - if (narg != 3 && !finitecutflag) error->all(FLERR, "Incorrect args for pair coefficients"); + if (narg > 2 && finitecutflag) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); + if (narg != 3 && !finitecutflag) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo, ihi, jlo, jhi; @@ -329,7 +329,7 @@ void PairTracker::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/ML-HDNNP/pair_hdnnp.cpp b/src/ML-HDNNP/pair_hdnnp.cpp index cfe1e0bb64..5b5802605c 100644 --- a/src/ML-HDNNP/pair_hdnnp.cpp +++ b/src/ML-HDNNP/pair_hdnnp.cpp @@ -189,10 +189,10 @@ void PairHDNNP::coeff(int narg, char **arg) if (!allocated) allocate(); - if (narg != 2 + n) error->all(FLERR, "Incorrect args for pair coefficients"); + if (narg != 2 + n) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); if (strcmp(arg[0], "*") != 0 || strcmp(arg[1], "*") != 0) - error->all(FLERR, "Incorrect args for pair coefficients"); + error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); int *map = new int[n + 1]; for (int i = 0; i < n; i++) map[i] = 0; @@ -214,7 +214,7 @@ void PairHDNNP::coeff(int narg, char **arg) count++; } - if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); delete[] map; } diff --git a/src/ML-IAP/pair_mliap.cpp b/src/ML-IAP/pair_mliap.cpp index 8585fffadb..b72e9bd481 100644 --- a/src/ML-IAP/pair_mliap.cpp +++ b/src/ML-IAP/pair_mliap.cpp @@ -226,7 +226,7 @@ void PairMLIAP::settings(int narg, char ** arg) void PairMLIAP::coeff(int narg, char **arg) { - if (narg < 3) error->all(FLERR,"Incorrect args for pair coefficients"); + if (narg < 3) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); char** elemtypes = &arg[2]; @@ -245,7 +245,7 @@ void PairMLIAP::coeff(int narg, char **arg) if (jelem < descriptor->nelements) map[i] = jelem; else if (strcmp(elemname,"NULL") == 0) map[i] = -1; - else error->all(FLERR,"Incorrect args for pair coefficients"); + else error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } // clear setflag since coeff() called once with I,J = * * @@ -265,7 +265,7 @@ void PairMLIAP::coeff(int narg, char **arg) count++; } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); // set up model, descriptor, and mliap data structures diff --git a/src/ML-QUIP/pair_quip.cpp b/src/ML-QUIP/pair_quip.cpp index 35ba4ff8e4..7f8e6fd6af 100644 --- a/src/ML-QUIP/pair_quip.cpp +++ b/src/ML-QUIP/pair_quip.cpp @@ -279,7 +279,7 @@ void PairQUIP::coeff(int narg, char **arg) count++; } - if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); // Initialise potential // First call initializes potential via the fortran code in memory, diff --git a/src/ML-RANN/pair_rann.cpp b/src/ML-RANN/pair_rann.cpp index 4ec1f45703..d1e4fc1671 100644 --- a/src/ML-RANN/pair_rann.cpp +++ b/src/ML-RANN/pair_rann.cpp @@ -302,8 +302,8 @@ void PairRANN::coeff(int narg, char **arg) int i,j; deallocate();//clear allocation from any previous coeff map = new int[atom->ntypes+1]; - if (narg != 3 + atom->ntypes) error->one(FLERR,"Incorrect args for pair coefficients"); - if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0) error->one(FLERR,"Incorrect args for pair coefficients"); + if (narg != 3 + atom->ntypes) error->one(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); + if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0) error->one(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); nelements = -1; read_file(arg[2]); // read args that map atom types to elements in potential file @@ -338,7 +338,7 @@ void PairRANN::coeff(int narg, char **arg) } } } - if (count == 0) error->one(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->one(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); for (i=0;iallocate(); diff --git a/src/MOFFF/pair_buck6d_coul_gauss_dsf.cpp b/src/MOFFF/pair_buck6d_coul_gauss_dsf.cpp index 71a6e7facf..ced0528ac6 100644 --- a/src/MOFFF/pair_buck6d_coul_gauss_dsf.cpp +++ b/src/MOFFF/pair_buck6d_coul_gauss_dsf.cpp @@ -274,7 +274,7 @@ void PairBuck6dCoulGaussDSF::settings(int narg, char **arg) void PairBuck6dCoulGaussDSF::coeff(int narg, char **arg) { if (narg < 7 || narg > 8) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -304,7 +304,7 @@ void PairBuck6dCoulGaussDSF::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/MOFFF/pair_buck6d_coul_gauss_long.cpp b/src/MOFFF/pair_buck6d_coul_gauss_long.cpp index 2ccc921448..72919312e5 100644 --- a/src/MOFFF/pair_buck6d_coul_gauss_long.cpp +++ b/src/MOFFF/pair_buck6d_coul_gauss_long.cpp @@ -289,7 +289,7 @@ void PairBuck6dCoulGaussLong::settings(int narg, char **arg) void PairBuck6dCoulGaussLong::coeff(int narg, char **arg) { if (narg < 7 || narg > 8) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -319,7 +319,7 @@ void PairBuck6dCoulGaussLong::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/MOLECULE/pair_hbond_dreiding_lj.cpp b/src/MOLECULE/pair_hbond_dreiding_lj.cpp index fd0e61edd2..2de43b6215 100644 --- a/src/MOLECULE/pair_hbond_dreiding_lj.cpp +++ b/src/MOLECULE/pair_hbond_dreiding_lj.cpp @@ -334,7 +334,7 @@ void PairHbondDreidingLJ::coeff(int narg, char **arg) // check settings if (narg < 6 || narg > maxarg) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); @@ -346,7 +346,7 @@ void PairHbondDreidingLJ::coeff(int narg, char **arg) int donor_flag; if (strcmp(arg[3],"i") == 0) donor_flag = 0; else if (strcmp(arg[3],"j") == 0) donor_flag = 1; - else error->all(FLERR,"Incorrect args for pair coefficients"); + else error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); double epsilon_one = utils::numeric(FLERR, arg[4], false, lmp); double sigma_one = utils::numeric(FLERR, arg[5], false, lmp); @@ -400,7 +400,7 @@ void PairHbondDreidingLJ::coeff(int narg, char **arg) } nparams++; - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/MOLECULE/pair_hbond_dreiding_morse.cpp b/src/MOLECULE/pair_hbond_dreiding_morse.cpp index 8506765984..c5465a076a 100644 --- a/src/MOLECULE/pair_hbond_dreiding_morse.cpp +++ b/src/MOLECULE/pair_hbond_dreiding_morse.cpp @@ -249,7 +249,7 @@ void PairHbondDreidingMorse::coeff(int narg, char **arg) int maxarg = 12; if (angle_offset_flag == 1) maxarg = 12; if (narg < 7 || narg > maxarg) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi,klo,khi; @@ -260,7 +260,7 @@ void PairHbondDreidingMorse::coeff(int narg, char **arg) int donor_flag; if (strcmp(arg[3],"i") == 0) donor_flag = 0; else if (strcmp(arg[3],"j") == 0) donor_flag = 1; - else error->all(FLERR,"Incorrect args for pair coefficients"); + else error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); double d0_one = utils::numeric(FLERR, arg[4], false, lmp); double alpha_one = utils::numeric(FLERR, arg[5], false, lmp); @@ -318,7 +318,7 @@ void PairHbondDreidingMorse::coeff(int narg, char **arg) } nparams++; - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/MOLECULE/pair_lj_charmm_coul_charmm.cpp b/src/MOLECULE/pair_lj_charmm_coul_charmm.cpp index 237b843ec5..d7986a67bd 100644 --- a/src/MOLECULE/pair_lj_charmm_coul_charmm.cpp +++ b/src/MOLECULE/pair_lj_charmm_coul_charmm.cpp @@ -243,7 +243,7 @@ void PairLJCharmmCoulCharmm::settings(int narg, char **arg) void PairLJCharmmCoulCharmm::coeff(int narg, char **arg) { if (narg != 4 && narg != 6) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -271,7 +271,7 @@ void PairLJCharmmCoulCharmm::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp b/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp index 65caa46153..ae3e680c65 100644 --- a/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp +++ b/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp @@ -267,7 +267,7 @@ void PairLJCharmmfswCoulCharmmfsh::settings(int narg, char **arg) void PairLJCharmmfswCoulCharmmfsh::coeff(int narg, char **arg) { if (narg != 4 && narg != 6) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -295,7 +295,7 @@ void PairLJCharmmfswCoulCharmmfsh::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/MOLECULE/pair_lj_cut_tip4p_cut.cpp b/src/MOLECULE/pair_lj_cut_tip4p_cut.cpp index b8946b67f4..504db90de0 100644 --- a/src/MOLECULE/pair_lj_cut_tip4p_cut.cpp +++ b/src/MOLECULE/pair_lj_cut_tip4p_cut.cpp @@ -458,7 +458,7 @@ void PairLJCutTIP4PCut::settings(int narg, char **arg) void PairLJCutTIP4PCut::coeff(int narg, char **arg) { if (narg < 4 || narg > 5) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); // set atom types from pair_style command unless we were restarted @@ -492,7 +492,7 @@ void PairLJCutTIP4PCut::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/MOLECULE/pair_tip4p_cut.cpp b/src/MOLECULE/pair_tip4p_cut.cpp index c914cb0ec0..fe3494ee85 100644 --- a/src/MOLECULE/pair_tip4p_cut.cpp +++ b/src/MOLECULE/pair_tip4p_cut.cpp @@ -393,7 +393,7 @@ void PairTIP4PCut::settings(int narg, char **arg) void PairTIP4PCut::coeff(int narg, char **arg) { if (narg != 2) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); // set atom types from pair_style command unless we were restarted @@ -418,7 +418,7 @@ void PairTIP4PCut::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/OPENMP/pair_coul_cut_global_omp.cpp b/src/OPENMP/pair_coul_cut_global_omp.cpp index c4236295a1..783cf9dc73 100644 --- a/src/OPENMP/pair_coul_cut_global_omp.cpp +++ b/src/OPENMP/pair_coul_cut_global_omp.cpp @@ -27,7 +27,7 @@ using namespace LAMMPS_NS; void PairCoulCutGlobalOMP::coeff(int narg, char **arg) { if (narg != 2) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); PairCoulCut::coeff(narg,arg); } diff --git a/src/OPENMP/pair_eam_alloy_omp.cpp b/src/OPENMP/pair_eam_alloy_omp.cpp index e78fafb193..6b9cbbe57e 100644 --- a/src/OPENMP/pair_eam_alloy_omp.cpp +++ b/src/OPENMP/pair_eam_alloy_omp.cpp @@ -99,7 +99,7 @@ void PairEAMAlloyOMP::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/OPENMP/pair_eam_fs_omp.cpp b/src/OPENMP/pair_eam_fs_omp.cpp index 1674c09e7a..423919013c 100644 --- a/src/OPENMP/pair_eam_fs_omp.cpp +++ b/src/OPENMP/pair_eam_fs_omp.cpp @@ -99,7 +99,7 @@ void PairEAMFSOMP::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/OPENMP/pair_hbond_dreiding_lj_angleoffset_omp.cpp b/src/OPENMP/pair_hbond_dreiding_lj_angleoffset_omp.cpp index 11c09ed549..9003268b77 100644 --- a/src/OPENMP/pair_hbond_dreiding_lj_angleoffset_omp.cpp +++ b/src/OPENMP/pair_hbond_dreiding_lj_angleoffset_omp.cpp @@ -51,7 +51,7 @@ void PairHbondDreidingLJAngleoffsetOMP::coeff(int narg, char **arg) { auto mylmp = PairHbondDreidingLJ::lmp; if (narg < 6 || narg > 11) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi,klo,khi; @@ -62,7 +62,7 @@ void PairHbondDreidingLJAngleoffsetOMP::coeff(int narg, char **arg) int donor_flag; if (strcmp(arg[3],"i") == 0) donor_flag = 0; else if (strcmp(arg[3],"j") == 0) donor_flag = 1; - else error->all(FLERR,"Incorrect args for pair coefficients"); + else error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); double epsilon_one = utils::numeric(FLERR, arg[4], false, mylmp); double sigma_one = utils::numeric(FLERR, arg[5], false, mylmp); @@ -123,5 +123,5 @@ void PairHbondDreidingLJAngleoffsetOMP::coeff(int narg, char **arg) } nparams++; - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } diff --git a/src/OPENMP/pair_hbond_dreiding_morse_angleoffset_omp.cpp b/src/OPENMP/pair_hbond_dreiding_morse_angleoffset_omp.cpp index e7c75f29e4..8011d25479 100644 --- a/src/OPENMP/pair_hbond_dreiding_morse_angleoffset_omp.cpp +++ b/src/OPENMP/pair_hbond_dreiding_morse_angleoffset_omp.cpp @@ -51,7 +51,7 @@ void PairHbondDreidingMorseAngleoffsetOMP::coeff(int narg, char **arg) { auto mylmp = PairHbondDreidingMorse::lmp; if (narg < 7 || narg > 12) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi,klo,khi; @@ -62,7 +62,7 @@ void PairHbondDreidingMorseAngleoffsetOMP::coeff(int narg, char **arg) int donor_flag; if (strcmp(arg[3],"i") == 0) donor_flag = 0; else if (strcmp(arg[3],"j") == 0) donor_flag = 1; - else error->all(FLERR,"Incorrect args for pair coefficients"); + else error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); double d0_one = utils::numeric(FLERR, arg[4], false, mylmp); double alpha_one = utils::numeric(FLERR, arg[5], false, mylmp); @@ -123,5 +123,5 @@ void PairHbondDreidingMorseAngleoffsetOMP::coeff(int narg, char **arg) } nparams++; - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } diff --git a/src/PERI/pair_peri_eps.cpp b/src/PERI/pair_peri_eps.cpp index 77d8c078c4..fccfee60c7 100644 --- a/src/PERI/pair_peri_eps.cpp +++ b/src/PERI/pair_peri_eps.cpp @@ -360,7 +360,7 @@ void PairPeriEPS::compute(int eflag, int vflag) void PairPeriEPS::coeff(int narg, char **arg) { - if (narg != 8) error->all(FLERR,"Incorrect args for pair coefficients"); + if (narg != 8) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -388,7 +388,7 @@ void PairPeriEPS::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/PERI/pair_peri_lps.cpp b/src/PERI/pair_peri_lps.cpp index 2e11b8c76f..34420b6ef2 100644 --- a/src/PERI/pair_peri_lps.cpp +++ b/src/PERI/pair_peri_lps.cpp @@ -306,7 +306,7 @@ void PairPeriLPS::compute(int eflag, int vflag) void PairPeriLPS::coeff(int narg, char **arg) { - if (narg != 7) error->all(FLERR,"Incorrect args for pair coefficients"); + if (narg != 7) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -332,7 +332,7 @@ void PairPeriLPS::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/PERI/pair_peri_pmb.cpp b/src/PERI/pair_peri_pmb.cpp index 1bed10a877..85c16f6ff8 100644 --- a/src/PERI/pair_peri_pmb.cpp +++ b/src/PERI/pair_peri_pmb.cpp @@ -245,7 +245,7 @@ void PairPeriPMB::compute(int eflag, int vflag) void PairPeriPMB::coeff(int narg, char **arg) { - if (narg != 6) error->all(FLERR,"Incorrect args for pair coefficients"); + if (narg != 6) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -269,7 +269,7 @@ void PairPeriPMB::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/PERI/pair_peri_ves.cpp b/src/PERI/pair_peri_ves.cpp index 7e43678919..24f6deb2d8 100644 --- a/src/PERI/pair_peri_ves.cpp +++ b/src/PERI/pair_peri_ves.cpp @@ -346,7 +346,7 @@ void PairPeriVES::compute(int eflag, int vflag) void PairPeriVES::coeff(int narg, char **arg) { - if (narg != 9) error->all(FLERR,"Incorrect args for pair coefficients"); + if (narg != 9) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -376,7 +376,7 @@ void PairPeriVES::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/PYTHON/pair_python.cpp b/src/PYTHON/pair_python.cpp index 695954604c..e954245e71 100644 --- a/src/PYTHON/pair_python.cpp +++ b/src/PYTHON/pair_python.cpp @@ -244,14 +244,14 @@ void PairPython::coeff(int narg, char **arg) const int ntypes = atom->ntypes; if (narg != 3+ntypes) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); // make sure I,J args are * * if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); // check if python potential class type exists diff --git a/src/REAXFF/pair_reaxff.cpp b/src/REAXFF/pair_reaxff.cpp index ca60e5248f..b36d9e79aa 100644 --- a/src/REAXFF/pair_reaxff.cpp +++ b/src/REAXFF/pair_reaxff.cpp @@ -278,7 +278,7 @@ void PairReaxFF::coeff(int nargs, char **args) if (!allocated) allocate(); if (nargs != 3 + atom->ntypes) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); // read ffield file @@ -328,7 +328,7 @@ void PairReaxFF::coeff(int nargs, char **args) count++; } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } diff --git a/src/RHEO/pair_rheo_solid.cpp b/src/RHEO/pair_rheo_solid.cpp index 6f6f7949ae..84446f5554 100644 --- a/src/RHEO/pair_rheo_solid.cpp +++ b/src/RHEO/pair_rheo_solid.cpp @@ -185,7 +185,7 @@ void PairRHEOSolid::settings(int narg, char ** /*arg*/) void PairRHEOSolid::coeff(int narg, char **arg) { - if (narg != 5) error->all(FLERR, "Incorrect args for pair coefficients"); + if (narg != 5) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo, ihi, jlo, jhi; @@ -196,7 +196,7 @@ void PairRHEOSolid::coeff(int narg, char **arg) double cut_one = utils::numeric(FLERR, arg[3], false, lmp); double gamma_one = utils::numeric(FLERR, arg[4], false, lmp); - if (cut_one <= 0.0) error->all(FLERR, "Incorrect args for pair coefficients"); + if (cut_one <= 0.0) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); int count = 0; for (int i = ilo; i <= ihi; i++) { @@ -210,7 +210,7 @@ void PairRHEOSolid::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/SMTBQ/pair_smatb.cpp b/src/SMTBQ/pair_smatb.cpp index ab6aee557e..0b97a62c32 100644 --- a/src/SMTBQ/pair_smatb.cpp +++ b/src/SMTBQ/pair_smatb.cpp @@ -329,7 +329,7 @@ void PairSMATB::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ------------------------------------------------------------------------ */ diff --git a/src/SMTBQ/pair_smatb_single.cpp b/src/SMTBQ/pair_smatb_single.cpp index 4506a1093c..fb72971c90 100644 --- a/src/SMTBQ/pair_smatb_single.cpp +++ b/src/SMTBQ/pair_smatb_single.cpp @@ -278,7 +278,7 @@ void PairSMATBSingle::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ------------------------------------------------------------------------ */ diff --git a/src/SPH/pair_sph_heatconduction.cpp b/src/SPH/pair_sph_heatconduction.cpp index 145d9cadee..0bff61d190 100644 --- a/src/SPH/pair_sph_heatconduction.cpp +++ b/src/SPH/pair_sph_heatconduction.cpp @@ -172,7 +172,7 @@ void PairSPHHeatConduction::settings(int narg, char **/*arg*/) void PairSPHHeatConduction::coeff(int narg, char **arg) { if (narg != 4) - error->all(FLERR,"Incorrect number of args for pair_style sph/heatconduction coefficients"); + error->all(FLERR,"Incorrect number of args for pair_style sph/heatconduction coefficients" + utils::errorurl(21)); if (!allocated) allocate(); @@ -194,7 +194,7 @@ void PairSPHHeatConduction::coeff(int narg, char **arg) } if (count == 0) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/SPH/pair_sph_lj.cpp b/src/SPH/pair_sph_lj.cpp index 63b84c630d..6f05c45638 100644 --- a/src/SPH/pair_sph_lj.cpp +++ b/src/SPH/pair_sph_lj.cpp @@ -224,7 +224,7 @@ void PairSPHLJ::coeff(int narg, char **arg) { if (narg != 4) error->all(FLERR, - "Incorrect args for pair_style sph/lj coefficients"); + "Incorrect args for pair_style sph/lj coefficients" + utils::errorurl(21)); if (!allocated) allocate(); @@ -246,7 +246,7 @@ void PairSPHLJ::coeff(int narg, char **arg) } if (count == 0) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/SPH/pair_sph_rhosum.cpp b/src/SPH/pair_sph_rhosum.cpp index 4fd96319ee..97062b16c1 100644 --- a/src/SPH/pair_sph_rhosum.cpp +++ b/src/SPH/pair_sph_rhosum.cpp @@ -218,7 +218,7 @@ void PairSPHRhoSum::settings(int narg, char **arg) void PairSPHRhoSum::coeff(int narg, char **arg) { if (narg != 3) - error->all(FLERR,"Incorrect number of args for sph/rhosum coefficients"); + error->all(FLERR,"Incorrect number of args for sph/rhosum coefficients" + utils::errorurl(21)); if (!allocated) allocate(); @@ -238,7 +238,7 @@ void PairSPHRhoSum::coeff(int narg, char **arg) } if (count == 0) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/SPH/pair_sph_taitwater.cpp b/src/SPH/pair_sph_taitwater.cpp index 41eef91d6e..442ac833cb 100644 --- a/src/SPH/pair_sph_taitwater.cpp +++ b/src/SPH/pair_sph_taitwater.cpp @@ -226,7 +226,7 @@ void PairSPHTaitwater::coeff(int narg, char **arg) { if (narg != 6) error->all(FLERR, - "Incorrect args for pair_style sph/taitwater coefficients"); + "Incorrect args for pair_style sph/taitwater coefficients" + utils::errorurl(21)); if (!allocated) allocate(); @@ -254,7 +254,7 @@ void PairSPHTaitwater::coeff(int narg, char **arg) } if (count == 0) - error->all(FLERR, "Incorrect args for pair coefficients"); + error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/SPH/pair_sph_taitwater_morris.cpp b/src/SPH/pair_sph_taitwater_morris.cpp index 2209cc4ecf..48493a1e09 100644 --- a/src/SPH/pair_sph_taitwater_morris.cpp +++ b/src/SPH/pair_sph_taitwater_morris.cpp @@ -226,7 +226,7 @@ void PairSPHTaitwaterMorris::coeff(int narg, char **arg) { if (narg != 6) error->all(FLERR, - "Incorrect args for pair_style sph/taitwater/morris coefficients"); + "Incorrect args for pair_style sph/taitwater/morris coefficients" + utils::errorurl(21)); if (!allocated) allocate(); @@ -255,7 +255,7 @@ void PairSPHTaitwaterMorris::coeff(int narg, char **arg) } if (count == 0) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/SPIN/pair_spin_dipole_cut.cpp b/src/SPIN/pair_spin_dipole_cut.cpp index 8470bbcfcc..8e5c125895 100644 --- a/src/SPIN/pair_spin_dipole_cut.cpp +++ b/src/SPIN/pair_spin_dipole_cut.cpp @@ -118,7 +118,7 @@ void PairSpinDipoleCut::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/SPIN/pair_spin_dipole_long.cpp b/src/SPIN/pair_spin_dipole_long.cpp index f3ef997d01..8f03c37b7c 100644 --- a/src/SPIN/pair_spin_dipole_long.cpp +++ b/src/SPIN/pair_spin_dipole_long.cpp @@ -115,7 +115,7 @@ void PairSpinDipoleLong::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/SPIN/pair_spin_exchange.cpp b/src/SPIN/pair_spin_exchange.cpp index b113b17d10..b0c9edef27 100644 --- a/src/SPIN/pair_spin_exchange.cpp +++ b/src/SPIN/pair_spin_exchange.cpp @@ -95,9 +95,9 @@ void PairSpinExchange::coeff(int narg, char **arg) // check if args correct if (strcmp(arg[2],"exchange") != 0) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if ((narg != 7) && (narg != 9)) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); int ilo,ihi,jlo,jhi; utils::bounds(FLERR,arg[0],1,atom->ntypes,ilo,ihi,error); @@ -117,7 +117,7 @@ void PairSpinExchange::coeff(int narg, char **arg) if (strcmp(arg[iarg],"offset") == 0) { e_offset = utils::logical(FLERR, arg[iarg+1], false, lmp); iarg += 2; - } else error->all(FLERR,"Incorrect args for pair coefficients"); + } else error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } int count = 0; diff --git a/src/SPIN/pair_spin_exchange_biquadratic.cpp b/src/SPIN/pair_spin_exchange_biquadratic.cpp index 51df3294d7..7c50659b45 100644 --- a/src/SPIN/pair_spin_exchange_biquadratic.cpp +++ b/src/SPIN/pair_spin_exchange_biquadratic.cpp @@ -99,9 +99,9 @@ void PairSpinExchangeBiquadratic::coeff(int narg, char **arg) // check if args correct if (strcmp(arg[2],"biquadratic") != 0) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if ((narg != 10) && (narg != 12)) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); int ilo,ihi,jlo,jhi; utils::bounds(FLERR,arg[0],1,atom->ntypes,ilo,ihi,error); @@ -124,7 +124,7 @@ void PairSpinExchangeBiquadratic::coeff(int narg, char **arg) if (strcmp(arg[iarg],"offset") == 0) { e_offset = utils::logical(FLERR,arg[iarg+1],false,lmp); iarg += 2; - } else error->all(FLERR,"Incorrect args for pair coefficients"); + } else error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } int count = 0; diff --git a/src/YAFF/pair_lj_switch3_coulgauss_long.cpp b/src/YAFF/pair_lj_switch3_coulgauss_long.cpp index 5fe9b886bf..e87c760e30 100644 --- a/src/YAFF/pair_lj_switch3_coulgauss_long.cpp +++ b/src/YAFF/pair_lj_switch3_coulgauss_long.cpp @@ -285,7 +285,7 @@ void PairLJSwitch3CoulGaussLong::settings(int narg, char **arg) void PairLJSwitch3CoulGaussLong::coeff(int narg, char **arg) { if (narg < 5 || narg > 6) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -311,7 +311,7 @@ void PairLJSwitch3CoulGaussLong::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/YAFF/pair_mm3_switch3_coulgauss_long.cpp b/src/YAFF/pair_mm3_switch3_coulgauss_long.cpp index c4f31f2059..98589ae85d 100644 --- a/src/YAFF/pair_mm3_switch3_coulgauss_long.cpp +++ b/src/YAFF/pair_mm3_switch3_coulgauss_long.cpp @@ -288,7 +288,7 @@ void PairMM3Switch3CoulGaussLong::settings(int narg, char **arg) void PairMM3Switch3CoulGaussLong::coeff(int narg, char **arg) { if (narg < 5 || narg > 6) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -314,7 +314,7 @@ void PairMM3Switch3CoulGaussLong::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/pair.cpp b/src/pair.cpp index 8f10d81d99..652f231908 100644 --- a/src/pair.cpp +++ b/src/pair.cpp @@ -865,7 +865,7 @@ void Pair::map_element2type(int narg, char **arg, bool update_setflag) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } } diff --git a/src/pair_born.cpp b/src/pair_born.cpp index c2a47be47f..fe041b2ada 100644 --- a/src/pair_born.cpp +++ b/src/pair_born.cpp @@ -197,7 +197,7 @@ void PairBorn::settings(int narg, char **arg) void PairBorn::coeff(int narg, char **arg) { - if (narg < 7 || narg > 8) error->all(FLERR,"Incorrect args for pair coefficients"); + if (narg < 7 || narg > 8) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -207,7 +207,7 @@ void PairBorn::coeff(int narg, char **arg) double a_one = utils::numeric(FLERR,arg[2],false,lmp); double rho_one = utils::numeric(FLERR,arg[3],false,lmp); double sigma_one = utils::numeric(FLERR,arg[4],false,lmp); - if (rho_one <= 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (rho_one <= 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); double c_one = utils::numeric(FLERR,arg[5],false,lmp); double d_one = utils::numeric(FLERR,arg[6],false,lmp); @@ -228,7 +228,7 @@ void PairBorn::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/pair_buck.cpp b/src/pair_buck.cpp index ff6fb5fbde..660a4b32ec 100644 --- a/src/pair_buck.cpp +++ b/src/pair_buck.cpp @@ -189,7 +189,7 @@ void PairBuck::settings(int narg, char **arg) void PairBuck::coeff(int narg, char **arg) { if (narg < 5 || narg > 6) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -198,7 +198,7 @@ void PairBuck::coeff(int narg, char **arg) double a_one = utils::numeric(FLERR,arg[2],false,lmp); double rho_one = utils::numeric(FLERR,arg[3],false,lmp); - if (rho_one <= 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (rho_one <= 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); double c_one = utils::numeric(FLERR,arg[4],false,lmp); double cut_one = cut_global; @@ -216,7 +216,7 @@ void PairBuck::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/pair_buck_coul_cut.cpp b/src/pair_buck_coul_cut.cpp index 933493eab6..cf342b4302 100644 --- a/src/pair_buck_coul_cut.cpp +++ b/src/pair_buck_coul_cut.cpp @@ -224,7 +224,7 @@ void PairBuckCoulCut::settings(int narg, char **arg) void PairBuckCoulCut::coeff(int narg, char **arg) { - if (narg < 5 || narg > 7) error->all(FLERR, "Incorrect args for pair coefficients"); + if (narg < 5 || narg > 7) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo, ihi, jlo, jhi; @@ -233,7 +233,7 @@ void PairBuckCoulCut::coeff(int narg, char **arg) double a_one = utils::numeric(FLERR, arg[2], false, lmp); double rho_one = utils::numeric(FLERR, arg[3], false, lmp); - if (rho_one <= 0) error->all(FLERR, "Incorrect args for pair coefficients"); + if (rho_one <= 0) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); double c_one = utils::numeric(FLERR, arg[4], false, lmp); double cut_lj_one = cut_lj_global; @@ -254,7 +254,7 @@ void PairBuckCoulCut::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/pair_coul_cut.cpp b/src/pair_coul_cut.cpp index 806d7a1066..91bb6014e7 100644 --- a/src/pair_coul_cut.cpp +++ b/src/pair_coul_cut.cpp @@ -171,7 +171,7 @@ void PairCoulCut::settings(int narg, char **arg) void PairCoulCut::coeff(int narg, char **arg) { - if (narg < 2 || narg > 3) error->all(FLERR, "Incorrect args for pair coefficients"); + if (narg < 2 || narg > 3) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo, ihi, jlo, jhi; @@ -191,7 +191,7 @@ void PairCoulCut::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/pair_coul_dsf.cpp b/src/pair_coul_dsf.cpp index 44dc9a7524..0d51d8e7ab 100644 --- a/src/pair_coul_dsf.cpp +++ b/src/pair_coul_dsf.cpp @@ -171,7 +171,7 @@ void PairCoulDSF::settings(int narg, char **arg) void PairCoulDSF::coeff(int narg, char **arg) { - if (narg != 2) error->all(FLERR, "Incorrect args for pair coefficients"); + if (narg != 2) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo, ihi, jlo, jhi; @@ -186,7 +186,7 @@ void PairCoulDSF::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/pair_coul_wolf.cpp b/src/pair_coul_wolf.cpp index 2bd3094a7c..fd4c0a1a61 100644 --- a/src/pair_coul_wolf.cpp +++ b/src/pair_coul_wolf.cpp @@ -179,7 +179,7 @@ void PairCoulWolf::settings(int narg, char **arg) void PairCoulWolf::coeff(int narg, char **arg) { - if (narg != 2) error->all(FLERR, "Incorrect args for pair coefficients"); + if (narg != 2) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo, ihi, jlo, jhi; @@ -194,7 +194,7 @@ void PairCoulWolf::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/pair_hybrid.cpp b/src/pair_hybrid.cpp index 09f233a4f6..4fb757cbab 100644 --- a/src/pair_hybrid.cpp +++ b/src/pair_hybrid.cpp @@ -578,7 +578,7 @@ void PairHybrid::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/pair_hybrid_overlay.cpp b/src/pair_hybrid_overlay.cpp index 4211d0e5cb..55b6477496 100644 --- a/src/pair_hybrid_overlay.cpp +++ b/src/pair_hybrid_overlay.cpp @@ -31,7 +31,7 @@ PairHybridOverlay::PairHybridOverlay(LAMMPS *lmp) : PairHybrid(lmp) {} void PairHybridOverlay::coeff(int narg, char **arg) { - if (narg < 3) error->all(FLERR,"Incorrect args for pair coefficients"); + if (narg < 3) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -50,7 +50,7 @@ void PairHybridOverlay::coeff(int narg, char **arg) if (strcmp(arg[2],keywords[m]) == 0) { if (multiple[m]) { multflag = 1; - if (narg < 4) error->all(FLERR,"Incorrect args for pair coefficients"); + if (narg < 4) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (multiple[m] == utils::inumeric(FLERR,arg[3],false,lmp)) break; else continue; } else break; @@ -76,7 +76,7 @@ void PairHybridOverlay::coeff(int narg, char **arg) if (!none && styles[m]->one_coeff) if ((strcmp(arg[0],"*") != 0) || (strcmp(arg[1],"*") != 0)) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); // invoke sub-style coeff() starting with 1st remaining arg @@ -106,7 +106,7 @@ void PairHybridOverlay::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } diff --git a/src/pair_hybrid_scaled.cpp b/src/pair_hybrid_scaled.cpp index 3ce6327370..22d4556769 100644 --- a/src/pair_hybrid_scaled.cpp +++ b/src/pair_hybrid_scaled.cpp @@ -584,7 +584,7 @@ void PairHybridScaled::born_matrix(int i, int j, int itype, int jtype, double rs void PairHybridScaled::coeff(int narg, char **arg) { - if (narg < 3) error->all(FLERR, "Incorrect args for pair coefficients"); + if (narg < 3) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo, ihi, jlo, jhi; @@ -603,7 +603,7 @@ void PairHybridScaled::coeff(int narg, char **arg) if (strcmp(arg[2], keywords[m]) == 0) { if (multiple[m]) { multflag = 1; - if (narg < 4) error->all(FLERR, "Incorrect args for pair coefficients"); + if (narg < 4) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); int index = utils::inumeric(FLERR, arg[3], false, lmp); if (index == multiple[m]) break; @@ -633,7 +633,7 @@ void PairHybridScaled::coeff(int narg, char **arg) if (!none && styles[m]->one_coeff) if ((strcmp(arg[0], "*") != 0) || (strcmp(arg[1], "*") != 0)) - error->all(FLERR, "Incorrect args for pair coefficients"); + error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); // invoke sub-style coeff() starting with 1st remaining arg @@ -663,7 +663,7 @@ void PairHybridScaled::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/pair_lj_cut.cpp b/src/pair_lj_cut.cpp index fae308c57f..ef339ba340 100644 --- a/src/pair_lj_cut.cpp +++ b/src/pair_lj_cut.cpp @@ -441,7 +441,7 @@ void PairLJCut::settings(int narg, char **arg) void PairLJCut::coeff(int narg, char **arg) { - if (narg < 4 || narg > 5) error->all(FLERR, "Incorrect args for pair coefficients"); + if (narg < 4 || narg > 5) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo, ihi, jlo, jhi; @@ -465,7 +465,7 @@ void PairLJCut::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/pair_lj_cut_coul_cut.cpp b/src/pair_lj_cut_coul_cut.cpp index 8e4e98a1ba..e188fc2020 100644 --- a/src/pair_lj_cut_coul_cut.cpp +++ b/src/pair_lj_cut_coul_cut.cpp @@ -217,7 +217,7 @@ void PairLJCutCoulCut::settings(int narg, char **arg) void PairLJCutCoulCut::coeff(int narg, char **arg) { - if (narg < 4 || narg > 6) error->all(FLERR, "Incorrect args for pair coefficients"); + if (narg < 4 || narg > 6) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo, ihi, jlo, jhi; @@ -244,7 +244,7 @@ void PairLJCutCoulCut::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/pair_lj_expand.cpp b/src/pair_lj_expand.cpp index 05b763429b..9c22f4ab75 100644 --- a/src/pair_lj_expand.cpp +++ b/src/pair_lj_expand.cpp @@ -186,7 +186,7 @@ void PairLJExpand::settings(int narg, char **arg) void PairLJExpand::coeff(int narg, char **arg) { - if (narg < 5 || narg > 6) error->all(FLERR, "Incorrect args for pair coefficients"); + if (narg < 5 || narg > 6) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo, ihi, jlo, jhi; @@ -212,7 +212,7 @@ void PairLJExpand::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/pair_morse.cpp b/src/pair_morse.cpp index efacd80ca3..83ca375818 100644 --- a/src/pair_morse.cpp +++ b/src/pair_morse.cpp @@ -174,7 +174,7 @@ void PairMorse::settings(int narg, char **arg) void PairMorse::coeff(int narg, char **arg) { - if (narg < 5 || narg > 6) error->all(FLERR, "Incorrect args for pair coefficients"); + if (narg < 5 || narg > 6) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo, ihi, jlo, jhi; @@ -200,7 +200,7 @@ void PairMorse::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/pair_soft.cpp b/src/pair_soft.cpp index cba6c742ab..726875052a 100644 --- a/src/pair_soft.cpp +++ b/src/pair_soft.cpp @@ -171,7 +171,7 @@ void PairSoft::settings(int narg, char **arg) void PairSoft::coeff(int narg, char **arg) { if (narg < 3 || narg > 4) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -193,7 +193,7 @@ void PairSoft::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/pair_yukawa.cpp b/src/pair_yukawa.cpp index 55a686e5f0..e4147ba90f 100644 --- a/src/pair_yukawa.cpp +++ b/src/pair_yukawa.cpp @@ -172,7 +172,7 @@ void PairYukawa::settings(int narg, char **arg) void PairYukawa::coeff(int narg, char **arg) { - if (narg < 3 || narg > 4) error->all(FLERR, "Incorrect args for pair coefficients"); + if (narg < 3 || narg > 4) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo, ihi, jlo, jhi; @@ -194,7 +194,7 @@ void PairYukawa::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/pair_zbl.cpp b/src/pair_zbl.cpp index bbbeea18d7..c0748b0f63 100644 --- a/src/pair_zbl.cpp +++ b/src/pair_zbl.cpp @@ -199,7 +199,7 @@ void PairZBL::coeff(int narg, char **arg) { double z_one, z_two; - if (narg != 4) error->all(FLERR, "Incorrect args for pair coefficients"); + if (narg != 4) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo, ihi; @@ -218,7 +218,7 @@ void PairZBL::coeff(int narg, char **arg) for (int i = ilo; i <= ihi; i++) { for (int j = MAX(jlo, i); j <= jhi; j++) { if (i == j) { - if (z_one != z_two) error->all(FLERR, "Incorrect args for pair coefficients"); + if (z_one != z_two) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); z[i] = z_one; } setflag[i][j] = 1; @@ -227,7 +227,7 @@ void PairZBL::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/pair_zero.cpp b/src/pair_zero.cpp index c62479d1c4..92733f12e7 100644 --- a/src/pair_zero.cpp +++ b/src/pair_zero.cpp @@ -123,7 +123,7 @@ void PairZero::settings(int narg, char **arg) void PairZero::coeff(int narg, char **arg) { if ((narg < 2) || (coeffflag && narg > 3)) - error->all(FLERR, "Incorrect args for pair coefficients"); + error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); if (!allocated) allocate(); @@ -143,7 +143,7 @@ void PairZero::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- From 02f98947f9ca33391704d8a4fbc4b876556ece1c Mon Sep 17 00:00:00 2001 From: megmcca Date: Mon, 3 Feb 2025 13:12:11 -0700 Subject: [PATCH 006/113] update unique coeff messages --- src/CG-DNA/pair_oxdna2_coaxstk.cpp | 4 ++-- src/CG-DNA/pair_oxdna2_dh.cpp | 4 ++-- src/CG-DNA/pair_oxdna_coaxstk.cpp | 4 ++-- src/CG-DNA/pair_oxdna_excv.cpp | 8 ++++---- src/CG-DNA/pair_oxdna_hbond.cpp | 4 ++-- src/CG-DNA/pair_oxdna_stk.cpp | 4 ++-- src/CG-DNA/pair_oxdna_xstk.cpp | 4 ++-- src/CG-DNA/pair_oxrna2_stk.cpp | 4 ++-- src/CG-DNA/pair_oxrna2_xstk.cpp | 4 ++-- src/EXTRA-PAIR/pair_cosine_squared.cpp | 12 ++++++------ 10 files changed, 26 insertions(+), 26 deletions(-) diff --git a/src/CG-DNA/pair_oxdna2_coaxstk.cpp b/src/CG-DNA/pair_oxdna2_coaxstk.cpp index a0f7c9e7e5..642ef2081a 100644 --- a/src/CG-DNA/pair_oxdna2_coaxstk.cpp +++ b/src/CG-DNA/pair_oxdna2_coaxstk.cpp @@ -560,7 +560,7 @@ void PairOxdna2Coaxstk::coeff(int narg, char **arg) { int count; - if (narg != 3 && narg != 21) error->all(FLERR,"Incorrect args for pair coefficients in oxdna2/coaxstk"); + if (narg != 3 && narg != 21) error->all(FLERR,"Incorrect args for pair coefficients in oxdna2/coaxstk" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -757,7 +757,7 @@ void PairOxdna2Coaxstk::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients in oxdna2/coaxstk"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients in oxdna2/coaxstk" + utils::errorurl(21)); } diff --git a/src/CG-DNA/pair_oxdna2_dh.cpp b/src/CG-DNA/pair_oxdna2_dh.cpp index 5c0c32b2d9..17cf613679 100644 --- a/src/CG-DNA/pair_oxdna2_dh.cpp +++ b/src/CG-DNA/pair_oxdna2_dh.cpp @@ -293,7 +293,7 @@ void PairOxdna2Dh::coeff(int narg, char **arg) { int count; - if (narg != 5) error->all(FLERR,"Incorrect args for pair coefficients in oxdna2/dh"); + if (narg != 5) error->all(FLERR,"Incorrect args for pair coefficients in oxdna2/dh" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -403,7 +403,7 @@ void PairOxdna2Dh::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients in oxdna2/dh"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients in oxdna2/dh" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/CG-DNA/pair_oxdna_coaxstk.cpp b/src/CG-DNA/pair_oxdna_coaxstk.cpp index d00e9fedf8..e62292c60d 100644 --- a/src/CG-DNA/pair_oxdna_coaxstk.cpp +++ b/src/CG-DNA/pair_oxdna_coaxstk.cpp @@ -694,7 +694,7 @@ void PairOxdnaCoaxstk::coeff(int narg, char **arg) { int count; - if (narg != 3 && narg != 23) error->all(FLERR,"Incorrect args for pair coefficients in oxdna/coaxstk"); + if (narg != 3 && narg != 23) error->all(FLERR,"Incorrect args for pair coefficients in oxdna/coaxstk" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -911,7 +911,7 @@ void PairOxdnaCoaxstk::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients in oxdna/coaxstk"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients in oxdna/coaxstk" + utils::errorurl(21)); } diff --git a/src/CG-DNA/pair_oxdna_excv.cpp b/src/CG-DNA/pair_oxdna_excv.cpp index a764679839..ee3500c6ae 100644 --- a/src/CG-DNA/pair_oxdna_excv.cpp +++ b/src/CG-DNA/pair_oxdna_excv.cpp @@ -503,7 +503,7 @@ void PairOxdnaExcv::coeff(int narg, char **arg) { int count; - if (narg != 3 && narg != 11) error->all(FLERR,"Incorrect args for pair coefficients in oxdna/excv"); + if (narg != 3 && narg != 11) error->all(FLERR,"Incorrect args for pair coefficients in oxdna/excv" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -612,7 +612,7 @@ void PairOxdnaExcv::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients in oxdna/excv"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients in oxdna/excv" + utils::errorurl(21)); count = 0; @@ -638,7 +638,7 @@ void PairOxdnaExcv::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients in oxdna/excv"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients in oxdna/excv" + utils::errorurl(21)); count = 0; @@ -664,7 +664,7 @@ void PairOxdnaExcv::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients in oxdna/excv"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients in oxdna/excv" + utils::errorurl(21)); } diff --git a/src/CG-DNA/pair_oxdna_hbond.cpp b/src/CG-DNA/pair_oxdna_hbond.cpp index ba82aeef83..f07581b356 100644 --- a/src/CG-DNA/pair_oxdna_hbond.cpp +++ b/src/CG-DNA/pair_oxdna_hbond.cpp @@ -636,7 +636,7 @@ void PairOxdnaHbond::coeff(int narg, char **arg) { int count; - if (narg != 4 && narg != 27) error->all(FLERR,"Incorrect args for pair coefficients in oxdna/hbond"); + if (narg != 4 && narg != 27) error->all(FLERR,"Incorrect args for pair coefficients in oxdna/hbond" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi,imod4,jmod4; @@ -901,7 +901,7 @@ void PairOxdnaHbond::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients in oxdna/hbond"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients in oxdna/hbond" + utils::errorurl(21)); } diff --git a/src/CG-DNA/pair_oxdna_stk.cpp b/src/CG-DNA/pair_oxdna_stk.cpp index 301782d212..83a098fb3f 100644 --- a/src/CG-DNA/pair_oxdna_stk.cpp +++ b/src/CG-DNA/pair_oxdna_stk.cpp @@ -778,7 +778,7 @@ void PairOxdnaStk::coeff(int narg, char **arg) { int count; - if (narg != 7 && narg != 24) error->all(FLERR,"Incorrect args for pair coefficients in oxdna/stk"); + if (narg != 7 && narg != 24) error->all(FLERR,"Incorrect args for pair coefficients in oxdna/stk" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi,imod4,jmod4; @@ -998,7 +998,7 @@ void PairOxdnaStk::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients in oxdna/stk"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients in oxdna/stk" + utils::errorurl(21)); } diff --git a/src/CG-DNA/pair_oxdna_xstk.cpp b/src/CG-DNA/pair_oxdna_xstk.cpp index 646c0f7216..4ea535f9a0 100644 --- a/src/CG-DNA/pair_oxdna_xstk.cpp +++ b/src/CG-DNA/pair_oxdna_xstk.cpp @@ -633,7 +633,7 @@ void PairOxdnaXstk::coeff(int narg, char **arg) { int count; - if (narg != 3 && narg != 25) error->all(FLERR,"Incorrect args for pair coefficients in oxdna/xstk"); + if (narg != 3 && narg != 25) error->all(FLERR,"Incorrect args for pair coefficients in oxdna/xstk" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -865,7 +865,7 @@ void PairOxdnaXstk::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients in oxdna/xstk"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients in oxdna/xstk" + utils::errorurl(21)); } diff --git a/src/CG-DNA/pair_oxrna2_stk.cpp b/src/CG-DNA/pair_oxrna2_stk.cpp index 423235b46a..35e727c7b1 100644 --- a/src/CG-DNA/pair_oxrna2_stk.cpp +++ b/src/CG-DNA/pair_oxrna2_stk.cpp @@ -847,7 +847,7 @@ void PairOxrna2Stk::coeff(int narg, char **arg) { int count; - if (narg != 7 && narg != 27) error->all(FLERR,"Incorrect args for pair coefficients in oxrna2/stk"); + if (narg != 7 && narg != 27) error->all(FLERR,"Incorrect args for pair coefficients in oxrna2/stk" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -1089,7 +1089,7 @@ void PairOxrna2Stk::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients in oxrna2/stk"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients in oxrna2/stk" + utils::errorurl(21)); } diff --git a/src/CG-DNA/pair_oxrna2_xstk.cpp b/src/CG-DNA/pair_oxrna2_xstk.cpp index ee7ca141f8..c8a09b5252 100644 --- a/src/CG-DNA/pair_oxrna2_xstk.cpp +++ b/src/CG-DNA/pair_oxrna2_xstk.cpp @@ -583,7 +583,7 @@ void PairOxrna2Xstk::coeff(int narg, char **arg) { int count; - if (narg != 3 && narg != 22) error->all(FLERR,"Incorrect args for pair coefficients in oxrna2/xstk"); + if (narg != 3 && narg != 22) error->all(FLERR,"Incorrect args for pair coefficients in oxrna2/xstk" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -790,7 +790,7 @@ void PairOxrna2Xstk::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients in oxrna2/xstk"); + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients in oxrna2/xstk" + utils::errorurl(21)); } diff --git a/src/EXTRA-PAIR/pair_cosine_squared.cpp b/src/EXTRA-PAIR/pair_cosine_squared.cpp index fafe0400d5..888938fa8d 100644 --- a/src/EXTRA-PAIR/pair_cosine_squared.cpp +++ b/src/EXTRA-PAIR/pair_cosine_squared.cpp @@ -120,7 +120,7 @@ void PairCosineSquared::settings(int narg, char **arg) void PairCosineSquared::coeff(int narg, char **arg) { if (narg < 4 || narg > 6) - error->all(FLERR, "Incorrect args for pair coefficients (too few or too many)"); + error->all(FLERR, "Incorrect args for pair coefficients (too few or too many)" + utils::errorurl(21)); if (!allocated) allocate(); @@ -139,7 +139,7 @@ void PairCosineSquared::coeff(int narg, char **arg) if (strcmp(arg[5], "wca") == 0) { wca_one = 1; } else { - error->all(FLERR, "Incorrect args for pair coefficients (unknown option)"); + error->all(FLERR, "Incorrect args for pair coefficients (unknown option)" + utils::errorurl(21)); } } else if (narg == 5) { if (strcmp(arg[4], "wca") == 0) { @@ -150,12 +150,12 @@ void PairCosineSquared::coeff(int narg, char **arg) } if (cut_one < sigma_one) { - error->all(FLERR, "Incorrect args for pair coefficients (cutoff < sigma)"); + error->all(FLERR, "Incorrect args for pair coefficients (cutoff < sigma)" + utils::errorurl(21)); } else if (cut_one == sigma_one) { if (wca_one == 0) { - error->all(FLERR, "Incorrect args for pair coefficients (cutoff = sigma w/o wca)"); + error->all(FLERR, "Incorrect args for pair coefficients (cutoff = sigma w/o wca)" + utils::errorurl(21)); } else { - error->warning(FLERR, "Cosine/squared set to WCA only (cutoff = sigma)"); + error->warning(FLERR, "Cosine/squared set to WCA only (cutoff = sigma)" + utils::errorurl(21)); } } @@ -172,7 +172,7 @@ void PairCosineSquared::coeff(int narg, char **arg) } if (count == 0) - error->all(FLERR, "Incorrect args for pair coefficients (none set)"); + error->all(FLERR, "Incorrect args for pair coefficients (none set)" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- From 3b8139d428a2abb1b5c75366c0899597d0abb1bf Mon Sep 17 00:00:00 2001 From: megmcca Date: Mon, 3 Feb 2025 15:08:12 -0700 Subject: [PATCH 007/113] update formatting (reflow) --- doc/src/Errors_details.rst | 19 +++++++++++++++++-- 1 file changed, 17 insertions(+), 2 deletions(-) diff --git a/doc/src/Errors_details.rst b/doc/src/Errors_details.rst index 2211333cd6..e608ca4a84 100644 --- a/doc/src/Errors_details.rst +++ b/doc/src/Errors_details.rst @@ -322,8 +322,23 @@ excessively grown the simulation box. Incorrect args for pair coefficients ------------------------------------ -The parameters in the :doc:`pair_coeff `, command for a specified :doc:`pair_style ` -have a missing or erroneous argument. Outside of normal typos, this error can have several sources. In all cases, the first step is to compare one's code to the expected format relevant :doc:`pair_style ` page. This can uncover cases where a pair style was changed, but the pair coefficients were not updated. This can happen especially with pair style variants such as :doc:`pair_style eam ` vs. :doc:`pair_style eam/alloy ` that are very similar but accept different numbers of coefficients. Note also that using multiple pair styles with commands such as :doc:`pair_style hybrid `. Using hybrid pair styles requires adding an extra "label" argument in the :doc:`pair_coeff ` commands that designates which pair style the command line refers to. Other errors might require a close look at files that are read in by the input script, such as data files or restart files. +The parameters in the :doc:`pair_coeff `, command for a specified +:doc:`pair_style ` have a missing or erroneous argument. Outside of +normal typos, this error can have several sources. In all cases, the first step +is to compare the command arguments to the expected format found in the +corresponding :doc:`pair_style ` page. This can reveal cases where, +for example, a pair style was changed, but the pair coefficients were not +updated. This can happen especially with pair style variants such as +:doc:`pair_style eam ` vs. :doc:`pair_style eam/alloy ` +that look very similar but accept different parameters (the latter 'eam/alloy' +variant takes element type names while 'eam' does not). + +Another common source of coefficient errors is when using multiple pair styles +with commands such as :doc:`pair_style hybrid `. Using hybrid pair +styles requires adding an extra "label" argument in the coefficient commands +that designates which pair style the command line refers to, and may require +different arguments per pair style. Other errors might require a close look at +files that are read in by the input script, such as data files or restart files. .. _err0024: From 75fd76aaa66005d6c78e82b7a10dcb5b3fb28e99 Mon Sep 17 00:00:00 2001 From: megmcca Date: Mon, 10 Feb 2025 09:26:08 -0700 Subject: [PATCH 008/113] update text for MOLECULE package --- doc/src/Errors_details.rst | 35 +++++++++++++++++++++-------------- 1 file changed, 21 insertions(+), 14 deletions(-) diff --git a/doc/src/Errors_details.rst b/doc/src/Errors_details.rst index e608ca4a84..b0d1393bf6 100644 --- a/doc/src/Errors_details.rst +++ b/doc/src/Errors_details.rst @@ -15,7 +15,7 @@ following are discussions of such cases. - :ref:`Too many neighbor bins ` - :ref:`Cannot use neighbor bins - box size \<\< cutoff ` - :ref:`Domain too large for neighbor bins ` -- :ref:`Incorrect args for pair coefficients ` +- :ref:`Incorrect args for pair coefficients (also bond/angle/dihedral/improper coefficients) ` - :ref:`Molecule topology/atom exceeds system topology/atom ` - :ref:`Molecule topology type exceeds system topology type ` - :ref:`Molecule attributes do not match system attributes ` @@ -288,7 +288,7 @@ Too many neighbor bins The simulation box has become too large relative to the size of a neighbor bin and LAMMPS is unable to store the needed number of bins. This typically implies the simulation box has expanded too far. -This can happen when some atoms move rapidly apart with shrinkwrap +This can happen when some atoms move rapidly apart with shrink-wrap boundaries or when a fix (like fix deform or a barostat) excessively grows the simulation box. @@ -319,15 +319,22 @@ excessively grown the simulation box. .. _err0021: -Incorrect args for pair coefficients ------------------------------------- +Incorrect args for pair coefficients (also bond/angle/dihedral/improper coefficients) +------------------------------------------------------------------------------------- -The parameters in the :doc:`pair_coeff `, command for a specified -:doc:`pair_style ` have a missing or erroneous argument. Outside of -normal typos, this error can have several sources. In all cases, the first step -is to compare the command arguments to the expected format found in the -corresponding :doc:`pair_style ` page. This can reveal cases where, -for example, a pair style was changed, but the pair coefficients were not +The parameters in the :doc:`pair_coeff ` command for a specified +:doc:`pair_style ` have a missing or erroneous argument. The same +applies when seeing this error for :doc:`bond_coeff `, +:doc:`angle_coeff `, :doc:`dihedral_coeff `, or +:doc:`improper_coeff ` and their respective style commands when +using the MOLECULE or EXTRA-MOLECULE packages. The cases below will describe +some ways to approach pair coefficient errors, but the same strategies will +apply to bonded systems as well. + +Outside of normal typos, this error can have several sources. In all cases, the +first step is to compare the command arguments to the expected format found in +the corresponding :doc:`pair_style ` page. This can reveal cases +where, for example, a pair style was changed, but the pair coefficients were not updated. This can happen especially with pair style variants such as :doc:`pair_style eam ` vs. :doc:`pair_style eam/alloy ` that look very similar but accept different parameters (the latter 'eam/alloy' @@ -345,10 +352,10 @@ files that are read in by the input script, such as data files or restart files. Molecule topology/atom exceeds system topology/atom --------------------------------------------------- -LAMMPS uses :doc:`domain decomposition ` to -distribute data (i.e. atoms) across the MPI processes in parallel runs. -This includes topology data, that is data about bonds, angles, -dihedrals, impropers and :doc:`"special" neighbors `. +LAMMPS uses :doc:`domain decomposition ` to distribute data +(i.e. atoms) across the MPI processes in parallel runs. This includes topology +data, that is data about bonds, angles, dihedrals, impropers and :doc:`"special" +neighbors `. This information is stored with either one or all atoms involved in such a topology entry (which of the two option applies depends on the :doc:`newton ` setting for bonds. When reading a data file, From 0a4eea6aa02257688a95f20b3d66f4918795f83b Mon Sep 17 00:00:00 2001 From: megmcca Date: Mon, 10 Feb 2025 09:36:22 -0700 Subject: [PATCH 009/113] add url to bond_coeff messages --- src/BPM/bond_bpm_rotational.cpp | 4 ++-- src/BPM/bond_bpm_spring.cpp | 4 ++-- src/CG-DNA/bond_oxdna_fene.cpp | 4 ++-- src/CLASS2/bond_class2.cpp | 4 ++-- src/EXTRA-MOLECULE/bond_fene_nm.cpp | 4 ++-- src/EXTRA-MOLECULE/bond_gaussian.cpp | 2 +- src/EXTRA-MOLECULE/bond_harmonic_restrain.cpp | 4 ++-- src/EXTRA-MOLECULE/bond_harmonic_shift.cpp | 4 ++-- src/EXTRA-MOLECULE/bond_harmonic_shift_cut.cpp | 4 ++-- src/EXTRA-MOLECULE/bond_nonlinear.cpp | 4 ++-- src/LEPTON/bond_lepton.cpp | 2 +- src/MISC/bond_special.cpp | 4 ++-- src/MOLECULE/bond_fene.cpp | 4 ++-- src/MOLECULE/bond_fene_expand.cpp | 4 ++-- src/MOLECULE/bond_gromos.cpp | 4 ++-- src/MOLECULE/bond_harmonic.cpp | 4 ++-- src/MOLECULE/bond_morse.cpp | 4 ++-- src/MOLECULE/bond_quartic.cpp | 4 ++-- src/RHEO/bond_rheo_shell.cpp | 4 ++-- src/YAFF/bond_mm3.cpp | 4 ++-- src/bond_zero.cpp | 4 ++-- 21 files changed, 40 insertions(+), 40 deletions(-) diff --git a/src/BPM/bond_bpm_rotational.cpp b/src/BPM/bond_bpm_rotational.cpp index abee373c5d..b8de3faca4 100644 --- a/src/BPM/bond_bpm_rotational.cpp +++ b/src/BPM/bond_bpm_rotational.cpp @@ -604,7 +604,7 @@ void BondBPMRotational::allocate() void BondBPMRotational::coeff(int narg, char **arg) { - if (narg != 13) error->all(FLERR, "Incorrect args for bond coefficients"); + if (narg != 13) error->all(FLERR, "Incorrect args for bond coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo, ihi; @@ -643,7 +643,7 @@ void BondBPMRotational::coeff(int narg, char **arg) if (Fcr[i] / Kr[i] > max_stretch) max_stretch = Fcr[i] / Kr[i]; } - if (count == 0) error->all(FLERR, "Incorrect args for bond coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for bond coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/BPM/bond_bpm_spring.cpp b/src/BPM/bond_bpm_spring.cpp index 0de93fea31..8da72cfb9e 100644 --- a/src/BPM/bond_bpm_spring.cpp +++ b/src/BPM/bond_bpm_spring.cpp @@ -399,7 +399,7 @@ void BondBPMSpring::allocate() void BondBPMSpring::coeff(int narg, char **arg) { if ((!volume_flag && narg != 4) || (volume_flag && narg != 5)) - error->all(FLERR, "Incorrect args for bond coefficients"); + error->all(FLERR, "Incorrect args for bond coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo, ihi; @@ -424,7 +424,7 @@ void BondBPMSpring::coeff(int narg, char **arg) if (1.0 + ecrit[i] > max_stretch) max_stretch = 1.0 + ecrit[i]; } - if (count == 0) error->all(FLERR, "Incorrect args for bond coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for bond coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/CG-DNA/bond_oxdna_fene.cpp b/src/CG-DNA/bond_oxdna_fene.cpp index f5edee9a05..381a131afd 100644 --- a/src/CG-DNA/bond_oxdna_fene.cpp +++ b/src/CG-DNA/bond_oxdna_fene.cpp @@ -318,7 +318,7 @@ void BondOxdnaFene::allocate() void BondOxdnaFene::coeff(int narg, char **arg) { - if (narg != 2 && narg != 4) error->all(FLERR, "Incorrect args for bond coefficients in oxdna/fene"); + if (narg != 2 && narg != 4) error->all(FLERR, "Incorrect args for bond coefficients in oxdna/fene" + utils::errorurl(21)); if (!allocated) allocate(); int ilo, ihi; @@ -374,7 +374,7 @@ void BondOxdnaFene::coeff(int narg, char **arg) count++; } - if (count == 0) error->all(FLERR, "Incorrect args for bond coefficients in oxdna/fene"); + if (count == 0) error->all(FLERR, "Incorrect args for bond coefficients in oxdna/fene" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/CLASS2/bond_class2.cpp b/src/CLASS2/bond_class2.cpp index da1e8199e0..8a7eec8215 100644 --- a/src/CLASS2/bond_class2.cpp +++ b/src/CLASS2/bond_class2.cpp @@ -134,7 +134,7 @@ void BondClass2::allocate() void BondClass2::coeff(int narg, char **arg) { - if (narg != 5) error->all(FLERR,"Incorrect args for bond coefficients"); + if (narg != 5) error->all(FLERR,"Incorrect args for bond coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi; @@ -155,7 +155,7 @@ void BondClass2::coeff(int narg, char **arg) count++; } - if (count == 0) error->all(FLERR,"Incorrect args for bond coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for bond coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/EXTRA-MOLECULE/bond_fene_nm.cpp b/src/EXTRA-MOLECULE/bond_fene_nm.cpp index 59f60379bd..5aa49265f4 100644 --- a/src/EXTRA-MOLECULE/bond_fene_nm.cpp +++ b/src/EXTRA-MOLECULE/bond_fene_nm.cpp @@ -139,7 +139,7 @@ void BondFENENM::allocate() void BondFENENM::coeff(int narg, char **arg) { - if (narg != 7) error->all(FLERR, "Incorrect args for bond coefficients"); + if (narg != 7) error->all(FLERR, "Incorrect args for bond coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo, ihi; @@ -164,7 +164,7 @@ void BondFENENM::coeff(int narg, char **arg) count++; } - if (count == 0) error->all(FLERR, "Incorrect args for bond coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for bond coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/EXTRA-MOLECULE/bond_gaussian.cpp b/src/EXTRA-MOLECULE/bond_gaussian.cpp index deb37042ad..ceb20c1487 100644 --- a/src/EXTRA-MOLECULE/bond_gaussian.cpp +++ b/src/EXTRA-MOLECULE/bond_gaussian.cpp @@ -189,7 +189,7 @@ void BondGaussian::coeff(int narg, char **arg) count++; } - if (count == 0) error->all(FLERR, "Incorrect args for bond coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for bond coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/EXTRA-MOLECULE/bond_harmonic_restrain.cpp b/src/EXTRA-MOLECULE/bond_harmonic_restrain.cpp index b4fe73c681..2a9a1e4e7f 100644 --- a/src/EXTRA-MOLECULE/bond_harmonic_restrain.cpp +++ b/src/EXTRA-MOLECULE/bond_harmonic_restrain.cpp @@ -133,7 +133,7 @@ void BondHarmonicRestrain::allocate() void BondHarmonicRestrain::coeff(int narg, char **arg) { - if (narg != 2) error->all(FLERR, "Incorrect args for bond coefficients"); + if (narg != 2) error->all(FLERR, "Incorrect args for bond coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo, ihi; @@ -148,7 +148,7 @@ void BondHarmonicRestrain::coeff(int narg, char **arg) count++; } - if (count == 0) error->all(FLERR, "Incorrect args for bond coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for bond coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/EXTRA-MOLECULE/bond_harmonic_shift.cpp b/src/EXTRA-MOLECULE/bond_harmonic_shift.cpp index 6c87d47f5e..227cf170e4 100644 --- a/src/EXTRA-MOLECULE/bond_harmonic_shift.cpp +++ b/src/EXTRA-MOLECULE/bond_harmonic_shift.cpp @@ -128,7 +128,7 @@ void BondHarmonicShift::allocate() void BondHarmonicShift::coeff(int narg, char **arg) { - if (narg != 4) error->all(FLERR,"Incorrect args for bond coefficients"); + if (narg != 4) error->all(FLERR,"Incorrect args for bond coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi; @@ -149,7 +149,7 @@ void BondHarmonicShift::coeff(int narg, char **arg) count++; } - if (count == 0) error->all(FLERR,"Incorrect args for bond coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for bond coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/EXTRA-MOLECULE/bond_harmonic_shift_cut.cpp b/src/EXTRA-MOLECULE/bond_harmonic_shift_cut.cpp index 7e2212b899..d8daad78d6 100644 --- a/src/EXTRA-MOLECULE/bond_harmonic_shift_cut.cpp +++ b/src/EXTRA-MOLECULE/bond_harmonic_shift_cut.cpp @@ -130,7 +130,7 @@ void BondHarmonicShiftCut::allocate() void BondHarmonicShiftCut::coeff(int narg, char **arg) { - if (narg != 4) error->all(FLERR,"Incorrect args for bond coefficients"); + if (narg != 4) error->all(FLERR,"Incorrect args for bond coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi; @@ -151,7 +151,7 @@ void BondHarmonicShiftCut::coeff(int narg, char **arg) count++; } - if (count == 0) error->all(FLERR,"Incorrect args for bond coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for bond coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/EXTRA-MOLECULE/bond_nonlinear.cpp b/src/EXTRA-MOLECULE/bond_nonlinear.cpp index 32de7276d2..debd100e76 100644 --- a/src/EXTRA-MOLECULE/bond_nonlinear.cpp +++ b/src/EXTRA-MOLECULE/bond_nonlinear.cpp @@ -123,7 +123,7 @@ void BondNonlinear::allocate() void BondNonlinear::coeff(int narg, char **arg) { - if (narg != 4) error->all(FLERR,"Incorrect args for bond coefficients"); + if (narg != 4) error->all(FLERR,"Incorrect args for bond coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi; @@ -142,7 +142,7 @@ void BondNonlinear::coeff(int narg, char **arg) count++; } - if (count == 0) error->all(FLERR,"Incorrect args for bond coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for bond coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- */ diff --git a/src/LEPTON/bond_lepton.cpp b/src/LEPTON/bond_lepton.cpp index 63c66011a1..26bcb6af81 100644 --- a/src/LEPTON/bond_lepton.cpp +++ b/src/LEPTON/bond_lepton.cpp @@ -247,7 +247,7 @@ void BondLepton::coeff(int narg, char **arg) count++; } - if (count == 0) error->all(FLERR, "Incorrect args for bond coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for bond coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/MISC/bond_special.cpp b/src/MISC/bond_special.cpp index d0c6652672..e8acba561a 100644 --- a/src/MISC/bond_special.cpp +++ b/src/MISC/bond_special.cpp @@ -137,7 +137,7 @@ void BondSpecial::allocate() void BondSpecial::coeff(int narg, char **arg) { - if (narg != 3) error->all(FLERR,"Incorrect args for bond coefficients"); + if (narg != 3) error->all(FLERR,"Incorrect args for bond coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi; @@ -154,7 +154,7 @@ void BondSpecial::coeff(int narg, char **arg) count++; } - if (count == 0) error->all(FLERR,"Incorrect args for bond coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for bond coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/MOLECULE/bond_fene.cpp b/src/MOLECULE/bond_fene.cpp index 7f55c89296..97b08c3f68 100644 --- a/src/MOLECULE/bond_fene.cpp +++ b/src/MOLECULE/bond_fene.cpp @@ -149,7 +149,7 @@ void BondFENE::allocate() void BondFENE::coeff(int narg, char **arg) { - if (narg != 5) error->all(FLERR, "Incorrect args for bond coefficients"); + if (narg != 5) error->all(FLERR, "Incorrect args for bond coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo, ihi; @@ -170,7 +170,7 @@ void BondFENE::coeff(int narg, char **arg) count++; } - if (count == 0) error->all(FLERR, "Incorrect args for bond coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for bond coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/MOLECULE/bond_fene_expand.cpp b/src/MOLECULE/bond_fene_expand.cpp index e115596eb1..fd3a376316 100644 --- a/src/MOLECULE/bond_fene_expand.cpp +++ b/src/MOLECULE/bond_fene_expand.cpp @@ -147,7 +147,7 @@ void BondFENEExpand::allocate() void BondFENEExpand::coeff(int narg, char **arg) { - if (narg != 6) error->all(FLERR, "Incorrect args for bond coefficients"); + if (narg != 6) error->all(FLERR, "Incorrect args for bond coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo, ihi; @@ -170,7 +170,7 @@ void BondFENEExpand::coeff(int narg, char **arg) count++; } - if (count == 0) error->all(FLERR, "Incorrect args for bond coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for bond coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/MOLECULE/bond_gromos.cpp b/src/MOLECULE/bond_gromos.cpp index 1917f18686..fb3872e402 100644 --- a/src/MOLECULE/bond_gromos.cpp +++ b/src/MOLECULE/bond_gromos.cpp @@ -120,7 +120,7 @@ void BondGromos::allocate() void BondGromos::coeff(int narg, char **arg) { - if (narg != 3) error->all(FLERR, "Incorrect args for bond coefficients"); + if (narg != 3) error->all(FLERR, "Incorrect args for bond coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo, ihi; @@ -137,7 +137,7 @@ void BondGromos::coeff(int narg, char **arg) count++; } - if (count == 0) error->all(FLERR, "Incorrect args for bond coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for bond coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/MOLECULE/bond_harmonic.cpp b/src/MOLECULE/bond_harmonic.cpp index a1e926abea..04529ea2eb 100644 --- a/src/MOLECULE/bond_harmonic.cpp +++ b/src/MOLECULE/bond_harmonic.cpp @@ -122,7 +122,7 @@ void BondHarmonic::allocate() void BondHarmonic::coeff(int narg, char **arg) { - if (narg != 3) error->all(FLERR, "Incorrect args for bond coefficients"); + if (narg != 3) error->all(FLERR, "Incorrect args for bond coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo, ihi; @@ -139,7 +139,7 @@ void BondHarmonic::coeff(int narg, char **arg) count++; } - if (count == 0) error->all(FLERR, "Incorrect args for bond coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for bond coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/MOLECULE/bond_morse.cpp b/src/MOLECULE/bond_morse.cpp index b0e19c359c..8b7c474f84 100644 --- a/src/MOLECULE/bond_morse.cpp +++ b/src/MOLECULE/bond_morse.cpp @@ -126,7 +126,7 @@ void BondMorse::allocate() void BondMorse::coeff(int narg, char **arg) { - if (narg != 4) error->all(FLERR, "Incorrect args for bond coefficients"); + if (narg != 4) error->all(FLERR, "Incorrect args for bond coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo, ihi; @@ -145,7 +145,7 @@ void BondMorse::coeff(int narg, char **arg) count++; } - if (count == 0) error->all(FLERR, "Incorrect args for bond coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for bond coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/MOLECULE/bond_quartic.cpp b/src/MOLECULE/bond_quartic.cpp index 4c9670447b..3cb766e0aa 100644 --- a/src/MOLECULE/bond_quartic.cpp +++ b/src/MOLECULE/bond_quartic.cpp @@ -197,7 +197,7 @@ void BondQuartic::allocate() void BondQuartic::coeff(int narg, char **arg) { - if (narg != 6) error->all(FLERR, "Incorrect args for bond coefficients"); + if (narg != 6) error->all(FLERR, "Incorrect args for bond coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo, ihi; @@ -220,7 +220,7 @@ void BondQuartic::coeff(int narg, char **arg) count++; } - if (count == 0) error->all(FLERR, "Incorrect args for bond coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for bond coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/RHEO/bond_rheo_shell.cpp b/src/RHEO/bond_rheo_shell.cpp index 7ef05bbc38..f7b74dbf70 100644 --- a/src/RHEO/bond_rheo_shell.cpp +++ b/src/RHEO/bond_rheo_shell.cpp @@ -325,7 +325,7 @@ void BondRHEOShell::allocate() void BondRHEOShell::coeff(int narg, char **arg) { - if (narg != 4) error->all(FLERR, "Incorrect args for bond coefficients"); + if (narg != 4) error->all(FLERR, "Incorrect args for bond coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo, ihi; @@ -346,7 +346,7 @@ void BondRHEOShell::coeff(int narg, char **arg) if (1.0 + ecrit[i] > max_stretch) max_stretch = 1.0 + ecrit[i]; } - if (count == 0) error->all(FLERR, "Incorrect args for bond coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for bond coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/YAFF/bond_mm3.cpp b/src/YAFF/bond_mm3.cpp index b3e69881e1..cbb83752f5 100644 --- a/src/YAFF/bond_mm3.cpp +++ b/src/YAFF/bond_mm3.cpp @@ -135,7 +135,7 @@ void BondMM3::allocate() void BondMM3::coeff(int narg, char **arg) { - if (narg != 3) error->all(FLERR,"Incorrect args for bond coefficients"); + if (narg != 3) error->all(FLERR,"Incorrect args for bond coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi; @@ -152,7 +152,7 @@ void BondMM3::coeff(int narg, char **arg) count++; } - if (count == 0) error->all(FLERR,"Incorrect args for bond coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for bond coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/bond_zero.cpp b/src/bond_zero.cpp index 66cedd4a29..78ef0b9915 100644 --- a/src/bond_zero.cpp +++ b/src/bond_zero.cpp @@ -80,7 +80,7 @@ void BondZero::allocate() void BondZero::coeff(int narg, char **arg) { if ((narg < 1) || (coeffflag && narg > 2)) - error->all(FLERR,"Incorrect args for bond coefficients"); + error->all(FLERR,"Incorrect args for bond coefficients" + utils::errorurl(21)); if (!allocated) allocate(); @@ -98,7 +98,7 @@ void BondZero::coeff(int narg, char **arg) count++; } - if (count == 0) error->all(FLERR,"Incorrect args for bond coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for bond coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- From 8025a494d9e4dfa15d37d3cffe5f50482b889244 Mon Sep 17 00:00:00 2001 From: megmcca Date: Mon, 10 Feb 2025 09:48:08 -0700 Subject: [PATCH 010/113] add url to angle_coeff messages --- src/AMOEBA/angle_amoeba.cpp | 10 +++++----- src/CG-SPICA/angle_spica.cpp | 6 +++--- src/CLASS2/angle_class2.cpp | 10 +++++----- src/DIPOLE/angle_dipole.cpp | 4 ++-- src/EXTRA-MOLECULE/angle_cosine_periodic.cpp | 6 +++--- src/EXTRA-MOLECULE/angle_cosine_shift.cpp | 4 ++-- src/EXTRA-MOLECULE/angle_cosine_shift_exp.cpp | 4 ++-- src/EXTRA-MOLECULE/angle_cosine_squared_restricted.cpp | 4 ++-- src/EXTRA-MOLECULE/angle_fourier.cpp | 4 ++-- src/EXTRA-MOLECULE/angle_fourier_simple.cpp | 4 ++-- src/EXTRA-MOLECULE/angle_gaussian.cpp | 2 +- src/EXTRA-MOLECULE/angle_mwlc.cpp | 4 ++-- src/EXTRA-MOLECULE/angle_quartic.cpp | 4 ++-- src/LEPTON/angle_lepton.cpp | 2 +- src/MOFFF/angle_class2_p6.cpp | 10 +++++----- src/MOFFF/angle_cosine_buck6d.cpp | 6 +++--- src/MOLECULE/angle_charmm.cpp | 4 ++-- src/MOLECULE/angle_cosine.cpp | 4 ++-- src/MOLECULE/angle_cosine_squared.cpp | 4 ++-- src/MOLECULE/angle_harmonic.cpp | 4 ++-- src/YAFF/angle_cross.cpp | 4 ++-- src/YAFF/angle_mm3.cpp | 4 ++-- src/angle_zero.cpp | 4 ++-- 23 files changed, 56 insertions(+), 56 deletions(-) diff --git a/src/AMOEBA/angle_amoeba.cpp b/src/AMOEBA/angle_amoeba.cpp index 3b937568ff..e2d26dd047 100644 --- a/src/AMOEBA/angle_amoeba.cpp +++ b/src/AMOEBA/angle_amoeba.cpp @@ -623,7 +623,7 @@ void AngleAmoeba::allocate() void AngleAmoeba::coeff(int narg, char **arg) { - if (narg < 2) error->all(FLERR,"Incorrect args for angle coefficients"); + if (narg < 2) error->all(FLERR,"Incorrect args for angle coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi; @@ -632,7 +632,7 @@ void AngleAmoeba::coeff(int narg, char **arg) int count = 0; if (strcmp(arg[1],"ba") == 0) { - if (narg != 6) error->all(FLERR,"Incorrect args for angle coefficients"); + if (narg != 6) error->all(FLERR,"Incorrect args for angle coefficients" + utils::errorurl(21)); double ba_k1_one = utils::numeric(FLERR,arg[2],false,lmp); double ba_k2_one = utils::numeric(FLERR,arg[3],false,lmp); @@ -649,7 +649,7 @@ void AngleAmoeba::coeff(int narg, char **arg) } } else if (strcmp(arg[1],"ub") == 0) { - if (narg != 4) error->all(FLERR,"Incorrect args for angle coefficients"); + if (narg != 4) error->all(FLERR,"Incorrect args for angle coefficients" + utils::errorurl(21)); double ub_k_one = utils::numeric(FLERR,arg[2],false,lmp); double ub_r0_one = utils::numeric(FLERR,arg[3],false,lmp); @@ -662,7 +662,7 @@ void AngleAmoeba::coeff(int narg, char **arg) } } else { - if (narg != 9) error->all(FLERR,"Incorrect args for angle coefficients"); + if (narg != 9) error->all(FLERR,"Incorrect args for angle coefficients" + utils::errorurl(21)); int pflag_one = utils::inumeric(FLERR,arg[1],false,lmp); int ubflag_one = utils::inumeric(FLERR,arg[2],false,lmp); @@ -689,7 +689,7 @@ void AngleAmoeba::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for angle coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for angle coefficients" + utils::errorurl(21)); for (int i = ilo; i <= ihi; i++) if (setflag_a[i] == 1 && setflag_ba[i] == 1 && setflag_ub[i]) diff --git a/src/CG-SPICA/angle_spica.cpp b/src/CG-SPICA/angle_spica.cpp index 913428cd9b..08e4217483 100644 --- a/src/CG-SPICA/angle_spica.cpp +++ b/src/CG-SPICA/angle_spica.cpp @@ -249,7 +249,7 @@ void AngleSPICA::allocate() void AngleSPICA::coeff(int narg, char **arg) { if ((narg < 3) || (narg > 6)) - error->all(FLERR,"Incorrect args for angle coefficients"); + error->all(FLERR,"Incorrect args for angle coefficients" + utils::errorurl(21)); if (!allocated) allocate(); @@ -270,7 +270,7 @@ void AngleSPICA::coeff(int narg, char **arg) if (repscale_one > 0.0) repscale_one = 1.0; } else if (narg == 4) repscale_one = utils::numeric(FLERR,arg[3],false,lmp); else if (narg == 3) repscale_one = 1.0; - else error->all(FLERR,"Incorrect args for angle coefficients"); + else error->all(FLERR,"Incorrect args for angle coefficients" + utils::errorurl(21)); // convert theta0 from degrees to radians and store coefficients @@ -283,7 +283,7 @@ void AngleSPICA::coeff(int narg, char **arg) count++; } - if (count == 0) error->all(FLERR,"Incorrect args for angle coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for angle coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/CLASS2/angle_class2.cpp b/src/CLASS2/angle_class2.cpp index 5000f9f629..04b7a9238c 100644 --- a/src/CLASS2/angle_class2.cpp +++ b/src/CLASS2/angle_class2.cpp @@ -272,7 +272,7 @@ void AngleClass2::allocate() void AngleClass2::coeff(int narg, char **arg) { - if (narg < 2) error->all(FLERR,"Incorrect args for angle coefficients"); + if (narg < 2) error->all(FLERR,"Incorrect args for angle coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi; @@ -281,7 +281,7 @@ void AngleClass2::coeff(int narg, char **arg) int count = 0; if (strcmp(arg[1],"bb") == 0) { - if (narg != 5) error->all(FLERR,"Incorrect args for angle coefficients"); + if (narg != 5) error->all(FLERR,"Incorrect args for angle coefficients" + utils::errorurl(21)); double bb_k_one = utils::numeric(FLERR,arg[2],false,lmp); double bb_r1_one = utils::numeric(FLERR,arg[3],false,lmp); @@ -296,7 +296,7 @@ void AngleClass2::coeff(int narg, char **arg) } } else if (strcmp(arg[1],"ba") == 0) { - if (narg != 6) error->all(FLERR,"Incorrect args for angle coefficients"); + if (narg != 6) error->all(FLERR,"Incorrect args for angle coefficients" + utils::errorurl(21)); double ba_k1_one = utils::numeric(FLERR,arg[2],false,lmp); double ba_k2_one = utils::numeric(FLERR,arg[3],false,lmp); @@ -313,7 +313,7 @@ void AngleClass2::coeff(int narg, char **arg) } } else { - if (narg != 5) error->all(FLERR,"Incorrect args for angle coefficients"); + if (narg != 5) error->all(FLERR,"Incorrect args for angle coefficients" + utils::errorurl(21)); double theta0_one = utils::numeric(FLERR,arg[1],false,lmp); double k2_one = utils::numeric(FLERR,arg[2],false,lmp); @@ -332,7 +332,7 @@ void AngleClass2::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for angle coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for angle coefficients" + utils::errorurl(21)); for (int i = ilo; i <= ihi; i++) if (setflag_a[i] == 1 && setflag_bb[i] == 1 && setflag_ba[i] == 1) diff --git a/src/DIPOLE/angle_dipole.cpp b/src/DIPOLE/angle_dipole.cpp index a66f3e1042..530f23f844 100644 --- a/src/DIPOLE/angle_dipole.cpp +++ b/src/DIPOLE/angle_dipole.cpp @@ -160,7 +160,7 @@ void AngleDipole::allocate() void AngleDipole::coeff(int narg, char **arg) { - if (narg != 3) error->all(FLERR, "Incorrect args for angle coefficients"); + if (narg != 3) error->all(FLERR, "Incorrect args for angle coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo, ihi; @@ -179,7 +179,7 @@ void AngleDipole::coeff(int narg, char **arg) count++; } - if (count == 0) error->all(FLERR, "Incorrect args for angle coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for angle coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/EXTRA-MOLECULE/angle_cosine_periodic.cpp b/src/EXTRA-MOLECULE/angle_cosine_periodic.cpp index 6aae8d3ff4..e0e7f31f39 100644 --- a/src/EXTRA-MOLECULE/angle_cosine_periodic.cpp +++ b/src/EXTRA-MOLECULE/angle_cosine_periodic.cpp @@ -201,7 +201,7 @@ void AngleCosinePeriodic::allocate() void AngleCosinePeriodic::coeff(int narg, char **arg) { - if (narg != 4) error->all(FLERR,"Incorrect args for angle coefficients"); + if (narg != 4) error->all(FLERR,"Incorrect args for angle coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi; @@ -210,7 +210,7 @@ void AngleCosinePeriodic::coeff(int narg, char **arg) double c_one = utils::numeric(FLERR,arg[1],false,lmp); int b_one = utils::inumeric(FLERR,arg[2],false,lmp); int n_one = utils::inumeric(FLERR,arg[3],false,lmp); - if (n_one <= 0) error->all(FLERR,"Incorrect args for angle coefficients"); + if (n_one <= 0) error->all(FLERR,"Incorrect args for angle coefficients" + utils::errorurl(21)); int count = 0; for (int i = ilo; i <= ihi; i++) { @@ -221,7 +221,7 @@ void AngleCosinePeriodic::coeff(int narg, char **arg) count++; } - if (count == 0) error->all(FLERR,"Incorrect args for angle coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for angle coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- */ diff --git a/src/EXTRA-MOLECULE/angle_cosine_shift.cpp b/src/EXTRA-MOLECULE/angle_cosine_shift.cpp index 53ecb35eaf..14640a5e12 100644 --- a/src/EXTRA-MOLECULE/angle_cosine_shift.cpp +++ b/src/EXTRA-MOLECULE/angle_cosine_shift.cpp @@ -172,7 +172,7 @@ void AngleCosineShift::allocate() void AngleCosineShift::coeff(int narg, char **arg) { - if (narg != 3) error->all(FLERR,"Incorrect args for angle coefficients"); + if (narg != 3) error->all(FLERR,"Incorrect args for angle coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi; @@ -194,7 +194,7 @@ void AngleCosineShift::coeff(int narg, char **arg) count++; } - if (count == 0) error->all(FLERR,"Incorrect args for angle coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for angle coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- */ diff --git a/src/EXTRA-MOLECULE/angle_cosine_shift_exp.cpp b/src/EXTRA-MOLECULE/angle_cosine_shift_exp.cpp index acca92c48e..185adea37d 100644 --- a/src/EXTRA-MOLECULE/angle_cosine_shift_exp.cpp +++ b/src/EXTRA-MOLECULE/angle_cosine_shift_exp.cpp @@ -200,7 +200,7 @@ void AngleCosineShiftExp::allocate() void AngleCosineShiftExp::coeff(int narg, char **arg) { - if (narg != 4) error->all(FLERR,"Incorrect args for angle coefficients"); + if (narg != 4) error->all(FLERR,"Incorrect args for angle coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi; @@ -225,7 +225,7 @@ void AngleCosineShiftExp::coeff(int narg, char **arg) count++; } - if (count == 0) error->all(FLERR,"Incorrect args for angle coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for angle coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- */ diff --git a/src/EXTRA-MOLECULE/angle_cosine_squared_restricted.cpp b/src/EXTRA-MOLECULE/angle_cosine_squared_restricted.cpp index c6d78ea133..37003b5b05 100644 --- a/src/EXTRA-MOLECULE/angle_cosine_squared_restricted.cpp +++ b/src/EXTRA-MOLECULE/angle_cosine_squared_restricted.cpp @@ -166,7 +166,7 @@ void AngleCosineSquaredRestricted::allocate() void AngleCosineSquaredRestricted::coeff(int narg, char **arg) { - if (narg != 3) error->all(FLERR, "Incorrect args for angle coefficients"); + if (narg != 3) error->all(FLERR, "Incorrect args for angle coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo, ihi; @@ -185,7 +185,7 @@ void AngleCosineSquaredRestricted::coeff(int narg, char **arg) count++; } - if (count == 0) error->all(FLERR, "Incorrect args for angle coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for angle coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- */ diff --git a/src/EXTRA-MOLECULE/angle_fourier.cpp b/src/EXTRA-MOLECULE/angle_fourier.cpp index abcda6d036..f6cd9f4c80 100644 --- a/src/EXTRA-MOLECULE/angle_fourier.cpp +++ b/src/EXTRA-MOLECULE/angle_fourier.cpp @@ -174,7 +174,7 @@ void AngleFourier::allocate() void AngleFourier::coeff(int narg, char **arg) { - if (narg != 5) error->all(FLERR,"Incorrect args for angle coefficients"); + if (narg != 5) error->all(FLERR,"Incorrect args for angle coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi; @@ -195,7 +195,7 @@ void AngleFourier::coeff(int narg, char **arg) count++; } - if (count == 0) error->all(FLERR,"Incorrect args for angle coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for angle coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- */ diff --git a/src/EXTRA-MOLECULE/angle_fourier_simple.cpp b/src/EXTRA-MOLECULE/angle_fourier_simple.cpp index 143a008039..e3497b5e81 100644 --- a/src/EXTRA-MOLECULE/angle_fourier_simple.cpp +++ b/src/EXTRA-MOLECULE/angle_fourier_simple.cpp @@ -191,7 +191,7 @@ void AngleFourierSimple::allocate() void AngleFourierSimple::coeff(int narg, char **arg) { - if (narg != 4) error->all(FLERR, "Incorrect args for angle coefficients"); + if (narg != 4) error->all(FLERR, "Incorrect args for angle coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo, ihi; @@ -210,7 +210,7 @@ void AngleFourierSimple::coeff(int narg, char **arg) count++; } - if (count == 0) error->all(FLERR, "Incorrect args for angle coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for angle coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- */ diff --git a/src/EXTRA-MOLECULE/angle_gaussian.cpp b/src/EXTRA-MOLECULE/angle_gaussian.cpp index 004fdd15ab..1272ada0bb 100644 --- a/src/EXTRA-MOLECULE/angle_gaussian.cpp +++ b/src/EXTRA-MOLECULE/angle_gaussian.cpp @@ -236,7 +236,7 @@ void AngleGaussian::coeff(int narg, char **arg) count++; } - if (count == 0) error->all(FLERR, "Incorrect args for angle coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for angle coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- */ diff --git a/src/EXTRA-MOLECULE/angle_mwlc.cpp b/src/EXTRA-MOLECULE/angle_mwlc.cpp index 1a1549fea6..804627cfa3 100644 --- a/src/EXTRA-MOLECULE/angle_mwlc.cpp +++ b/src/EXTRA-MOLECULE/angle_mwlc.cpp @@ -174,7 +174,7 @@ void AngleMWLC::allocate() void AngleMWLC::coeff(int narg, char **arg) { - if (narg != 5) error->all(FLERR, "Incorrect args for angle coefficients"); + if (narg != 5) error->all(FLERR, "Incorrect args for angle coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo, ihi; @@ -195,7 +195,7 @@ void AngleMWLC::coeff(int narg, char **arg) count++; } - if (count == 0) error->all(FLERR, "Incorrect args for angle coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for angle coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- */ diff --git a/src/EXTRA-MOLECULE/angle_quartic.cpp b/src/EXTRA-MOLECULE/angle_quartic.cpp index 616c81c749..92e84e79a5 100644 --- a/src/EXTRA-MOLECULE/angle_quartic.cpp +++ b/src/EXTRA-MOLECULE/angle_quartic.cpp @@ -183,7 +183,7 @@ void AngleQuartic::allocate() void AngleQuartic::coeff(int narg, char **arg) { - if (narg != 5) error->all(FLERR,"Incorrect args for angle coefficients"); + if (narg != 5) error->all(FLERR,"Incorrect args for angle coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi; @@ -206,7 +206,7 @@ void AngleQuartic::coeff(int narg, char **arg) count++; } - if (count == 0) error->all(FLERR,"Incorrect args for angle coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for angle coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- */ diff --git a/src/LEPTON/angle_lepton.cpp b/src/LEPTON/angle_lepton.cpp index 6efded950f..4907086ab1 100644 --- a/src/LEPTON/angle_lepton.cpp +++ b/src/LEPTON/angle_lepton.cpp @@ -298,7 +298,7 @@ void AngleLepton::coeff(int narg, char **arg) count++; } - if (count == 0) error->all(FLERR, "Incorrect args for angle coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for angle coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- */ diff --git a/src/MOFFF/angle_class2_p6.cpp b/src/MOFFF/angle_class2_p6.cpp index f2667fb17b..d7cedb0bcf 100644 --- a/src/MOFFF/angle_class2_p6.cpp +++ b/src/MOFFF/angle_class2_p6.cpp @@ -279,7 +279,7 @@ void AngleClass2P6::allocate() void AngleClass2P6::coeff(int narg, char **arg) { - if (narg < 2) error->all(FLERR,"Incorrect args for angle coefficients"); + if (narg < 2) error->all(FLERR,"Incorrect args for angle coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi; @@ -288,7 +288,7 @@ void AngleClass2P6::coeff(int narg, char **arg) int count = 0; if (strcmp(arg[1],"bb") == 0) { - if (narg != 5) error->all(FLERR,"Incorrect args for angle coefficients"); + if (narg != 5) error->all(FLERR,"Incorrect args for angle coefficients" + utils::errorurl(21)); double bb_k_one = utils::numeric(FLERR,arg[2],false,lmp); double bb_r1_one = utils::numeric(FLERR,arg[3],false,lmp); @@ -303,7 +303,7 @@ void AngleClass2P6::coeff(int narg, char **arg) } } else if (strcmp(arg[1],"ba") == 0) { - if (narg != 6) error->all(FLERR,"Incorrect args for angle coefficients"); + if (narg != 6) error->all(FLERR,"Incorrect args for angle coefficients" + utils::errorurl(21)); double ba_k1_one = utils::numeric(FLERR,arg[2],false,lmp); double ba_k2_one = utils::numeric(FLERR,arg[3],false,lmp); @@ -320,7 +320,7 @@ void AngleClass2P6::coeff(int narg, char **arg) } } else { - if (narg != 7) error->all(FLERR,"Incorrect args for angle coefficients"); + if (narg != 7) error->all(FLERR,"Incorrect args for angle coefficients" + utils::errorurl(21)); double theta0_one = utils::numeric(FLERR,arg[1],false,lmp); double k2_one = utils::numeric(FLERR,arg[2],false,lmp); @@ -343,7 +343,7 @@ void AngleClass2P6::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for angle coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for angle coefficients" + utils::errorurl(21)); for (int i = ilo; i <= ihi; i++) if (setflag_a[i] == 1 && setflag_bb[i] == 1 && setflag_ba[i] == 1) diff --git a/src/MOFFF/angle_cosine_buck6d.cpp b/src/MOFFF/angle_cosine_buck6d.cpp index e1f5f54bf6..bf7390a6f8 100644 --- a/src/MOFFF/angle_cosine_buck6d.cpp +++ b/src/MOFFF/angle_cosine_buck6d.cpp @@ -248,7 +248,7 @@ void AngleCosineBuck6d::allocate() void AngleCosineBuck6d::coeff(int narg, char **arg) { - if (narg != 4) error->all(FLERR,"Incorrect args for angle coefficients"); + if (narg != 4) error->all(FLERR,"Incorrect args for angle coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi; @@ -257,7 +257,7 @@ void AngleCosineBuck6d::coeff(int narg, char **arg) double c_one = utils::numeric(FLERR,arg[1],false,lmp); int n_one = utils::inumeric(FLERR,arg[2],false,lmp); int th0_one = utils::numeric(FLERR,arg[3],false,lmp); - if (n_one <= 0) error->all(FLERR,"Incorrect args for angle coefficients"); + if (n_one <= 0) error->all(FLERR,"Incorrect args for angle coefficients" + utils::errorurl(21)); int count = 0; @@ -271,7 +271,7 @@ void AngleCosineBuck6d::coeff(int narg, char **arg) count++; } - if (count == 0) error->all(FLERR,"Incorrect args for angle coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for angle coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/MOLECULE/angle_charmm.cpp b/src/MOLECULE/angle_charmm.cpp index 11b5abd699..92f4d65723 100644 --- a/src/MOLECULE/angle_charmm.cpp +++ b/src/MOLECULE/angle_charmm.cpp @@ -196,7 +196,7 @@ void AngleCharmm::allocate() void AngleCharmm::coeff(int narg, char **arg) { - if (narg != 5) error->all(FLERR, "Incorrect args for angle coefficients"); + if (narg != 5) error->all(FLERR, "Incorrect args for angle coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo, ihi; @@ -219,7 +219,7 @@ void AngleCharmm::coeff(int narg, char **arg) count++; } - if (count == 0) error->all(FLERR, "Incorrect args for angle coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for angle coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- */ diff --git a/src/MOLECULE/angle_cosine.cpp b/src/MOLECULE/angle_cosine.cpp index 86d67f94aa..6a6d838bc0 100644 --- a/src/MOLECULE/angle_cosine.cpp +++ b/src/MOLECULE/angle_cosine.cpp @@ -155,7 +155,7 @@ void AngleCosine::allocate() void AngleCosine::coeff(int narg, char **arg) { - if (narg != 2) error->all(FLERR, "Incorrect args for angle coefficients"); + if (narg != 2) error->all(FLERR, "Incorrect args for angle coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo, ihi; @@ -170,7 +170,7 @@ void AngleCosine::coeff(int narg, char **arg) count++; } - if (count == 0) error->all(FLERR, "Incorrect args for angle coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for angle coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- */ diff --git a/src/MOLECULE/angle_cosine_squared.cpp b/src/MOLECULE/angle_cosine_squared.cpp index 0ce9d4a064..2074b822eb 100644 --- a/src/MOLECULE/angle_cosine_squared.cpp +++ b/src/MOLECULE/angle_cosine_squared.cpp @@ -169,7 +169,7 @@ void AngleCosineSquared::allocate() void AngleCosineSquared::coeff(int narg, char **arg) { - if (narg != 3) error->all(FLERR, "Incorrect args for angle coefficients"); + if (narg != 3) error->all(FLERR, "Incorrect args for angle coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo, ihi; @@ -188,7 +188,7 @@ void AngleCosineSquared::coeff(int narg, char **arg) count++; } - if (count == 0) error->all(FLERR, "Incorrect args for angle coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for angle coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- */ diff --git a/src/MOLECULE/angle_harmonic.cpp b/src/MOLECULE/angle_harmonic.cpp index 040cbe7530..e04cecfe0d 100644 --- a/src/MOLECULE/angle_harmonic.cpp +++ b/src/MOLECULE/angle_harmonic.cpp @@ -172,7 +172,7 @@ void AngleHarmonic::allocate() void AngleHarmonic::coeff(int narg, char **arg) { - if (narg != 3) error->all(FLERR, "Incorrect args for angle coefficients"); + if (narg != 3) error->all(FLERR, "Incorrect args for angle coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo, ihi; @@ -191,7 +191,7 @@ void AngleHarmonic::coeff(int narg, char **arg) count++; } - if (count == 0) error->all(FLERR, "Incorrect args for angle coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for angle coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- */ diff --git a/src/YAFF/angle_cross.cpp b/src/YAFF/angle_cross.cpp index 067fe986e9..0ff3580715 100644 --- a/src/YAFF/angle_cross.cpp +++ b/src/YAFF/angle_cross.cpp @@ -220,7 +220,7 @@ void AngleCross::allocate() void AngleCross::coeff(int narg, char **arg) { - if (narg != 7) error->all(FLERR,"Incorrect args for angle coefficients"); + if (narg != 7) error->all(FLERR,"Incorrect args for angle coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi; @@ -247,7 +247,7 @@ void AngleCross::coeff(int narg, char **arg) count++; } - if (count == 0) error->all(FLERR,"Incorrect args for angle coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for angle coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- */ diff --git a/src/YAFF/angle_mm3.cpp b/src/YAFF/angle_mm3.cpp index 920041f7e9..9cc53e21de 100644 --- a/src/YAFF/angle_mm3.cpp +++ b/src/YAFF/angle_mm3.cpp @@ -180,7 +180,7 @@ void AngleMM3::allocate() void AngleMM3::coeff(int narg, char **arg) { - if (narg != 3) error->all(FLERR,"Incorrect args for angle coefficients"); + if (narg != 3) error->all(FLERR,"Incorrect args for angle coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi; @@ -200,7 +200,7 @@ void AngleMM3::coeff(int narg, char **arg) count++; } - if (count == 0) error->all(FLERR,"Incorrect args for angle coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for angle coefficients" + utils::errorurl(21)); } diff --git a/src/angle_zero.cpp b/src/angle_zero.cpp index 39ff64d2bb..4f41509771 100644 --- a/src/angle_zero.cpp +++ b/src/angle_zero.cpp @@ -83,7 +83,7 @@ void AngleZero::allocate() void AngleZero::coeff(int narg, char **arg) { if ((narg < 1) || (coeffflag && narg > 2)) - error->all(FLERR, "Incorrect args for angle coefficients"); + error->all(FLERR, "Incorrect args for angle coefficients" + utils::errorurl(21)); if (!allocated) allocate(); @@ -102,7 +102,7 @@ void AngleZero::coeff(int narg, char **arg) count++; } - if (count == 0) error->all(FLERR, "Incorrect args for angle coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for angle coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- */ From 0f66e665297d3a698eecc4c48527a9b66bbd4a77 Mon Sep 17 00:00:00 2001 From: megmcca Date: Mon, 10 Feb 2025 09:57:04 -0700 Subject: [PATCH 011/113] add url to dihedral_coeff messages --- src/CLASS2/dihedral_class2.cpp | 14 +++++++------- src/EXTRA-MOLECULE/dihedral_cosine_shift_exp.cpp | 4 ++-- .../dihedral_cosine_squared_restricted.cpp | 4 ++-- src/EXTRA-MOLECULE/dihedral_fourier.cpp | 4 ++-- src/EXTRA-MOLECULE/dihedral_helix.cpp | 4 ++-- src/EXTRA-MOLECULE/dihedral_nharmonic.cpp | 6 +++--- src/EXTRA-MOLECULE/dihedral_quadratic.cpp | 4 ++-- src/EXTRA-MOLECULE/dihedral_spherical.cpp | 4 ++-- src/EXTRA-MOLECULE/dihedral_table_cut.cpp | 4 ++-- src/LEPTON/dihedral_lepton.cpp | 2 +- src/MOLECULE/dihedral_charmm.cpp | 4 ++-- src/MOLECULE/dihedral_charmmfsw.cpp | 4 ++-- src/MOLECULE/dihedral_harmonic.cpp | 4 ++-- src/MOLECULE/dihedral_multi_harmonic.cpp | 4 ++-- src/MOLECULE/dihedral_opls.cpp | 4 ++-- src/MOLECULE/dihedral_table.cpp | 2 +- src/dihedral_zero.cpp | 4 ++-- 17 files changed, 38 insertions(+), 38 deletions(-) diff --git a/src/CLASS2/dihedral_class2.cpp b/src/CLASS2/dihedral_class2.cpp index 288fac2e92..9c4c1ad871 100644 --- a/src/CLASS2/dihedral_class2.cpp +++ b/src/CLASS2/dihedral_class2.cpp @@ -632,7 +632,7 @@ void DihedralClass2::coeff(int narg, char **arg) int count = 0; if (strcmp(arg[1],"mbt") == 0) { - if (narg != 6) error->all(FLERR,"Incorrect args for dihedral coefficients"); + if (narg != 6) error->all(FLERR,"Incorrect args for dihedral coefficients" + utils::errorurl(21)); double f1_one = utils::numeric(FLERR,arg[2],false,lmp); double f2_one = utils::numeric(FLERR,arg[3],false,lmp); @@ -650,7 +650,7 @@ void DihedralClass2::coeff(int narg, char **arg) } else if (strcmp(arg[1],"ebt") == 0) { if (narg != 10) - error->all(FLERR,"Incorrect args for dihedral coefficients"); + error->all(FLERR,"Incorrect args for dihedral coefficients" + utils::errorurl(21)); double f1_1_one = utils::numeric(FLERR,arg[2],false,lmp); double f2_1_one = utils::numeric(FLERR,arg[3],false,lmp); @@ -676,7 +676,7 @@ void DihedralClass2::coeff(int narg, char **arg) } else if (strcmp(arg[1],"at") == 0) { if (narg != 10) - error->all(FLERR,"Incorrect args for dihedral coefficients"); + error->all(FLERR,"Incorrect args for dihedral coefficients" + utils::errorurl(21)); double f1_1_one = utils::numeric(FLERR,arg[2],false,lmp); double f2_1_one = utils::numeric(FLERR,arg[3],false,lmp); @@ -703,7 +703,7 @@ void DihedralClass2::coeff(int narg, char **arg) } } else if (strcmp(arg[1],"aat") == 0) { - if (narg != 5) error->all(FLERR,"Incorrect args for dihedral coefficients"); + if (narg != 5) error->all(FLERR,"Incorrect args for dihedral coefficients" + utils::errorurl(21)); double k_one = utils::numeric(FLERR,arg[2],false,lmp); double theta0_1_one = utils::numeric(FLERR,arg[3],false,lmp); @@ -720,7 +720,7 @@ void DihedralClass2::coeff(int narg, char **arg) } } else if (strcmp(arg[1],"bb13") == 0) { - if (narg != 5) error->all(FLERR,"Incorrect args for dihedral coefficients"); + if (narg != 5) error->all(FLERR,"Incorrect args for dihedral coefficients" + utils::errorurl(21)); double k_one = utils::numeric(FLERR,arg[2],false,lmp); double r10_one = utils::numeric(FLERR,arg[3],false,lmp); @@ -735,7 +735,7 @@ void DihedralClass2::coeff(int narg, char **arg) } } else { - if (narg != 7) error->all(FLERR,"Incorrect args for dihedral coefficients"); + if (narg != 7) error->all(FLERR,"Incorrect args for dihedral coefficients" + utils::errorurl(21)); double k1_one = utils::numeric(FLERR,arg[1],false,lmp); double phi1_one = utils::numeric(FLERR,arg[2],false,lmp); @@ -758,7 +758,7 @@ void DihedralClass2::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for dihedral coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for dihedral coefficients" + utils::errorurl(21)); for (int i = ilo; i <= ihi; i++) if (setflag_d[i] == 1 && setflag_mbt[i] == 1 && setflag_ebt[i] == 1 && diff --git a/src/EXTRA-MOLECULE/dihedral_cosine_shift_exp.cpp b/src/EXTRA-MOLECULE/dihedral_cosine_shift_exp.cpp index 28015b0c36..53cad49d92 100644 --- a/src/EXTRA-MOLECULE/dihedral_cosine_shift_exp.cpp +++ b/src/EXTRA-MOLECULE/dihedral_cosine_shift_exp.cpp @@ -252,7 +252,7 @@ void DihedralCosineShiftExp::allocate() void DihedralCosineShiftExp::coeff(int narg, char **arg) { - if (narg != 4) error->all(FLERR,"Incorrect args for dihedral coefficients"); + if (narg != 4) error->all(FLERR,"Incorrect args for dihedral coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi; @@ -277,7 +277,7 @@ void DihedralCosineShiftExp::coeff(int narg, char **arg) count++; } - if (count == 0) error->all(FLERR,"Incorrect args for dihedral coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for dihedral coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/EXTRA-MOLECULE/dihedral_cosine_squared_restricted.cpp b/src/EXTRA-MOLECULE/dihedral_cosine_squared_restricted.cpp index 5b2feb6897..d8e34189d9 100644 --- a/src/EXTRA-MOLECULE/dihedral_cosine_squared_restricted.cpp +++ b/src/EXTRA-MOLECULE/dihedral_cosine_squared_restricted.cpp @@ -245,7 +245,7 @@ void DihedralCosineSquaredRestricted::allocate() void DihedralCosineSquaredRestricted::coeff(int narg, char **arg) { - if (narg != 3) error->all(FLERR, "Incorrect args for dihedral coefficients"); + if (narg != 3) error->all(FLERR, "Incorrect args for dihedral coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo, ihi; @@ -262,7 +262,7 @@ void DihedralCosineSquaredRestricted::coeff(int narg, char **arg) count++; } - if (count == 0) error->all(FLERR, "Incorrect args for dihedral coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for dihedral coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/EXTRA-MOLECULE/dihedral_fourier.cpp b/src/EXTRA-MOLECULE/dihedral_fourier.cpp index 37e1ae8328..a6f2052b16 100644 --- a/src/EXTRA-MOLECULE/dihedral_fourier.cpp +++ b/src/EXTRA-MOLECULE/dihedral_fourier.cpp @@ -273,7 +273,7 @@ void DihedralFourier::allocate() void DihedralFourier::coeff(int narg, char **arg) { - if (narg < 4) error->all(FLERR,"Incorrect args for dihedral coefficients"); + if (narg < 4) error->all(FLERR,"Incorrect args for dihedral coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi; @@ -322,7 +322,7 @@ void DihedralFourier::coeff(int narg, char **arg) count++; } - if (count == 0) error->all(FLERR,"Incorrect args for dihedral coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for dihedral coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/EXTRA-MOLECULE/dihedral_helix.cpp b/src/EXTRA-MOLECULE/dihedral_helix.cpp index 0111da9f99..4693d29cd7 100644 --- a/src/EXTRA-MOLECULE/dihedral_helix.cpp +++ b/src/EXTRA-MOLECULE/dihedral_helix.cpp @@ -263,7 +263,7 @@ void DihedralHelix::allocate() void DihedralHelix::coeff(int narg, char **arg) { - if (narg != 4) error->all(FLERR,"Incorrect args for dihedral coefficients"); + if (narg != 4) error->all(FLERR,"Incorrect args for dihedral coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi; @@ -282,7 +282,7 @@ void DihedralHelix::coeff(int narg, char **arg) count++; } - if (count == 0) error->all(FLERR,"Incorrect args for dihedral coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for dihedral coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/EXTRA-MOLECULE/dihedral_nharmonic.cpp b/src/EXTRA-MOLECULE/dihedral_nharmonic.cpp index 4c3cd3be2c..a88593dd20 100644 --- a/src/EXTRA-MOLECULE/dihedral_nharmonic.cpp +++ b/src/EXTRA-MOLECULE/dihedral_nharmonic.cpp @@ -257,11 +257,11 @@ void DihedralNHarmonic::allocate() void DihedralNHarmonic::coeff(int narg, char **arg) { - if (narg < 3) error->all(FLERR,"Incorrect args for dihedral coefficients"); + if (narg < 3) error->all(FLERR,"Incorrect args for dihedral coefficients" + utils::errorurl(21)); int n = utils::inumeric(FLERR,arg[1],false,lmp); if (narg != n + 2) - error->all(FLERR,"Incorrect args for dihedral coefficients"); + error->all(FLERR,"Incorrect args for dihedral coefficients" + utils::errorurl(21)); if (!allocated) allocate(); @@ -280,7 +280,7 @@ void DihedralNHarmonic::coeff(int narg, char **arg) count++; } - if (count == 0) error->all(FLERR,"Incorrect args for dihedral coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for dihedral coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/EXTRA-MOLECULE/dihedral_quadratic.cpp b/src/EXTRA-MOLECULE/dihedral_quadratic.cpp index 1bef5956fa..2350095f0d 100644 --- a/src/EXTRA-MOLECULE/dihedral_quadratic.cpp +++ b/src/EXTRA-MOLECULE/dihedral_quadratic.cpp @@ -267,7 +267,7 @@ void DihedralQuadratic::allocate() void DihedralQuadratic::coeff(int narg, char **arg) { - if (narg != 3) error->all(FLERR,"Incorrect args for dihedral coefficients"); + if (narg != 3) error->all(FLERR,"Incorrect args for dihedral coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi; @@ -288,7 +288,7 @@ void DihedralQuadratic::coeff(int narg, char **arg) count++; } - if (count == 0) error->all(FLERR,"Incorrect args for dihedral coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for dihedral coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/EXTRA-MOLECULE/dihedral_spherical.cpp b/src/EXTRA-MOLECULE/dihedral_spherical.cpp index fc22a4a46c..15e403ef03 100644 --- a/src/EXTRA-MOLECULE/dihedral_spherical.cpp +++ b/src/EXTRA-MOLECULE/dihedral_spherical.cpp @@ -639,7 +639,7 @@ void DihedralSpherical::allocate() void DihedralSpherical::coeff(int narg, char **arg) { - if (narg < 4) error->all(FLERR, "Incorrect args for dihedral coefficients"); + if (narg < 4) error->all(FLERR, "Incorrect args for dihedral coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo, ihi; @@ -692,7 +692,7 @@ void DihedralSpherical::coeff(int narg, char **arg) count++; } - if (count == 0) error->all(FLERR, "Incorrect args for dihedral coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for dihedral coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/EXTRA-MOLECULE/dihedral_table_cut.cpp b/src/EXTRA-MOLECULE/dihedral_table_cut.cpp index a06df279f3..9a73db7660 100644 --- a/src/EXTRA-MOLECULE/dihedral_table_cut.cpp +++ b/src/EXTRA-MOLECULE/dihedral_table_cut.cpp @@ -451,7 +451,7 @@ void DihedralTableCut::allocate() void DihedralTableCut::coeff(int narg, char **arg) { - if (narg != 7) error->all(FLERR,"Incorrect args for dihedral coefficients"); + if (narg != 7) error->all(FLERR,"Incorrect args for dihedral coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi; @@ -628,5 +628,5 @@ void DihedralTableCut::coeff(int narg, char **arg) } ntables++; - if (count == 0) error->all(FLERR,"Incorrect args for dihedral coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for dihedral coefficients" + utils::errorurl(21)); } diff --git a/src/LEPTON/dihedral_lepton.cpp b/src/LEPTON/dihedral_lepton.cpp index 16975a8f52..2cee9fba8a 100644 --- a/src/LEPTON/dihedral_lepton.cpp +++ b/src/LEPTON/dihedral_lepton.cpp @@ -407,7 +407,7 @@ void DihedralLepton::coeff(int narg, char **arg) count++; } - if (count == 0) error->all(FLERR, "Incorrect args for dihedral coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for dihedral coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/MOLECULE/dihedral_charmm.cpp b/src/MOLECULE/dihedral_charmm.cpp index 78ff0c9d08..de6d59c1d4 100644 --- a/src/MOLECULE/dihedral_charmm.cpp +++ b/src/MOLECULE/dihedral_charmm.cpp @@ -307,7 +307,7 @@ void DihedralCharmm::allocate() void DihedralCharmm::coeff(int narg, char **arg) { - if (narg != 5) error->all(FLERR, "Incorrect args for dihedral coefficients"); + if (narg != 5) error->all(FLERR, "Incorrect args for dihedral coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo, ihi; @@ -340,7 +340,7 @@ void DihedralCharmm::coeff(int narg, char **arg) count++; } - if (count == 0) error->all(FLERR, "Incorrect args for dihedral coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for dihedral coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/MOLECULE/dihedral_charmmfsw.cpp b/src/MOLECULE/dihedral_charmmfsw.cpp index a84eee8ade..a46fb8680c 100644 --- a/src/MOLECULE/dihedral_charmmfsw.cpp +++ b/src/MOLECULE/dihedral_charmmfsw.cpp @@ -326,7 +326,7 @@ void DihedralCharmmfsw::allocate() void DihedralCharmmfsw::coeff(int narg, char **arg) { - if (narg != 5) error->all(FLERR, "Incorrect args for dihedral coefficients"); + if (narg != 5) error->all(FLERR, "Incorrect args for dihedral coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo, ihi; @@ -359,7 +359,7 @@ void DihedralCharmmfsw::coeff(int narg, char **arg) count++; } - if (count == 0) error->all(FLERR, "Incorrect args for dihedral coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for dihedral coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/MOLECULE/dihedral_harmonic.cpp b/src/MOLECULE/dihedral_harmonic.cpp index b7dfa17575..790c388eaf 100644 --- a/src/MOLECULE/dihedral_harmonic.cpp +++ b/src/MOLECULE/dihedral_harmonic.cpp @@ -248,7 +248,7 @@ void DihedralHarmonic::allocate() void DihedralHarmonic::coeff(int narg, char **arg) { - if (narg != 4) error->all(FLERR, "Incorrect args for dihedral coefficients"); + if (narg != 4) error->all(FLERR, "Incorrect args for dihedral coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo, ihi; @@ -283,7 +283,7 @@ void DihedralHarmonic::coeff(int narg, char **arg) count++; } - if (count == 0) error->all(FLERR, "Incorrect args for dihedral coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for dihedral coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/MOLECULE/dihedral_multi_harmonic.cpp b/src/MOLECULE/dihedral_multi_harmonic.cpp index 2d1e16b9e4..bbf1bf5d34 100644 --- a/src/MOLECULE/dihedral_multi_harmonic.cpp +++ b/src/MOLECULE/dihedral_multi_harmonic.cpp @@ -251,7 +251,7 @@ void DihedralMultiHarmonic::allocate() void DihedralMultiHarmonic::coeff(int narg, char **arg) { - if (narg != 6) error->all(FLERR, "Incorrect args for dihedral coefficients"); + if (narg != 6) error->all(FLERR, "Incorrect args for dihedral coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo, ihi; @@ -274,7 +274,7 @@ void DihedralMultiHarmonic::coeff(int narg, char **arg) count++; } - if (count == 0) error->all(FLERR, "Incorrect args for dihedral coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for dihedral coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/MOLECULE/dihedral_opls.cpp b/src/MOLECULE/dihedral_opls.cpp index e99d83f631..1ec2f869a5 100644 --- a/src/MOLECULE/dihedral_opls.cpp +++ b/src/MOLECULE/dihedral_opls.cpp @@ -264,7 +264,7 @@ void DihedralOPLS::allocate() void DihedralOPLS::coeff(int narg, char **arg) { - if (narg != 5) error->all(FLERR, "Incorrect args for dihedral coefficients"); + if (narg != 5) error->all(FLERR, "Incorrect args for dihedral coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo, ihi; @@ -287,7 +287,7 @@ void DihedralOPLS::coeff(int narg, char **arg) count++; } - if (count == 0) error->all(FLERR, "Incorrect args for dihedral coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for dihedral coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/MOLECULE/dihedral_table.cpp b/src/MOLECULE/dihedral_table.cpp index 1fb05c211c..a731a03b5e 100644 --- a/src/MOLECULE/dihedral_table.cpp +++ b/src/MOLECULE/dihedral_table.cpp @@ -890,7 +890,7 @@ void DihedralTable::coeff(int narg, char **arg) } ntables++; - if (count == 0) error->all(FLERR,"Incorrect args for dihedral coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for dihedral coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/dihedral_zero.cpp b/src/dihedral_zero.cpp index a4f7524e02..70bb8c19d0 100644 --- a/src/dihedral_zero.cpp +++ b/src/dihedral_zero.cpp @@ -78,7 +78,7 @@ void DihedralZero::allocate() void DihedralZero::coeff(int narg, char **arg) { if ((narg < 1) || (coeffflag && narg > 1)) - error->all(FLERR, "Incorrect args for dihedral coefficients"); + error->all(FLERR, "Incorrect args for dihedral coefficients" + utils::errorurl(21)); if (!allocated) allocate(); @@ -91,7 +91,7 @@ void DihedralZero::coeff(int narg, char **arg) count++; } - if (count == 0) error->all(FLERR, "Incorrect args for dihedral coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for dihedral coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- From c9bd1a7877c6dcf88e1d00c6c088f977561034d1 Mon Sep 17 00:00:00 2001 From: megmcca Date: Mon, 10 Feb 2025 09:59:04 -0700 Subject: [PATCH 012/113] add url to improper_coeff messages --- src/AMOEBA/improper_amoeba.cpp | 4 ++-- src/CLASS2/improper_class2.cpp | 8 ++++---- src/EXTRA-MOLECULE/improper_cossq.cpp | 2 +- src/EXTRA-MOLECULE/improper_distance.cpp | 4 ++-- src/EXTRA-MOLECULE/improper_fourier.cpp | 4 ++-- src/EXTRA-MOLECULE/improper_ring.cpp | 2 +- src/MOFFF/improper_inversion_harmonic.cpp | 4 ++-- src/MOLECULE/improper_cvff.cpp | 4 ++-- src/MOLECULE/improper_harmonic.cpp | 4 ++-- src/MOLECULE/improper_umbrella.cpp | 4 ++-- src/YAFF/improper_distharm.cpp | 4 ++-- src/YAFF/improper_sqdistharm.cpp | 4 ++-- src/improper_zero.cpp | 4 ++-- 13 files changed, 26 insertions(+), 26 deletions(-) diff --git a/src/AMOEBA/improper_amoeba.cpp b/src/AMOEBA/improper_amoeba.cpp index cbc7fbd8d2..f14713cd20 100644 --- a/src/AMOEBA/improper_amoeba.cpp +++ b/src/AMOEBA/improper_amoeba.cpp @@ -257,7 +257,7 @@ void ImproperAmoeba::allocate() void ImproperAmoeba::coeff(int narg, char **arg) { - if (narg != 2) error->all(FLERR,"Incorrect args for improper coefficients"); + if (narg != 2) error->all(FLERR,"Incorrect args for improper coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi; @@ -274,7 +274,7 @@ void ImproperAmoeba::coeff(int narg, char **arg) count++; } - if (count == 0) error->all(FLERR,"Incorrect args for improper coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for improper coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/CLASS2/improper_class2.cpp b/src/CLASS2/improper_class2.cpp index 73f21600bb..e53b06969c 100644 --- a/src/CLASS2/improper_class2.cpp +++ b/src/CLASS2/improper_class2.cpp @@ -509,7 +509,7 @@ void ImproperClass2::allocate() void ImproperClass2::coeff(int narg, char **arg) { - if (narg < 2) error->all(FLERR,"Incorrect args for improper coefficients"); + if (narg < 2) error->all(FLERR,"Incorrect args for improper coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi; @@ -518,7 +518,7 @@ void ImproperClass2::coeff(int narg, char **arg) int count = 0; if (strcmp(arg[1],"aa") == 0) { - if (narg != 8) error->all(FLERR,"Incorrect args for improper coefficients"); + if (narg != 8) error->all(FLERR,"Incorrect args for improper coefficients" + utils::errorurl(21)); double k1_one = utils::numeric(FLERR,arg[2],false,lmp); double k2_one = utils::numeric(FLERR,arg[3],false,lmp); @@ -541,7 +541,7 @@ void ImproperClass2::coeff(int narg, char **arg) } } else { - if (narg != 3) error->all(FLERR,"Incorrect args for improper coefficients"); + if (narg != 3) error->all(FLERR,"Incorrect args for improper coefficients" + utils::errorurl(21)); double k0_one = utils::numeric(FLERR,arg[1],false,lmp); double chi0_one = utils::numeric(FLERR,arg[2],false,lmp); @@ -556,7 +556,7 @@ void ImproperClass2::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for improper coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for improper coefficients" + utils::errorurl(21)); for (int i = ilo; i <= ihi; i++) if (setflag_i[i] == 1 && setflag_aa[i] == 1) setflag[i] = 1; diff --git a/src/EXTRA-MOLECULE/improper_cossq.cpp b/src/EXTRA-MOLECULE/improper_cossq.cpp index 864ec28927..bcf9715990 100644 --- a/src/EXTRA-MOLECULE/improper_cossq.cpp +++ b/src/EXTRA-MOLECULE/improper_cossq.cpp @@ -270,7 +270,7 @@ void ImproperCossq::coeff(int narg, char **arg) count++; } - if (count == 0) error->all(FLERR,"Incorrect args for improper coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for improper coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/EXTRA-MOLECULE/improper_distance.cpp b/src/EXTRA-MOLECULE/improper_distance.cpp index 934eeb285d..b8376020dd 100644 --- a/src/EXTRA-MOLECULE/improper_distance.cpp +++ b/src/EXTRA-MOLECULE/improper_distance.cpp @@ -209,7 +209,7 @@ void ImproperDistance::allocate() void ImproperDistance::coeff(int narg, char **arg) { // if (which > 0) return; - if (narg != 3) error->all(FLERR,"Incorrect args for improper coefficients"); + if (narg != 3) error->all(FLERR,"Incorrect args for improper coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi; @@ -228,7 +228,7 @@ void ImproperDistance::coeff(int narg, char **arg) count++; } - if (count == 0) error->all(FLERR,"Incorrect args for improper coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for improper coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/EXTRA-MOLECULE/improper_fourier.cpp b/src/EXTRA-MOLECULE/improper_fourier.cpp index 1db8b3697c..b2814f4d1f 100644 --- a/src/EXTRA-MOLECULE/improper_fourier.cpp +++ b/src/EXTRA-MOLECULE/improper_fourier.cpp @@ -261,7 +261,7 @@ void ImproperFourier::allocate() void ImproperFourier::coeff(int narg, char **arg) { - if (narg != 5 && narg != 6) error->all(FLERR,"Incorrect args for improper coefficients"); + if (narg != 5 && narg != 6) error->all(FLERR,"Incorrect args for improper coefficients" + utils::errorurl(21)); if (!allocated) allocate(); @@ -288,7 +288,7 @@ void ImproperFourier::coeff(int narg, char **arg) count++; } - if (count == 0) error->all(FLERR,"Incorrect args for improper coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for improper coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/EXTRA-MOLECULE/improper_ring.cpp b/src/EXTRA-MOLECULE/improper_ring.cpp index 3d8b672e1e..8fee93055e 100644 --- a/src/EXTRA-MOLECULE/improper_ring.cpp +++ b/src/EXTRA-MOLECULE/improper_ring.cpp @@ -309,7 +309,7 @@ void ImproperRing ::coeff(int narg, char **arg) count++; } - if (count == 0) error->all(FLERR,"Incorrect args for improper coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for improper coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/MOFFF/improper_inversion_harmonic.cpp b/src/MOFFF/improper_inversion_harmonic.cpp index c0de968626..0a4661c6b1 100644 --- a/src/MOFFF/improper_inversion_harmonic.cpp +++ b/src/MOFFF/improper_inversion_harmonic.cpp @@ -273,7 +273,7 @@ void ImproperInversionHarmonic::allocate() void ImproperInversionHarmonic::coeff(int narg, char **arg) { - if (narg != 3) error->all(FLERR,"Incorrect args for improper coefficients"); + if (narg != 3) error->all(FLERR,"Incorrect args for improper coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi; @@ -292,7 +292,7 @@ void ImproperInversionHarmonic::coeff(int narg, char **arg) count++; } - if (count == 0) error->all(FLERR,"Incorrect args for improper coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for improper coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/MOLECULE/improper_cvff.cpp b/src/MOLECULE/improper_cvff.cpp index ad8f709541..11dace26d1 100644 --- a/src/MOLECULE/improper_cvff.cpp +++ b/src/MOLECULE/improper_cvff.cpp @@ -275,7 +275,7 @@ void ImproperCvff::allocate() void ImproperCvff::coeff(int narg, char **arg) { - if (narg != 4) error->all(FLERR, "Incorrect args for improper coefficients"); + if (narg != 4) error->all(FLERR, "Incorrect args for improper coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo, ihi; @@ -294,7 +294,7 @@ void ImproperCvff::coeff(int narg, char **arg) count++; } - if (count == 0) error->all(FLERR, "Incorrect args for improper coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for improper coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/MOLECULE/improper_harmonic.cpp b/src/MOLECULE/improper_harmonic.cpp index 06647fb93b..5f25d678db 100644 --- a/src/MOLECULE/improper_harmonic.cpp +++ b/src/MOLECULE/improper_harmonic.cpp @@ -217,7 +217,7 @@ void ImproperHarmonic::allocate() void ImproperHarmonic::coeff(int narg, char **arg) { - if (narg != 3) error->all(FLERR, "Incorrect args for improper coefficients"); + if (narg != 3) error->all(FLERR, "Incorrect args for improper coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo, ihi; @@ -236,7 +236,7 @@ void ImproperHarmonic::coeff(int narg, char **arg) count++; } - if (count == 0) error->all(FLERR, "Incorrect args for improper coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for improper coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/MOLECULE/improper_umbrella.cpp b/src/MOLECULE/improper_umbrella.cpp index 1558adc337..d3dcf4da41 100644 --- a/src/MOLECULE/improper_umbrella.cpp +++ b/src/MOLECULE/improper_umbrella.cpp @@ -256,7 +256,7 @@ void ImproperUmbrella::allocate() void ImproperUmbrella::coeff(int narg, char **arg) { - if (narg != 3) error->all(FLERR, "Incorrect args for improper coefficients"); + if (narg != 3) error->all(FLERR, "Incorrect args for improper coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo, ihi; @@ -279,7 +279,7 @@ void ImproperUmbrella::coeff(int narg, char **arg) count++; } - if (count == 0) error->all(FLERR, "Incorrect args for improper coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for improper coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/YAFF/improper_distharm.cpp b/src/YAFF/improper_distharm.cpp index 257cbce1b3..c056b310ee 100644 --- a/src/YAFF/improper_distharm.cpp +++ b/src/YAFF/improper_distharm.cpp @@ -217,7 +217,7 @@ void ImproperDistHarm::allocate() void ImproperDistHarm::coeff(int narg, char **arg) { // if (which > 0) return; - if (narg != 3) error->all(FLERR,"Incorrect args for improper coefficients"); + if (narg != 3) error->all(FLERR,"Incorrect args for improper coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi; @@ -237,7 +237,7 @@ void ImproperDistHarm::coeff(int narg, char **arg) count++; } - if (count == 0) error->all(FLERR,"Incorrect args for improper coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for improper coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/YAFF/improper_sqdistharm.cpp b/src/YAFF/improper_sqdistharm.cpp index f4beab3587..f3a34f3976 100644 --- a/src/YAFF/improper_sqdistharm.cpp +++ b/src/YAFF/improper_sqdistharm.cpp @@ -217,7 +217,7 @@ void ImproperSQDistHarm::allocate() void ImproperSQDistHarm::coeff(int narg, char **arg) { // if (which > 0) return; - if (narg != 3) error->all(FLERR,"Incorrect args for improper coefficients"); + if (narg != 3) error->all(FLERR,"Incorrect args for improper coefficients" + utils::errorurl(21)); if (!allocated) allocate(); int ilo,ihi; @@ -237,7 +237,7 @@ void ImproperSQDistHarm::coeff(int narg, char **arg) count++; } - if (count == 0) error->all(FLERR,"Incorrect args for improper coefficients"); + if (count == 0) error->all(FLERR,"Incorrect args for improper coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- diff --git a/src/improper_zero.cpp b/src/improper_zero.cpp index e8497795ae..2487520a94 100644 --- a/src/improper_zero.cpp +++ b/src/improper_zero.cpp @@ -78,7 +78,7 @@ void ImproperZero::allocate() void ImproperZero::coeff(int narg, char **arg) { if ((narg < 1) || (coeffflag && narg > 1)) - error->all(FLERR, "Incorrect args for improper coefficients"); + error->all(FLERR, "Incorrect args for improper coefficients" + utils::errorurl(21)); if (!allocated) allocate(); @@ -91,7 +91,7 @@ void ImproperZero::coeff(int narg, char **arg) count++; } - if (count == 0) error->all(FLERR, "Incorrect args for improper coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for improper coefficients" + utils::errorurl(21)); } /* ---------------------------------------------------------------------- From 0b55587b1df189a6bf6f7bf0d0fa85f05376ebf5 Mon Sep 17 00:00:00 2001 From: megmcca Date: Mon, 10 Feb 2025 10:56:04 -0700 Subject: [PATCH 013/113] add error 10 URL and text --- doc/src/Errors_details.rst | 27 ++++++++++++++++++++++++--- 1 file changed, 24 insertions(+), 3 deletions(-) diff --git a/doc/src/Errors_details.rst b/doc/src/Errors_details.rst index b0d1393bf6..3ab843a6ea 100644 --- a/doc/src/Errors_details.rst +++ b/doc/src/Errors_details.rst @@ -12,7 +12,9 @@ following are discussions of such cases. - :ref:`Incorrect format in ... section of data file ` - :ref:`Illegal variable command: expected X arguments but found Y ` - :ref:`Out of range atoms - cannot compute ... ` +- :ref:`Lost atoms ... ` - :ref:`Too many neighbor bins ` +- :ref:`Unrecognized pair style ... is part of ... package which is not enabled in this LAMMPS binary ` - :ref:`Cannot use neighbor bins - box size \<\< cutoff ` - :ref:`Domain too large for neighbor bins ` - :ref:`Incorrect args for pair coefficients (also bond/angle/dihedral/improper coefficients) ` @@ -288,9 +290,28 @@ Too many neighbor bins The simulation box has become too large relative to the size of a neighbor bin and LAMMPS is unable to store the needed number of bins. This typically implies the simulation box has expanded too far. -This can happen when some atoms move rapidly apart with shrink-wrap -boundaries or when a fix (like fix deform or a barostat) excessively -grows the simulation box. +This can happen when some atoms move rapidly apart with shrink-wrap boundaries +or when a fix (like fix deform or a barostat) excessively grows the simulation +box. + +.. _err0010: + +Unrecognized pair style ... is part of ... package which is not enabled in this LAMMPS binary +--------------------------------------------------------------------------------------------- + +The LAMMPS executable (binary) being used was not compiled with a package +containing the specified pair style. This indicates that the executable needs to +be re-built after enabling the correct package in the relevant Makefile or CMake +build directory, see :ref:`Section 3. Build LAMMPS ` for more details. +One can check if the expected package and pair style is present in the +executable by running it with the ``-help`` (or ``-h``) flag on the command +line. One common oversight, especially for beginner LAMMPS users, is to enable +the package, but to forget to run commands to rebuild (e.g., to run the final +``make`` or ``cmake`` command). + +If this error is occurring with an executable that the user does not control +(e.g., through a module on HPC clusters), the user will need to get in contact +with the relevant person or people who can update the executable. .. _err0015: From 5479ac32d4c97ee10ffa5176e41b30aa517dc8e2 Mon Sep 17 00:00:00 2001 From: jtclemm Date: Tue, 11 Feb 2025 16:06:20 -0700 Subject: [PATCH 014/113] Adding errorurl for missing bond atom error --- doc/src/Errors_details.rst | 23 ++++++++++++++++++++++- src/KOKKOS/neigh_bond_kokkos.cpp | 32 ++++++++++++++++---------------- src/ntopo_angle_all.cpp | 4 ++-- src/ntopo_angle_partial.cpp | 4 ++-- src/ntopo_angle_template.cpp | 4 ++-- src/ntopo_bond_all.cpp | 4 ++-- src/ntopo_bond_partial.cpp | 4 ++-- src/ntopo_bond_template.cpp | 4 ++-- src/ntopo_dihedral_all.cpp | 4 ++-- src/ntopo_dihedral_partial.cpp | 4 ++-- src/ntopo_dihedral_template.cpp | 4 ++-- src/ntopo_improper_all.cpp | 4 ++-- src/ntopo_improper_partial.cpp | 4 ++-- src/ntopo_improper_template.cpp | 4 ++-- 14 files changed, 62 insertions(+), 41 deletions(-) diff --git a/doc/src/Errors_details.rst b/doc/src/Errors_details.rst index 3ab843a6ea..894e02fa29 100644 --- a/doc/src/Errors_details.rst +++ b/doc/src/Errors_details.rst @@ -311,7 +311,7 @@ the package, but to forget to run commands to rebuild (e.g., to run the final If this error is occurring with an executable that the user does not control (e.g., through a module on HPC clusters), the user will need to get in contact -with the relevant person or people who can update the executable. +with the relevant person or people who can update the executable. .. _err0015: @@ -419,3 +419,24 @@ example, are usually not a per-atom property, but defined through the atom type. Thus it would not be required to have a Masses section and the included data would be ignored. LAMMPS prints this warning to inform about this case. + +.. _err0030: + +Bond (or angle, dihedral, or improper) atoms missing +---------------------------------------------------- + +The second atom needed to compute a particular bond (or the third or fourth +atom for angle, dihedral, or improper) is missing on the indicated timestep +and processor. Typically, this is because the two bonded atoms have become +too far apart relative to the communication cutoff distance for ghost atoms. +Typically, the communication cutoff is set by the pair cutoff, but it can +be manually adjusted using :doc:`comm_modify ` to accommodate +larger distances between topologically connected atoms at the cost of increased +communication and more ghost atoms. However, missing bond atoms may also +indicate unstable dynamics caused the atoms blow apart such that increasing +the communication distance will not solve the underlying issue. + +If the simulation has open boundary conditions where atoms can leave, +potentially at different times than other atoms they are bonded to, this +error can be converted to a warning or turned off using the *lost/bond* +keyword in the :doc:`thermo_modify ` command. diff --git a/src/KOKKOS/neigh_bond_kokkos.cpp b/src/KOKKOS/neigh_bond_kokkos.cpp index 9e1c8c273b..de68dfbf99 100644 --- a/src/KOKKOS/neigh_bond_kokkos.cpp +++ b/src/KOKKOS/neigh_bond_kokkos.cpp @@ -259,7 +259,7 @@ void NeighBondKokkos::bond_all() } while (h_fail_flag()); if (nmissing && lostbond == Thermo::ERROR) - error->one(FLERR,"Bond atoms missing at step {}", update->ntimestep); + error->one(FLERR,"Bond atoms missing at step {}" + utils::errorurl(30), update->ntimestep); if (neighbor->cluster_check) bond_check(); if (lostbond == Thermo::IGNORE) return; @@ -267,7 +267,7 @@ void NeighBondKokkos::bond_all() int all; MPI_Allreduce(&nmissing,&all,1,MPI_INT,MPI_SUM,world); if (all && me == 0) - error->warning(FLERR,"Bond atoms missing at step {}", update->ntimestep); + error->warning(FLERR,"Bond atoms missing at step {}" + utils::errorurl(30), update->ntimestep); k_bondlist.modify(); } @@ -338,7 +338,7 @@ void NeighBondKokkos::bond_partial() } while (h_fail_flag()); if (nmissing && lostbond == Thermo::ERROR) - error->one(FLERR,"Bond atoms missing at step {}", update->ntimestep); + error->one(FLERR,"Bond atoms missing at step {}" + utils::errorurl(30), update->ntimestep); if (neighbor->cluster_check) bond_check(); if (lostbond == Thermo::IGNORE) return; @@ -346,7 +346,7 @@ void NeighBondKokkos::bond_partial() int all; MPI_Allreduce(&nmissing,&all,1,MPI_INT,MPI_SUM,world); if (all && me == 0) - error->warning(FLERR,"Bond atoms missing at step {}", update->ntimestep); + error->warning(FLERR,"Bond atoms missing at step {}" + utils::errorurl(30), update->ntimestep); k_bondlist.modify(); } @@ -443,7 +443,7 @@ void NeighBondKokkos::angle_all() } while (h_fail_flag()); if (nmissing && lostbond == Thermo::ERROR) - error->one(FLERR,"Angle atoms missing at step {}", update->ntimestep); + error->one(FLERR,"Angle atoms missing at step {}" + utils::errorurl(30), update->ntimestep); if (neighbor->cluster_check) angle_check(); if (lostbond == Thermo::IGNORE) return; @@ -451,7 +451,7 @@ void NeighBondKokkos::angle_all() int all; MPI_Allreduce(&nmissing,&all,1,MPI_INT,MPI_SUM,world); if (all && (me == 0)) - error->warning(FLERR,"Angle atoms missing at step {}", update->ntimestep); + error->warning(FLERR,"Angle atoms missing at step {}" + utils::errorurl(30), update->ntimestep); k_anglelist.modify(); } @@ -529,7 +529,7 @@ void NeighBondKokkos::angle_partial() } while (h_fail_flag()); if (nmissing && lostbond == Thermo::ERROR) - error->one(FLERR,"Angle atoms missing at step {}", update->ntimestep); + error->one(FLERR,"Angle atoms missing at step {}" + utils::errorurl(30), update->ntimestep); if (neighbor->cluster_check) angle_check(); if (lostbond == Thermo::IGNORE) return; @@ -537,7 +537,7 @@ void NeighBondKokkos::angle_partial() int all; MPI_Allreduce(&nmissing,&all,1,MPI_INT,MPI_SUM,world); if (all && (me == 0)) - error->warning(FLERR,"Angle atoms missing at step {}", update->ntimestep); + error->warning(FLERR,"Angle atoms missing at step {}" + utils::errorurl(30), update->ntimestep); k_anglelist.modify(); } @@ -654,7 +654,7 @@ void NeighBondKokkos::dihedral_all() } while (h_fail_flag()); if (nmissing && lostbond == Thermo::ERROR) - error->one(FLERR,"Dihedral atoms missing at step {}", update->ntimestep); + error->one(FLERR,"Dihedral atoms missing at step {}" + utils::errorurl(30), update->ntimestep); if (neighbor->cluster_check) dihedral_check(neighbor->ndihedrallist,v_dihedrallist); if (lostbond == Thermo::IGNORE) return; @@ -662,7 +662,7 @@ void NeighBondKokkos::dihedral_all() int all; MPI_Allreduce(&nmissing,&all,1,MPI_INT,MPI_SUM,world); if (all && (me == 0)) - error->warning(FLERR,"Dihedral atoms missing at step {}", update->ntimestep); + error->warning(FLERR,"Dihedral atoms missing at step {}" + utils::errorurl(30), update->ntimestep); k_dihedrallist.modify(); } @@ -745,7 +745,7 @@ void NeighBondKokkos::dihedral_partial() } while (h_fail_flag()); if (nmissing && lostbond == Thermo::ERROR) - error->one(FLERR,"Dihedral atoms missing at step {}", update->ntimestep); + error->one(FLERR,"Dihedral atoms missing at step {}" + utils::errorurl(30), update->ntimestep); if (neighbor->cluster_check) dihedral_check(neighbor->ndihedrallist,v_dihedrallist); if (lostbond == Thermo::IGNORE) return; @@ -753,7 +753,7 @@ void NeighBondKokkos::dihedral_partial() int all; MPI_Allreduce(&nmissing,&all,1,MPI_INT,MPI_SUM,world); if (all && (me == 0)) - error->warning(FLERR,"Dihedral atoms missing at step {}", update->ntimestep); + error->warning(FLERR,"Dihedral atoms missing at step {}" + utils::errorurl(30), update->ntimestep); k_dihedrallist.modify(); } @@ -892,7 +892,7 @@ void NeighBondKokkos::improper_all() } while (h_fail_flag()); if (nmissing && lostbond == Thermo::ERROR) - error->one(FLERR,"Improper atoms missing at step {}", update->ntimestep); + error->one(FLERR,"Improper atoms missing at step {}" + utils::errorurl(30), update->ntimestep); if (neighbor->cluster_check) dihedral_check(neighbor->nimproperlist,v_improperlist); if (lostbond == Thermo::IGNORE) return; @@ -900,7 +900,7 @@ void NeighBondKokkos::improper_all() int all; MPI_Allreduce(&nmissing,&all,1,MPI_INT,MPI_SUM,world); if (all && (me == 0)) - error->warning(FLERR,"Improper atoms missing at step {}", update->ntimestep); + error->warning(FLERR,"Improper atoms missing at step {}" + utils::errorurl(30), update->ntimestep); k_improperlist.modify(); } @@ -983,7 +983,7 @@ void NeighBondKokkos::improper_partial() } while (h_fail_flag()); if (nmissing && lostbond == Thermo::ERROR) - error->one(FLERR,"Improper atoms missing at step {}", update->ntimestep); + error->one(FLERR,"Improper atoms missing at step {}" + utils::errorurl(30), update->ntimestep); if (neighbor->cluster_check) dihedral_check(neighbor->nimproperlist,v_improperlist); if (lostbond == Thermo::IGNORE) return; @@ -991,7 +991,7 @@ void NeighBondKokkos::improper_partial() int all; MPI_Allreduce(&nmissing,&all,1,MPI_INT,MPI_SUM,world); if (all && (me == 0)) - error->warning(FLERR,"Improper atoms missing at step {}", update->ntimestep); + error->warning(FLERR,"Improper atoms missing at step {}" + utils::errorurl(30), update->ntimestep); k_improperlist.modify(); } diff --git a/src/ntopo_angle_all.cpp b/src/ntopo_angle_all.cpp index 593750c7b7..8e15a5e197 100644 --- a/src/ntopo_angle_all.cpp +++ b/src/ntopo_angle_all.cpp @@ -59,7 +59,7 @@ void NTopoAngleAll::build() if (atom1 == -1 || atom2 == -1 || atom3 == -1) { nmissing++; if (lostbond == Thermo::ERROR) - error->one(FLERR, "Angle atoms {} {} {} missing on proc {} at step {}", angle_atom1[i][m], + error->one(FLERR, "Angle atoms {} {} {} missing on proc {} at step {}" + utils::errorurl(30), angle_atom1[i][m], angle_atom2[i][m], angle_atom3[i][m], me, update->ntimestep); continue; } @@ -84,5 +84,5 @@ void NTopoAngleAll::build() int all; MPI_Allreduce(&nmissing, &all, 1, MPI_INT, MPI_SUM, world); - if (all && (me == 0)) error->warning(FLERR, "Angle atoms missing at step {}", update->ntimestep); + if (all && (me == 0)) error->warning(FLERR, "Angle atoms missing at step {}" + utils::errorurl(30), update->ntimestep); } diff --git a/src/ntopo_angle_partial.cpp b/src/ntopo_angle_partial.cpp index 277621f0bd..0d3d6d78d8 100644 --- a/src/ntopo_angle_partial.cpp +++ b/src/ntopo_angle_partial.cpp @@ -60,7 +60,7 @@ void NTopoAnglePartial::build() if (atom1 == -1 || atom2 == -1 || atom3 == -1) { nmissing++; if (lostbond == Thermo::ERROR) - error->one(FLERR, "Angle atoms {} {} {} missing on proc {} at step {}", angle_atom1[i][m], + error->one(FLERR, "Angle atoms {} {} {} missing on proc {} at step {}" + utils::errorurl(30), angle_atom1[i][m], angle_atom2[i][m], angle_atom3[i][m], me, update->ntimestep); continue; } @@ -85,5 +85,5 @@ void NTopoAnglePartial::build() int all; MPI_Allreduce(&nmissing, &all, 1, MPI_INT, MPI_SUM, world); - if (all && (me == 0)) error->warning(FLERR, "Angle atoms missing at step {}", update->ntimestep); + if (all && (me == 0)) error->warning(FLERR, "Angle atoms missing at step {}" + utils::errorurl(30), update->ntimestep); } diff --git a/src/ntopo_angle_template.cpp b/src/ntopo_angle_template.cpp index 982ef90a9d..48e5f5eff6 100644 --- a/src/ntopo_angle_template.cpp +++ b/src/ntopo_angle_template.cpp @@ -77,7 +77,7 @@ void NTopoAngleTemplate::build() if (atom1 == -1 || atom2 == -1 || atom3 == -1) { nmissing++; if (lostbond == Thermo::ERROR) - error->one(FLERR, "Angle atoms {} {} {} missing on proc {} at step {}", + error->one(FLERR, "Angle atoms {} {} {} missing on proc {} at step {}" + utils::errorurl(30), angle_atom1[iatom][m] + tagprev, angle_atom2[iatom][m] + tagprev, angle_atom3[iatom][m] + tagprev, me, update->ntimestep); continue; @@ -104,5 +104,5 @@ void NTopoAngleTemplate::build() int all; MPI_Allreduce(&nmissing, &all, 1, MPI_INT, MPI_SUM, world); - if (all && (me == 0)) error->warning(FLERR, "Angle atoms missing at step {}", update->ntimestep); + if (all && (me == 0)) error->warning(FLERR, "Angle atoms missing at step {}" + utils::errorurl(30), update->ntimestep); } diff --git a/src/ntopo_bond_all.cpp b/src/ntopo_bond_all.cpp index 7e051744e2..c5d511fa1d 100644 --- a/src/ntopo_bond_all.cpp +++ b/src/ntopo_bond_all.cpp @@ -56,7 +56,7 @@ void NTopoBondAll::build() if (atom1 == -1) { nmissing++; if (lostbond == Thermo::ERROR) - error->one(FLERR, "Bond atoms {} {} missing on proc {} at step {}", tag[i], + error->one(FLERR, "Bond atoms {} {} missing on proc {} at step {}" + utils::errorurl(30), tag[i], bond_atom[i][m], me, update->ntimestep); continue; } @@ -78,5 +78,5 @@ void NTopoBondAll::build() int all; MPI_Allreduce(&nmissing, &all, 1, MPI_INT, MPI_SUM, world); - if (all && (me == 0)) error->warning(FLERR, "Bond atoms missing at step {}", update->ntimestep); + if (all && (me == 0)) error->warning(FLERR, "Bond atoms missing at step {}" + utils::errorurl(30), update->ntimestep); } diff --git a/src/ntopo_bond_partial.cpp b/src/ntopo_bond_partial.cpp index 4df72f9ab8..2dc0b3c530 100644 --- a/src/ntopo_bond_partial.cpp +++ b/src/ntopo_bond_partial.cpp @@ -57,7 +57,7 @@ void NTopoBondPartial::build() if (atom1 == -1) { nmissing++; if (lostbond == Thermo::ERROR) - error->one(FLERR, "Bond atoms {} {} missing on proc {} at step {}", tag[i], + error->one(FLERR, "Bond atoms {} {} missing on proc {} at step {}" + utils::errorurl(30), tag[i], bond_atom[i][m], me, update->ntimestep); continue; } @@ -79,5 +79,5 @@ void NTopoBondPartial::build() int all; MPI_Allreduce(&nmissing, &all, 1, MPI_INT, MPI_SUM, world); - if (all && (me == 0)) error->warning(FLERR, "Bond atoms missing at step {}", update->ntimestep); + if (all && (me == 0)) error->warning(FLERR, "Bond atoms missing at step {}" + utils::errorurl(30), update->ntimestep); } diff --git a/src/ntopo_bond_template.cpp b/src/ntopo_bond_template.cpp index c8f4bc51d8..a949fdae8e 100644 --- a/src/ntopo_bond_template.cpp +++ b/src/ntopo_bond_template.cpp @@ -73,7 +73,7 @@ void NTopoBondTemplate::build() if (atom1 == -1) { nmissing++; if (lostbond == Thermo::ERROR) - error->one(FLERR, "Bond atoms {} {} missing on proc {} at step {}", tag[i], + error->one(FLERR, "Bond atoms {} {} missing on proc {} at step {}" + utils::errorurl(30), tag[i], bond_atom[iatom][m] + tagprev, me, update->ntimestep); continue; } @@ -96,5 +96,5 @@ void NTopoBondTemplate::build() int all; MPI_Allreduce(&nmissing, &all, 1, MPI_INT, MPI_SUM, world); - if (all && (me == 0)) error->warning(FLERR, "Bond atoms missing at step {}", update->ntimestep); + if (all && (me == 0)) error->warning(FLERR, "Bond atoms missing at step {}" + utils::errorurl(30), update->ntimestep); } diff --git a/src/ntopo_dihedral_all.cpp b/src/ntopo_dihedral_all.cpp index 9f62cda07d..2d2f2bf289 100644 --- a/src/ntopo_dihedral_all.cpp +++ b/src/ntopo_dihedral_all.cpp @@ -61,7 +61,7 @@ void NTopoDihedralAll::build() if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) { nmissing++; if (lostbond == Thermo::ERROR) - error->one(FLERR, "Dihedral atoms {} {} {} {} missing on proc {} at step {}", + error->one(FLERR, "Dihedral atoms {} {} {} {} missing on proc {} at step {}" + utils::errorurl(30), dihedral_atom1[i][m], dihedral_atom2[i][m], dihedral_atom3[i][m], dihedral_atom4[i][m], me, update->ntimestep); continue; @@ -90,5 +90,5 @@ void NTopoDihedralAll::build() int all; MPI_Allreduce(&nmissing, &all, 1, MPI_INT, MPI_SUM, world); if (all && (me == 0)) - error->warning(FLERR, "Dihedral atoms missing at step {}", update->ntimestep); + error->warning(FLERR, "Dihedral atoms missing at step {}" + utils::errorurl(30), update->ntimestep); } diff --git a/src/ntopo_dihedral_partial.cpp b/src/ntopo_dihedral_partial.cpp index 98246b7b4f..5437624b71 100644 --- a/src/ntopo_dihedral_partial.cpp +++ b/src/ntopo_dihedral_partial.cpp @@ -62,7 +62,7 @@ void NTopoDihedralPartial::build() if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) { nmissing++; if (lostbond == Thermo::ERROR) - error->one(FLERR, "Dihedral atoms {} {} {} {} missing on proc {} at step {}", + error->one(FLERR, "Dihedral atoms {} {} {} {} missing on proc {} at step {}" + utils::errorurl(30), dihedral_atom1[i][m], dihedral_atom2[i][m], dihedral_atom3[i][m], dihedral_atom4[i][m], me, update->ntimestep); continue; @@ -91,5 +91,5 @@ void NTopoDihedralPartial::build() int all; MPI_Allreduce(&nmissing, &all, 1, MPI_INT, MPI_SUM, world); if (all && (me == 0)) - error->warning(FLERR, "Dihedral atoms missing at step {}", update->ntimestep); + error->warning(FLERR, "Dihedral atoms missing at step {}" + utils::errorurl(30), update->ntimestep); } diff --git a/src/ntopo_dihedral_template.cpp b/src/ntopo_dihedral_template.cpp index 2cc41f4a8f..89d4f202f8 100644 --- a/src/ntopo_dihedral_template.cpp +++ b/src/ntopo_dihedral_template.cpp @@ -78,7 +78,7 @@ void NTopoDihedralTemplate::build() if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) { nmissing++; if (lostbond == Thermo::ERROR) - error->one(FLERR, "Dihedral atoms {} {} {} {} missing on proc {} at step {}", + error->one(FLERR, "Dihedral atoms {} {} {} {} missing on proc {} at step {}" + utils::errorurl(30), dihedral_atom1[iatom][m] + tagprev, dihedral_atom2[iatom][m] + tagprev, dihedral_atom3[iatom][m] + tagprev, dihedral_atom4[iatom][m] + tagprev, me, update->ntimestep); @@ -109,5 +109,5 @@ void NTopoDihedralTemplate::build() int all; MPI_Allreduce(&nmissing, &all, 1, MPI_INT, MPI_SUM, world); if (all && (me == 0)) - error->warning(FLERR, "Dihedral atoms missing at step {}", update->ntimestep); + error->warning(FLERR, "Dihedral atoms missing at step {}" + utils::errorurl(30), update->ntimestep); } diff --git a/src/ntopo_improper_all.cpp b/src/ntopo_improper_all.cpp index 2786fdbfa8..7e6b4c6e60 100644 --- a/src/ntopo_improper_all.cpp +++ b/src/ntopo_improper_all.cpp @@ -61,7 +61,7 @@ void NTopoImproperAll::build() if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) { nmissing++; if (lostbond == Thermo::ERROR) - error->one(FLERR, "Improper atoms {} {} {} {} missing on proc {} at step {}", + error->one(FLERR, "Improper atoms {} {} {} {} missing on proc {} at step {}" + utils::errorurl(30), improper_atom1[i][m], improper_atom2[i][m], improper_atom3[i][m], improper_atom4[i][m], me, update->ntimestep); continue; @@ -90,5 +90,5 @@ void NTopoImproperAll::build() int all; MPI_Allreduce(&nmissing, &all, 1, MPI_INT, MPI_SUM, world); if (all && (me == 0)) - error->warning(FLERR, "Improper atoms missing at step {}", update->ntimestep); + error->warning(FLERR, "Improper atoms missing at step {}" + utils::errorurl(30), update->ntimestep); } diff --git a/src/ntopo_improper_partial.cpp b/src/ntopo_improper_partial.cpp index 559a7b3d7d..7266c5c2a1 100644 --- a/src/ntopo_improper_partial.cpp +++ b/src/ntopo_improper_partial.cpp @@ -62,7 +62,7 @@ void NTopoImproperPartial::build() if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) { nmissing++; if (lostbond == Thermo::ERROR) - error->one(FLERR, "Improper atoms {} {} {} {} missing on proc {} at step {}", + error->one(FLERR, "Improper atoms {} {} {} {} missing on proc {} at step {}" + utils::errorurl(30), improper_atom1[i][m], improper_atom2[i][m], improper_atom3[i][m], improper_atom4[i][m], me, update->ntimestep); continue; @@ -90,5 +90,5 @@ void NTopoImproperPartial::build() int all; MPI_Allreduce(&nmissing, &all, 1, MPI_INT, MPI_SUM, world); - if (all && me == 0) error->warning(FLERR, "Improper atoms missing at step {}", update->ntimestep); + if (all && me == 0) error->warning(FLERR, "Improper atoms missing at step {}" + utils::errorurl(30), update->ntimestep); } diff --git a/src/ntopo_improper_template.cpp b/src/ntopo_improper_template.cpp index 79712f4ed1..bfd097a812 100644 --- a/src/ntopo_improper_template.cpp +++ b/src/ntopo_improper_template.cpp @@ -78,7 +78,7 @@ void NTopoImproperTemplate::build() if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) { nmissing++; if (lostbond == Thermo::ERROR) - error->one(FLERR, "Improper atoms {} {} {} {} missing on proc {} at step {}", + error->one(FLERR, "Improper atoms {} {} {} {} missing on proc {} at step {}" + utils::errorurl(30), improper_atom1[iatom][m] + tagprev, improper_atom2[iatom][m] + tagprev, improper_atom3[iatom][m] + tagprev, improper_atom4[iatom][m] + tagprev, me, update->ntimestep); @@ -109,5 +109,5 @@ void NTopoImproperTemplate::build() int all; MPI_Allreduce(&nmissing, &all, 1, MPI_INT, MPI_SUM, world); if (all && (me == 0)) - error->warning(FLERR, "Improper atoms missing at step {}", update->ntimestep); + error->warning(FLERR, "Improper atoms missing at step {}" + utils::errorurl(30), update->ntimestep); } From 8dc7d254dc541969f1c60602f38977b0848d7652 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 13 Feb 2025 17:55:55 -0500 Subject: [PATCH 015/113] add section about segmentation faults --- doc/src/Errors_details.rst | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) diff --git a/doc/src/Errors_details.rst b/doc/src/Errors_details.rst index 894e02fa29..c699ee1e37 100644 --- a/doc/src/Errors_details.rst +++ b/doc/src/Errors_details.rst @@ -58,6 +58,35 @@ only the symptoms are not triggering an error quickly. Correspondingly, errors may be triggered faster with more processors and thus smaller sub-domains. +Segmentation Fault +^^^^^^^^^^^^^^^^^^ + +A segmentation fault is an error reported by the **operating system** +and not LAMMPS itself. It happens when a process tries to access a +memory address that is not available. This can have **many** reasons: +memory has not been allocated, a memory buffer is not large enough, a +memory address is computed from an incorrect index, a memory buffer is +used after it has been freed, some general memory corruption. When +investigating a segmentation fault (aka segfault), it is important to +determine which process is causing it; it may not always be LAMMPS. For +example, some MPI library implementation report a segmentation fault +from their "mpirun" or "mpiexec" command when the application has been +terminated unexpectedly. + +While a segmentation fault is likely an indication of a bug in LAMMPS, +it need not always be; it can also be the consequence of too aggressive +simulation settings. For time critical code paths, LAMMPS will assume +the user has chosen the settings carefully and will not make any checks +to avoid to avoid performance penalties. + +A crucial step in resolving segmentation faults is to identify the exact +location in the code where this happens. Please see `Errors_debug` for +a couple of examples showing how to do this on a Linux machine. With +this information, a simple way to reproduce the segmentation fault, and +the information about the :doc:`exact LAMMPS version ` +and platform you are running on, you can contact the LAMMPS developers +or post in the LAMMPS forum to get assistance. + Fast moving atoms ^^^^^^^^^^^^^^^^^ From ad51ef5aff092d5c987e2a81c3701ddc9af744a7 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 13 Feb 2025 17:56:14 -0500 Subject: [PATCH 016/113] don't use :ref: on a docpage --- doc/src/Errors_details.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/src/Errors_details.rst b/doc/src/Errors_details.rst index c699ee1e37..91b11742cb 100644 --- a/doc/src/Errors_details.rst +++ b/doc/src/Errors_details.rst @@ -331,7 +331,7 @@ Unrecognized pair style ... is part of ... package which is not enabled in this The LAMMPS executable (binary) being used was not compiled with a package containing the specified pair style. This indicates that the executable needs to be re-built after enabling the correct package in the relevant Makefile or CMake -build directory, see :ref:`Section 3. Build LAMMPS ` for more details. +build directory, see :doc:`Section 3. Build LAMMPS ` for more details. One can check if the expected package and pair style is present in the executable by running it with the ``-help`` (or ``-h``) flag on the command line. One common oversight, especially for beginner LAMMPS users, is to enable From f4d2653cdaae8e34c5840e46d150b14103691ce0 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 13 Feb 2025 17:57:31 -0500 Subject: [PATCH 017/113] add dummy section that is referenced from local TOC --- doc/src/Errors_details.rst | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/doc/src/Errors_details.rst b/doc/src/Errors_details.rst index 91b11742cb..b151132b5f 100644 --- a/doc/src/Errors_details.rst +++ b/doc/src/Errors_details.rst @@ -311,6 +311,11 @@ help to temporarily use a cutoff-Coulomb pair style and no kspace style until the system has somewhat equilibrated and then switch to the long-range solver. +.. _err0008: + +Lost atoms ... +-------------- + .. _err0009: Too many neighbor bins From 3ed6b617f0ac3d4ead7e959963af403a8f99ee0a Mon Sep 17 00:00:00 2001 From: Aidan Thompson Date: Mon, 17 Feb 2025 13:08:42 -0700 Subject: [PATCH 018/113] tweaked number 11 --- doc/src/Errors_details.rst | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/doc/src/Errors_details.rst b/doc/src/Errors_details.rst index b151132b5f..8d87e74799 100644 --- a/doc/src/Errors_details.rst +++ b/doc/src/Errors_details.rst @@ -398,9 +398,13 @@ variant takes element type names while 'eam' does not). Another common source of coefficient errors is when using multiple pair styles with commands such as :doc:`pair_style hybrid `. Using hybrid pair styles requires adding an extra "label" argument in the coefficient commands -that designates which pair style the command line refers to, and may require -different arguments per pair style. Other errors might require a close look at -files that are read in by the input script, such as data files or restart files. +that designates which pair style the command line refers to. Moreover, if +the same pair style is used multiple times, this label must be followed by +an additional numeric argument. Also, different pair styles may require +different arguments. + +This error message might also require a close look at other LAMMPS input files +that are read in by the input script, such as data files or restart files. .. _err0024: From 25774943d575b7d4c88120a99ee5c155d0c003b1 Mon Sep 17 00:00:00 2001 From: Aidan Thompson Date: Mon, 17 Feb 2025 17:25:07 -0700 Subject: [PATCH 019/113] Added advice on error 21 --- doc/src/Errors_details.rst | 42 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 42 insertions(+) diff --git a/doc/src/Errors_details.rst b/doc/src/Errors_details.rst index 8d87e74799..3b97f245e2 100644 --- a/doc/src/Errors_details.rst +++ b/doc/src/Errors_details.rst @@ -406,6 +406,48 @@ different arguments. This error message might also require a close look at other LAMMPS input files that are read in by the input script, such as data files or restart files. +.. _err0021: + +Energy was not tallied on needed timestep (also virial, per-atom energy, per-atom virial) +----------------------------------------------------------------------------------------- + +This error is generated when LAMMPS attempts to access an out-of-date +or non-existent energy, pressure, or virial. +For efficiency reasons, +LAMMPS does *not* calculate these quantities when the forces are calculated +on every timestep or iteration. Global quantities are only calculated +when they are needed for :doc:`thermo ` output (at the beginning, end, +and at regular intervals specified by the :doc:`thermo ` command). Similarly, +per-atom quantities are only calculated if they are needed to write per-atom +energy or virial to a dump file. +This system works fine for simple input scripts. +However, the many user-specified `variable`, `fix`, and `compute` commands +that LAMMPS provides make it difficult to anticipate when a quantity will +be requested. In some use cases, LAMMPS will figure out that a quantity is needed +and arrange for it to be calculated on that timestep e.g. if it is requested by +:doc:`fix ave/time ` or similar commands. +If that fails, it can be detected by a mismatch +between the current timestep and when a quantity was last calculated, +in which case an error message of this type is generated. + +The most common cause of this type of error is requesting a quantity before +the start of the simulation. + +.. code-block:: LAMMPS + + # run 0 post no # this will fix the error + variable e equal pe # requesting energy compute + print "Potential energy = $e" # this will generate the error + run 1000 # start of simulation + +This situation can be avoided by adding in a "run 0" command, as explained in +more detail in the "Variable Accuracy" section of the +:doc:`variable ` doc page. + +Another cause is requesting a quantity on a timestep that is not +a thermo or dump output timestep. This can often be +remedied by increasing the frequency of thermo or dump output. + .. _err0024: Molecule topology/atom exceeds system topology/atom From 841e459b67631390262929d7ab8cb4bc42c914c2 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 17 Feb 2025 23:05:42 -0500 Subject: [PATCH 020/113] provide URL to explain fmt::format_error --- doc/src/Errors_details.rst | 14 ++++++++++++++ src/main.cpp | 2 +- 2 files changed, 15 insertions(+), 1 deletion(-) diff --git a/doc/src/Errors_details.rst b/doc/src/Errors_details.rst index 8d87e74799..ace74e8ae3 100644 --- a/doc/src/Errors_details.rst +++ b/doc/src/Errors_details.rst @@ -347,6 +347,20 @@ If this error is occurring with an executable that the user does not control (e.g., through a module on HPC clusters), the user will need to get in contact with the relevant person or people who can update the executable. +.. _err0012: + +fmt::format_error +----------------- + +LAMMPS uses the `{fmt} library `_ for advanced string +formatting tasks. This is similar to the ``printf()`` family of +functions from the standard C library, but more flexible. If there is a +bug in the LAMMPS code and the format string does not match the list of +arguments or has some other error, this error message will be shown. +You should contact the LAMMPS developers and report the bug as a `GitHub +Bug Report Issue `_ along with +sufficient information to easily reproduce it. + .. _err0015: Cannot use neighbor bins - box size \<\< cutoff diff --git a/src/main.cpp b/src/main.cpp index da80d66b52..a1f9772455 100644 --- a/src/main.cpp +++ b/src/main.cpp @@ -86,7 +86,7 @@ int main(int argc, char **argv) MPI_Finalize(); exit(1); } catch (fmt::format_error &fe) { - fprintf(stderr, "fmt::format_error: %s\n", fe.what()); + fprintf(stderr, "\nfmt::format_error: %s%s\n", fe.what(), utils::errorurl(12).c_str()); finalize(); MPI_Abort(MPI_COMM_WORLD, 1); exit(1); From fe5d6b154a8a7130722d14a734b714180bbeb838 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 17 Feb 2025 23:42:04 -0500 Subject: [PATCH 021/113] simplify building of mini TOC at the top, renumber and reformat block 22 --- doc/src/Errors_details.rst | 51 ++++++++++++++------------------------ 1 file changed, 19 insertions(+), 32 deletions(-) diff --git a/doc/src/Errors_details.rst b/doc/src/Errors_details.rst index c82a5498bb..e166a38c4e 100644 --- a/doc/src/Errors_details.rst +++ b/doc/src/Errors_details.rst @@ -8,19 +8,7 @@ not the exact cause, or where the explanation needs to be more detailed than what can be fit into a message printed by the program. The following are discussions of such cases. -- :ref:`Unknown identifier in data file ` -- :ref:`Incorrect format in ... section of data file ` -- :ref:`Illegal variable command: expected X arguments but found Y ` -- :ref:`Out of range atoms - cannot compute ... ` -- :ref:`Lost atoms ... ` -- :ref:`Too many neighbor bins ` -- :ref:`Unrecognized pair style ... is part of ... package which is not enabled in this LAMMPS binary ` -- :ref:`Cannot use neighbor bins - box size \<\< cutoff ` -- :ref:`Domain too large for neighbor bins ` -- :ref:`Incorrect args for pair coefficients (also bond/angle/dihedral/improper coefficients) ` -- :ref:`Molecule topology/atom exceeds system topology/atom ` -- :ref:`Molecule topology type exceeds system topology type ` -- :ref:`Molecule attributes do not match system attributes ` +.. contents:: ------ @@ -420,29 +408,28 @@ different arguments. This error message might also require a close look at other LAMMPS input files that are read in by the input script, such as data files or restart files. -.. _err0021: +.. _err0022: Energy was not tallied on needed timestep (also virial, per-atom energy, per-atom virial) ----------------------------------------------------------------------------------------- -This error is generated when LAMMPS attempts to access an out-of-date -or non-existent energy, pressure, or virial. -For efficiency reasons, -LAMMPS does *not* calculate these quantities when the forces are calculated -on every timestep or iteration. Global quantities are only calculated -when they are needed for :doc:`thermo ` output (at the beginning, end, -and at regular intervals specified by the :doc:`thermo ` command). Similarly, -per-atom quantities are only calculated if they are needed to write per-atom -energy or virial to a dump file. -This system works fine for simple input scripts. -However, the many user-specified `variable`, `fix`, and `compute` commands -that LAMMPS provides make it difficult to anticipate when a quantity will -be requested. In some use cases, LAMMPS will figure out that a quantity is needed -and arrange for it to be calculated on that timestep e.g. if it is requested by -:doc:`fix ave/time ` or similar commands. -If that fails, it can be detected by a mismatch -between the current timestep and when a quantity was last calculated, -in which case an error message of this type is generated. +This error is generated when LAMMPS attempts to access an out-of-date or +non-existent energy, pressure, or virial. For efficiency reasons, +LAMMPS does *not* calculate these quantities when the forces are +calculated on every timestep or iteration. Global quantities are only +calculated when they are needed for :doc:`thermo ` output +(at the beginning, end, and at regular intervals specified by the +:doc:`thermo ` command). Similarly, per-atom quantities are only +calculated if they are needed to write per-atom energy or virial to a +dump file. This system works fine for simple input scripts. However, +the many user-specified `variable`, `fix`, and `compute` commands that +LAMMPS provides make it difficult to anticipate when a quantity will be +requested. In some use cases, LAMMPS will figure out that a quantity is +needed and arrange for it to be calculated on that timestep e.g. if it +is requested by :doc:`fix ave/time ` or similar commands. +If that fails, it can be detected by a mismatch between the current +timestep and when a quantity was last calculated, in which case an error +message of this type is generated. The most common cause of this type of error is requesting a quantity before the start of the simulation. From 0e07eab97f9779d4e2430f2ecf0617e339a0216d Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 17 Feb 2025 23:50:41 -0500 Subject: [PATCH 022/113] add some calls to utils::errorurl(22) --- src/BOCS/compute_pressure_bocs.cpp | 4 ++-- src/DIELECTRIC/compute_efield_atom.cpp | 2 +- src/EXTRA-COMPUTE/compute_ti.cpp | 2 +- src/REPLICA/compute_pressure_alchemy.cpp | 4 ++-- src/REPLICA/compute_pressure_grem.cpp | 4 ++-- src/TALLY/compute_force_tally.cpp | 4 ++-- src/TALLY/compute_heat_flux_tally.cpp | 2 +- src/TALLY/compute_heat_flux_virial_tally.cpp | 4 ++-- src/TALLY/compute_pe_mol_tally.cpp | 2 +- src/TALLY/compute_pe_tally.cpp | 4 ++-- src/TALLY/compute_stress_tally.cpp | 4 ++-- src/UEF/compute_pressure_uef.cpp | 2 +- src/compute_angle.cpp | 2 +- src/compute_bond.cpp | 2 +- src/compute_centroid_stress_atom.cpp | 2 +- src/compute_dihedral.cpp | 2 +- src/compute_improper.cpp | 2 +- src/compute_pair.cpp | 6 ++++-- src/compute_pe.cpp | 2 +- src/compute_pe_atom.cpp | 2 +- src/compute_pressure.cpp | 4 ++-- src/compute_stress_atom.cpp | 2 +- src/thermo.cpp | 5 +++-- 23 files changed, 36 insertions(+), 33 deletions(-) diff --git a/src/BOCS/compute_pressure_bocs.cpp b/src/BOCS/compute_pressure_bocs.cpp index 16d6c91a1f..12ca17093f 100644 --- a/src/BOCS/compute_pressure_bocs.cpp +++ b/src/BOCS/compute_pressure_bocs.cpp @@ -293,7 +293,7 @@ double ComputePressureBocs::compute_scalar() { invoked_scalar = update->ntimestep; if (update->vflag_global != invoked_scalar) - error->all(FLERR,"Virial was not tallied on needed timestep"); + error->all(FLERR, Error::NOLASTLINE, "Virial was not tallied on needed timestep{}", utils::errorurl(22)); // invoke temperature if it hasn't been already @@ -354,7 +354,7 @@ void ComputePressureBocs::compute_vector() { invoked_vector = update->ntimestep; if (update->vflag_global != invoked_vector) - error->all(FLERR,"Virial was not tallied on needed timestep"); + error->all(FLERR, Error::NOLASTLINE, "Virial was not tallied on needed timestep{}", utils::errorurl(22)); if (force->kspace && kspace_virial && force->kspace->scalar_pressure_flag) error->all(FLERR,"Must use 'kspace_modify pressure/scalar no' for " diff --git a/src/DIELECTRIC/compute_efield_atom.cpp b/src/DIELECTRIC/compute_efield_atom.cpp index 5e847a2a28..78688e5c0a 100644 --- a/src/DIELECTRIC/compute_efield_atom.cpp +++ b/src/DIELECTRIC/compute_efield_atom.cpp @@ -133,7 +133,7 @@ void ComputeEfieldAtom::compute_peratom() invoked_peratom = update->ntimestep; if (update->vflag_atom != invoked_peratom) - error->all(FLERR, "Per-atom virial was not tallied on needed timestep"); + error->all(FLERR, Error::NOLASTLINE, "Per-atom virial was not tallied on needed timestep{}", utils::errorurl(22)); // grow local stress array if necessary // needs to be atom->nmax in length diff --git a/src/EXTRA-COMPUTE/compute_ti.cpp b/src/EXTRA-COMPUTE/compute_ti.cpp index d405ba86e9..187ed953ef 100644 --- a/src/EXTRA-COMPUTE/compute_ti.cpp +++ b/src/EXTRA-COMPUTE/compute_ti.cpp @@ -154,7 +154,7 @@ double ComputeTI::compute_scalar() invoked_scalar = update->ntimestep; if (update->eflag_global != invoked_scalar) - error->all(FLERR,"Energy was not tallied on needed timestep"); + error->all(FLERR, Error::NOLASTLINE, "Energy was not tallied on needed timestep{}", utils::errorurl(22)); const int nlocal = atom->nlocal; const int * const type = atom->type; diff --git a/src/REPLICA/compute_pressure_alchemy.cpp b/src/REPLICA/compute_pressure_alchemy.cpp index bad2785fb8..e91860445a 100644 --- a/src/REPLICA/compute_pressure_alchemy.cpp +++ b/src/REPLICA/compute_pressure_alchemy.cpp @@ -72,7 +72,7 @@ double ComputePressureAlchemy::compute_scalar() { invoked_scalar = update->ntimestep; if (update->vflag_global != invoked_scalar) - error->all(FLERR, "Virial was not tallied on needed timestep"); + error->all(FLERR, Error::NOLASTLINE, "Virial was not tallied on needed timestep{}", utils::errorurl(22)); compute_vector(); @@ -92,7 +92,7 @@ void ComputePressureAlchemy::compute_vector() { invoked_vector = update->ntimestep; if (update->vflag_global != invoked_vector) - error->all(FLERR, "Virial was not tallied on needed timestep"); + error->all(FLERR, Error::NOLASTLINE, "Virial was not tallied on needed timestep{}", utils::errorurl(22)); int dim = 0; double *pressure = (double *) fix->extract("pressure", dim); diff --git a/src/REPLICA/compute_pressure_grem.cpp b/src/REPLICA/compute_pressure_grem.cpp index 50790ead2e..4fbef504dc 100644 --- a/src/REPLICA/compute_pressure_grem.cpp +++ b/src/REPLICA/compute_pressure_grem.cpp @@ -66,7 +66,7 @@ double ComputePressureGrem::compute_scalar() { invoked_scalar = update->ntimestep; if (update->vflag_global != invoked_scalar) - error->all(FLERR,"Virial was not tallied on needed timestep"); + error->all(FLERR, Error::NOLASTLINE, "Virial was not tallied on needed timestep{}", utils::errorurl(22)); // invoke temperature if it hasn't been already @@ -107,7 +107,7 @@ void ComputePressureGrem::compute_vector() { invoked_vector = update->ntimestep; if (update->vflag_global != invoked_vector) - error->all(FLERR,"Virial was not tallied on needed timestep"); + error->all(FLERR, Error::NOLASTLINE, "Virial was not tallied on needed timestep{}", utils::errorurl(22)); if (force->kspace && kspace_virial && force->kspace->scalar_pressure_flag) error->all(FLERR,"Must use 'kspace_modify pressure/scalar no' for " diff --git a/src/TALLY/compute_force_tally.cpp b/src/TALLY/compute_force_tally.cpp index e2243e02a7..6b09cac785 100644 --- a/src/TALLY/compute_force_tally.cpp +++ b/src/TALLY/compute_force_tally.cpp @@ -179,7 +179,7 @@ double ComputeForceTally::compute_scalar() { invoked_scalar = update->ntimestep; if ((did_setup != invoked_scalar) || (update->eflag_global != invoked_scalar)) - error->all(FLERR, "Stress was not tallied on needed timestep"); + error->all(FLERR, Error::NOLASTLINE, "Stress was not tallied on needed timestep{}", utils::errorurl(22)); if ((comm->me == 0) && !force->pair->did_tally_callback()) error->warning(FLERR, "Stress was not tallied by pair style"); @@ -198,7 +198,7 @@ void ComputeForceTally::compute_peratom() { invoked_peratom = update->ntimestep; if ((did_setup != invoked_peratom) || (update->eflag_global != invoked_peratom)) - error->all(FLERR, "Stress was not tallied on needed timestep"); + error->all(FLERR, Error::NOLASTLINE, "Stress was not tallied on needed timestep{}", utils::errorurl(22)); if ((comm->me == 0) && !force->pair->did_tally_callback()) error->warning(FLERR, "Stress was not tallied by pair style"); diff --git a/src/TALLY/compute_heat_flux_tally.cpp b/src/TALLY/compute_heat_flux_tally.cpp index 47b9fb5681..65b66db7d0 100644 --- a/src/TALLY/compute_heat_flux_tally.cpp +++ b/src/TALLY/compute_heat_flux_tally.cpp @@ -205,7 +205,7 @@ void ComputeHeatFluxTally::compute_vector() { invoked_vector = update->ntimestep; if ((did_setup != invoked_vector) || (update->eflag_global != invoked_vector)) - error->all(FLERR, "Stress was not tallied on needed timestep"); + error->all(FLERR, Error::NOLASTLINE, "Stress was not tallied on needed timestep{}", utils::errorurl(22)); if ((comm->me == 0) && !force->pair->did_tally_callback()) error->warning(FLERR, "Stress was not tallied by pair style"); diff --git a/src/TALLY/compute_heat_flux_virial_tally.cpp b/src/TALLY/compute_heat_flux_virial_tally.cpp index 7e4b27f361..a87732c15e 100644 --- a/src/TALLY/compute_heat_flux_virial_tally.cpp +++ b/src/TALLY/compute_heat_flux_virial_tally.cpp @@ -191,7 +191,7 @@ double ComputeHeatFluxVirialTally::compute_scalar() invoked_scalar = update->ntimestep; if ((did_setup != invoked_scalar) || (update->eflag_global != invoked_scalar)) - error->all(FLERR, "Stress was not tallied on needed timestep"); + error->all(FLERR, Error::NOLASTLINE, "Stress was not tallied on needed timestep{}", utils::errorurl(22)); if ((comm->me == 0) && !force->pair->did_tally_callback()) error->warning(FLERR, "Stress was not tallied by pair style"); @@ -213,7 +213,7 @@ void ComputeHeatFluxVirialTally::compute_peratom() { invoked_peratom = update->ntimestep; if ((did_setup != invoked_peratom) || (update->eflag_global != invoked_peratom)) - error->all(FLERR, "Stress was not tallied on needed timestep"); + error->all(FLERR, Error::NOLASTLINE, "Stress was not tallied on needed timestep{}", utils::errorurl(22)); if ((comm->me == 0) && !force->pair->did_tally_callback()) error->warning(FLERR, "Stress was not tallied by pair style"); diff --git a/src/TALLY/compute_pe_mol_tally.cpp b/src/TALLY/compute_pe_mol_tally.cpp index 66e9972464..e5ddb57568 100644 --- a/src/TALLY/compute_pe_mol_tally.cpp +++ b/src/TALLY/compute_pe_mol_tally.cpp @@ -126,7 +126,7 @@ void ComputePEMolTally::compute_vector() { invoked_vector = update->ntimestep; if ((did_setup != invoked_vector) || (update->eflag_global != invoked_vector)) - error->all(FLERR, "Energy was not tallied on needed timestep"); + error->all(FLERR, Error::NOLASTLINE, "Energy was not tallied on needed timestep{}", utils::errorurl(22)); if ((comm->me == 0) && !force->pair->did_tally_callback()) error->warning(FLERR, "Energy was not tallied by pair style"); diff --git a/src/TALLY/compute_pe_tally.cpp b/src/TALLY/compute_pe_tally.cpp index c2dd133016..d77cfe2646 100644 --- a/src/TALLY/compute_pe_tally.cpp +++ b/src/TALLY/compute_pe_tally.cpp @@ -167,7 +167,7 @@ double ComputePETally::compute_scalar() { invoked_scalar = update->ntimestep; if ((did_setup != invoked_scalar) || (update->eflag_global != invoked_scalar)) - error->all(FLERR, "Energy was not tallied on needed timestep"); + error->all(FLERR, Error::NOLASTLINE, "Energy was not tallied on needed timestep{}", utils::errorurl(22)); if ((comm->me == 0) && !force->pair->did_tally_callback()) error->warning(FLERR, "Energy was not tallied by pair style"); @@ -186,7 +186,7 @@ void ComputePETally::compute_peratom() { invoked_peratom = update->ntimestep; if ((did_setup != invoked_peratom) || (update->eflag_global != invoked_peratom)) - error->all(FLERR, "Energy was not tallied on needed timestep"); + error->all(FLERR, Error::NOLASTLINE, "Energy was not tallied on needed timestep{}", utils::errorurl(22)); if ((comm->me == 0) && !force->pair->did_tally_callback()) error->warning(FLERR, "Energy was not tallied by pair style"); diff --git a/src/TALLY/compute_stress_tally.cpp b/src/TALLY/compute_stress_tally.cpp index b5b54c495c..c16e046dcf 100644 --- a/src/TALLY/compute_stress_tally.cpp +++ b/src/TALLY/compute_stress_tally.cpp @@ -202,7 +202,7 @@ double ComputeStressTally::compute_scalar() { invoked_scalar = update->ntimestep; if ((did_setup != invoked_scalar) || (update->eflag_global != invoked_scalar)) - error->all(FLERR, "Stress was not tallied on needed timestep"); + error->all(FLERR, Error::NOLASTLINE, "Stress was not tallied on needed timestep{}", utils::errorurl(22)); if ((comm->me == 0) && !force->pair->did_tally_callback()) error->warning(FLERR, "Stress was not tallied by pair style"); @@ -225,7 +225,7 @@ void ComputeStressTally::compute_peratom() { invoked_peratom = update->ntimestep; if ((did_setup != invoked_peratom) || (update->eflag_global != invoked_peratom)) - error->all(FLERR, "Stress was not tallied on needed timestep"); + error->all(FLERR, Error::NOLASTLINE, "Stress was not tallied on needed timestep{}", utils::errorurl(22)); if ((comm->me == 0) && !force->pair->did_tally_callback()) error->warning(FLERR, "Stress was not tallied by pair style"); diff --git a/src/UEF/compute_pressure_uef.cpp b/src/UEF/compute_pressure_uef.cpp index 16fe6137bf..040fe3df03 100644 --- a/src/UEF/compute_pressure_uef.cpp +++ b/src/UEF/compute_pressure_uef.cpp @@ -104,7 +104,7 @@ void ComputePressureUef::compute_vector() { invoked_vector = update->ntimestep; if (update->vflag_global != invoked_vector) - error->all(FLERR,"Virial was not tallied on needed timestep"); + error->all(FLERR, Error::NOLASTLINE, "Virial was not tallied on needed timestep{}", utils::errorurl(22)); if (force->kspace && kspace_virial && force->kspace->scalar_pressure_flag) error->all(FLERR,"Must use 'kspace_modify pressure/scalar no' for " diff --git a/src/compute_angle.cpp b/src/compute_angle.cpp index 71c13ebc7f..9fdd20513e 100644 --- a/src/compute_angle.cpp +++ b/src/compute_angle.cpp @@ -69,7 +69,7 @@ void ComputeAngle::compute_vector() { invoked_vector = update->ntimestep; if (update->eflag_global != invoked_vector) - error->all(FLERR, "Energy was not tallied on needed timestep"); + error->all(FLERR, Error::NOLASTLINE, "Energy was not tallied on needed timestep{}", utils::errorurl(22)); for (int i = 0; i < nsub; i++) emine[i] = angle->styles[i]->energy; diff --git a/src/compute_bond.cpp b/src/compute_bond.cpp index 8070c13231..a88b95d6c7 100644 --- a/src/compute_bond.cpp +++ b/src/compute_bond.cpp @@ -68,7 +68,7 @@ void ComputeBond::compute_vector() { invoked_vector = update->ntimestep; if (update->eflag_global != invoked_vector) - error->all(FLERR, "Energy was not tallied on needed timestep"); + error->all(FLERR, Error::NOLASTLINE, "Energy was not tallied on needed timestep{}", utils::errorurl(22)); for (int i = 0; i < nsub; i++) emine[i] = bond->styles[i]->energy; diff --git a/src/compute_centroid_stress_atom.cpp b/src/compute_centroid_stress_atom.cpp index c6854737a8..682e7a5e63 100644 --- a/src/compute_centroid_stress_atom.cpp +++ b/src/compute_centroid_stress_atom.cpp @@ -210,7 +210,7 @@ void ComputeCentroidStressAtom::compute_peratom() invoked_peratom = update->ntimestep; if (update->vflag_atom != invoked_peratom) - error->all(FLERR, "Per-atom virial was not tallied on needed timestep"); + error->all(FLERR, Error::NOLASTLINE, "Per-atom virial was not tallied on needed timestep{}", utils::errorurl(22)); // grow local stress array if necessary // needs to be atom->nmax in length diff --git a/src/compute_dihedral.cpp b/src/compute_dihedral.cpp index 39d5179d30..29c15e2917 100644 --- a/src/compute_dihedral.cpp +++ b/src/compute_dihedral.cpp @@ -69,7 +69,7 @@ void ComputeDihedral::compute_vector() { invoked_vector = update->ntimestep; if (update->eflag_global != invoked_vector) - error->all(FLERR, "Energy was not tallied on needed timestep"); + error->all(FLERR, Error::NOLASTLINE, "Energy was not tallied on needed timestep{}", utils::errorurl(22)); for (int i = 0; i < nsub; i++) emine[i] = dihedral->styles[i]->energy; diff --git a/src/compute_improper.cpp b/src/compute_improper.cpp index 36a38a48f8..9643a9d499 100644 --- a/src/compute_improper.cpp +++ b/src/compute_improper.cpp @@ -69,7 +69,7 @@ void ComputeImproper::compute_vector() { invoked_vector = update->ntimestep; if (update->eflag_global != invoked_vector) - error->all(FLERR, "Energy was not tallied on needed timestep"); + error->all(FLERR, Error::NOLASTLINE, "Energy was not tallied on needed timestep{}", utils::errorurl(22)); for (int i = 0; i < nsub; i++) emine[i] = improper->styles[i]->energy; diff --git a/src/compute_pair.cpp b/src/compute_pair.cpp index 1cb22a006f..2bf5ef6e83 100644 --- a/src/compute_pair.cpp +++ b/src/compute_pair.cpp @@ -113,7 +113,8 @@ double ComputePair::compute_scalar() { invoked_scalar = update->ntimestep; if (update->eflag_global != invoked_scalar) - error->all(FLERR, "Energy was not tallied on needed timestep"); + error->all(FLERR, Error::NOLASTLINE, "Energy was not tallied on needed timestep{}", + utils::errorurl(22)); double eng; if (evalue == EPAIR) @@ -133,7 +134,8 @@ void ComputePair::compute_vector() { invoked_vector = update->ntimestep; if (update->eflag_global != invoked_vector) - error->all(FLERR, "Energy was not tallied on needed timestep"); + error->all(FLERR, Error::NOLASTLINE, "Energy was not tallied on needed timestep{}", + utils::errorurl(22)); for (int i = 0; i < npair; i++) one[i] = pair->pvector[i]; MPI_Allreduce(one, vector, npair, MPI_DOUBLE, MPI_SUM, world); diff --git a/src/compute_pe.cpp b/src/compute_pe.cpp index f4207408f9..c430add751 100644 --- a/src/compute_pe.cpp +++ b/src/compute_pe.cpp @@ -85,7 +85,7 @@ double ComputePE::compute_scalar() { invoked_scalar = update->ntimestep; if (update->eflag_global != invoked_scalar) - error->all(FLERR, "Energy was not tallied on needed timestep"); + error->all(FLERR, Error::NOLASTLINE, "Energy was not tallied on needed timestep{}", utils::errorurl(22)); double one = 0.0; if (pairflag && force->pair) one += force->pair->eng_vdwl + force->pair->eng_coul; diff --git a/src/compute_pe_atom.cpp b/src/compute_pe_atom.cpp index 2e1973ceca..05f35ca9a6 100644 --- a/src/compute_pe_atom.cpp +++ b/src/compute_pe_atom.cpp @@ -94,7 +94,7 @@ void ComputePEAtom::compute_peratom() invoked_peratom = update->ntimestep; if (update->eflag_atom != invoked_peratom) - error->all(FLERR, "Per-atom energy was not tallied on needed timestep"); + error->all(FLERR, Error::NOLASTLINE, "Per-atom energy was not tallied on needed timestep{}", utils::errorurl(22)); // grow local energy array if necessary // needs to be atom->nmax in length diff --git a/src/compute_pressure.cpp b/src/compute_pressure.cpp index 65cb612390..57a884bc3e 100644 --- a/src/compute_pressure.cpp +++ b/src/compute_pressure.cpp @@ -235,7 +235,7 @@ double ComputePressure::compute_scalar() { invoked_scalar = update->ntimestep; if (update->vflag_global != invoked_scalar) - error->all(FLERR,"Virial was not tallied on needed timestep"); + error->all(FLERR, Error::NOLASTLINE, "Virial was not tallied on needed timestep{}", utils::errorurl(22)); // invoke temperature if it hasn't been already @@ -274,7 +274,7 @@ void ComputePressure::compute_vector() { invoked_vector = update->ntimestep; if (update->vflag_global != invoked_vector) - error->all(FLERR,"Virial was not tallied on needed timestep"); + error->all(FLERR, Error::NOLASTLINE, "Virial was not tallied on needed timestep{}", utils::errorurl(22)); if (force->kspace && kspace_virial && force->kspace->scalar_pressure_flag) error->all(FLERR,"Must use 'kspace_modify pressure/scalar no' for " diff --git a/src/compute_stress_atom.cpp b/src/compute_stress_atom.cpp index 3560570163..a9037ae1a8 100644 --- a/src/compute_stress_atom.cpp +++ b/src/compute_stress_atom.cpp @@ -142,7 +142,7 @@ void ComputeStressAtom::compute_peratom() invoked_peratom = update->ntimestep; if (update->vflag_atom != invoked_peratom) - error->all(FLERR, "Per-atom virial was not tallied on needed timestep"); + error->all(FLERR, Error::NOLASTLINE, "Per-atom virial was not tallied on needed timestep{}", utils::errorurl(22)); // grow local stress array if necessary // needs to be atom->nmax in length diff --git a/src/thermo.cpp b/src/thermo.cpp index c7e53f8c85..ca60b48687 100644 --- a/src/thermo.cpp +++ b/src/thermo.cpp @@ -1220,7 +1220,7 @@ void Thermo::check_temp(const std::string &keyword) void Thermo::check_pe(const std::string &keyword) { if (update->eflag_global != update->ntimestep) - error->all(FLERR, "Energy was not tallied on needed timestep"); + error->all(FLERR, Error::NOLASTLINE, "Energy was not tallied on needed timestep{}", utils::errorurl(22)); if (!pe) error->all(FLERR, "Thermo keyword {} in variable requires thermo to use/init potential energy", keyword); @@ -1419,7 +1419,8 @@ int Thermo::evaluate_keyword(const std::string &word, double *answer) } else if (word == "etail") { if (update->eflag_global != update->ntimestep) - error->all(FLERR, "Energy was not tallied on needed timestep for thermo keyword etail"); + error->all(FLERR, Error::NOLASTLINE, "Energy was not tallied on needed timestep for thermo " + "keyword etail{}", utils::errorurl(22)); compute_etail(); } else if (word == "enthalpy") { From 3138f62ac8cb999db84ab5c3b83abc20d436bc28 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 18 Feb 2025 00:26:15 -0500 Subject: [PATCH 023/113] renumber error 30 to 5 to match list of errors. Update error calls --- doc/src/Errors_details.rst | 42 ++++++++++++++-------------- src/KOKKOS/neigh_bond_kokkos.cpp | 47 ++++++++++++++++---------------- src/ntopo_angle_all.cpp | 4 +-- src/ntopo_angle_partial.cpp | 4 +-- src/ntopo_angle_template.cpp | 4 +-- src/ntopo_bond_all.cpp | 4 +-- src/ntopo_bond_partial.cpp | 4 +-- src/ntopo_bond_template.cpp | 4 +-- src/ntopo_dihedral_all.cpp | 4 +-- src/ntopo_dihedral_partial.cpp | 4 +-- src/ntopo_dihedral_template.cpp | 4 +-- src/ntopo_improper_all.cpp | 4 +-- src/ntopo_improper_partial.cpp | 4 +-- src/ntopo_improper_template.cpp | 4 +-- 14 files changed, 69 insertions(+), 68 deletions(-) diff --git a/doc/src/Errors_details.rst b/doc/src/Errors_details.rst index e166a38c4e..32ebafbae2 100644 --- a/doc/src/Errors_details.rst +++ b/doc/src/Errors_details.rst @@ -299,6 +299,27 @@ help to temporarily use a cutoff-Coulomb pair style and no kspace style until the system has somewhat equilibrated and then switch to the long-range solver. +.. _err0005: + +Bond (or angle, dihedral, or improper) atoms missing +---------------------------------------------------- + +The second atom needed to compute a particular bond (or the third or fourth +atom for angle, dihedral, or improper) is missing on the indicated timestep +and processor. Typically, this is because the two bonded atoms have become +too far apart relative to the communication cutoff distance for ghost atoms. +Typically, the communication cutoff is set by the pair cutoff, but it can +be manually adjusted using :doc:`comm_modify ` to accommodate +larger distances between topologically connected atoms at the cost of increased +communication and more ghost atoms. However, missing bond atoms may also +indicate unstable dynamics caused the atoms blow apart such that increasing +the communication distance will not solve the underlying issue. + +If the simulation has open boundary conditions where atoms can leave, +potentially at different times than other atoms they are bonded to, this +error can be converted to a warning or turned off using the *lost/bond* +keyword in the :doc:`thermo_modify ` command. + .. _err0008: Lost atoms ... @@ -500,24 +521,3 @@ example, are usually not a per-atom property, but defined through the atom type. Thus it would not be required to have a Masses section and the included data would be ignored. LAMMPS prints this warning to inform about this case. - -.. _err0030: - -Bond (or angle, dihedral, or improper) atoms missing ----------------------------------------------------- - -The second atom needed to compute a particular bond (or the third or fourth -atom for angle, dihedral, or improper) is missing on the indicated timestep -and processor. Typically, this is because the two bonded atoms have become -too far apart relative to the communication cutoff distance for ghost atoms. -Typically, the communication cutoff is set by the pair cutoff, but it can -be manually adjusted using :doc:`comm_modify ` to accommodate -larger distances between topologically connected atoms at the cost of increased -communication and more ghost atoms. However, missing bond atoms may also -indicate unstable dynamics caused the atoms blow apart such that increasing -the communication distance will not solve the underlying issue. - -If the simulation has open boundary conditions where atoms can leave, -potentially at different times than other atoms they are bonded to, this -error can be converted to a warning or turned off using the *lost/bond* -keyword in the :doc:`thermo_modify ` command. diff --git a/src/KOKKOS/neigh_bond_kokkos.cpp b/src/KOKKOS/neigh_bond_kokkos.cpp index de68dfbf99..840e0bff55 100644 --- a/src/KOKKOS/neigh_bond_kokkos.cpp +++ b/src/KOKKOS/neigh_bond_kokkos.cpp @@ -259,7 +259,8 @@ void NeighBondKokkos::bond_all() } while (h_fail_flag()); if (nmissing && lostbond == Thermo::ERROR) - error->one(FLERR,"Bond atoms missing at step {}" + utils::errorurl(30), update->ntimestep); + error->one(FLERR, Error::NOLASTLINE, "Bond atoms missing at step {}" + utils::errorurl(5), + update->ntimestep); if (neighbor->cluster_check) bond_check(); if (lostbond == Thermo::IGNORE) return; @@ -267,7 +268,7 @@ void NeighBondKokkos::bond_all() int all; MPI_Allreduce(&nmissing,&all,1,MPI_INT,MPI_SUM,world); if (all && me == 0) - error->warning(FLERR,"Bond atoms missing at step {}" + utils::errorurl(30), update->ntimestep); + error->warning(FLERR,"Bond atoms missing at step {}" + utils::errorurl(5), update->ntimestep); k_bondlist.modify(); } @@ -300,7 +301,7 @@ void NeighBondKokkos::operator()(TagNeighBondBondAll, const int &i, template void NeighBondKokkos::bond_template() { - error->all(FLERR,"Cannot (yet) use molecular templates with Kokkos"); + error->all(FLERR, Error::NOLASTLINE, "Cannot (yet) use molecular templates with Kokkos"); } /* ---------------------------------------------------------------------- */ @@ -338,7 +339,7 @@ void NeighBondKokkos::bond_partial() } while (h_fail_flag()); if (nmissing && lostbond == Thermo::ERROR) - error->one(FLERR,"Bond atoms missing at step {}" + utils::errorurl(30), update->ntimestep); + error->one(FLERR, Error::NOLASTLINE, "Bond atoms missing at step {}" + utils::errorurl(5), update->ntimestep); if (neighbor->cluster_check) bond_check(); if (lostbond == Thermo::IGNORE) return; @@ -346,7 +347,7 @@ void NeighBondKokkos::bond_partial() int all; MPI_Allreduce(&nmissing,&all,1,MPI_INT,MPI_SUM,world); if (all && me == 0) - error->warning(FLERR,"Bond atoms missing at step {}" + utils::errorurl(30), update->ntimestep); + error->warning(FLERR, "Bond atoms missing at step {}" + utils::errorurl(5), update->ntimestep); k_bondlist.modify(); } @@ -389,7 +390,7 @@ void NeighBondKokkos::bond_check() int flag_all; MPI_Allreduce(&flag,&flag_all,1,MPI_INT,MPI_SUM,world); - if (flag_all) error->all(FLERR,"Bond extent > half of periodic box length"); + if (flag_all) error->all(FLERR, Error::NOLASTLINE, "Bond extent > half of periodic box length"); } template @@ -443,7 +444,7 @@ void NeighBondKokkos::angle_all() } while (h_fail_flag()); if (nmissing && lostbond == Thermo::ERROR) - error->one(FLERR,"Angle atoms missing at step {}" + utils::errorurl(30), update->ntimestep); + error->one(FLERR, Error::NOLASTLINE, "Angle atoms missing at step {}" + utils::errorurl(5), update->ntimestep); if (neighbor->cluster_check) angle_check(); if (lostbond == Thermo::IGNORE) return; @@ -451,7 +452,7 @@ void NeighBondKokkos::angle_all() int all; MPI_Allreduce(&nmissing,&all,1,MPI_INT,MPI_SUM,world); if (all && (me == 0)) - error->warning(FLERR,"Angle atoms missing at step {}" + utils::errorurl(30), update->ntimestep); + error->warning(FLERR, "Angle atoms missing at step {}" + utils::errorurl(5), update->ntimestep); k_anglelist.modify(); } @@ -489,7 +490,7 @@ void NeighBondKokkos::operator()(TagNeighBondAngleAll, const int &i, template void NeighBondKokkos::angle_template() { - error->all(FLERR,"Cannot (yet) use molecular templates with Kokkos"); + error->all(FLERR, Error::NOLASTLINE, "Cannot (yet) use molecular templates with Kokkos"); } /* ---------------------------------------------------------------------- */ @@ -529,7 +530,7 @@ void NeighBondKokkos::angle_partial() } while (h_fail_flag()); if (nmissing && lostbond == Thermo::ERROR) - error->one(FLERR,"Angle atoms missing at step {}" + utils::errorurl(30), update->ntimestep); + error->one(FLERR, Error::NOLASTLINE, "Angle atoms missing at step {}" + utils::errorurl(5), update->ntimestep); if (neighbor->cluster_check) angle_check(); if (lostbond == Thermo::IGNORE) return; @@ -537,7 +538,7 @@ void NeighBondKokkos::angle_partial() int all; MPI_Allreduce(&nmissing,&all,1,MPI_INT,MPI_SUM,world); if (all && (me == 0)) - error->warning(FLERR,"Angle atoms missing at step {}" + utils::errorurl(30), update->ntimestep); + error->warning(FLERR, "Angle atoms missing at step {}" + utils::errorurl(5), update->ntimestep); k_anglelist.modify(); } @@ -588,7 +589,7 @@ void NeighBondKokkos::angle_check() int flag_all; MPI_Allreduce(&flag,&flag_all,1,MPI_INT,MPI_SUM,world); - if (flag_all) error->all(FLERR,"Angle extent > half of periodic box length"); + if (flag_all) error->all(FLERR, Error::NOLASTLINE, "Angle extent > half of periodic box length"); } template @@ -654,7 +655,7 @@ void NeighBondKokkos::dihedral_all() } while (h_fail_flag()); if (nmissing && lostbond == Thermo::ERROR) - error->one(FLERR,"Dihedral atoms missing at step {}" + utils::errorurl(30), update->ntimestep); + error->one(FLERR, Error::NOLASTLINE, "Dihedral atoms missing at step {}" + utils::errorurl(5), update->ntimestep); if (neighbor->cluster_check) dihedral_check(neighbor->ndihedrallist,v_dihedrallist); if (lostbond == Thermo::IGNORE) return; @@ -662,7 +663,7 @@ void NeighBondKokkos::dihedral_all() int all; MPI_Allreduce(&nmissing,&all,1,MPI_INT,MPI_SUM,world); if (all && (me == 0)) - error->warning(FLERR,"Dihedral atoms missing at step {}" + utils::errorurl(30), update->ntimestep); + error->warning(FLERR, "Dihedral atoms missing at step {}" + utils::errorurl(5), update->ntimestep); k_dihedrallist.modify(); } @@ -704,7 +705,7 @@ void NeighBondKokkos::operator()(TagNeighBondDihedralAll, const int template void NeighBondKokkos::dihedral_template() { - error->all(FLERR,"Cannot (yet) use molecular templates with Kokkos"); + error->all(FLERR, Error::NOLASTLINE, "Cannot (yet) use molecular templates with Kokkos"); } /* ---------------------------------------------------------------------- */ @@ -745,7 +746,7 @@ void NeighBondKokkos::dihedral_partial() } while (h_fail_flag()); if (nmissing && lostbond == Thermo::ERROR) - error->one(FLERR,"Dihedral atoms missing at step {}" + utils::errorurl(30), update->ntimestep); + error->one(FLERR, Error::NOLASTLINE, "Dihedral atoms missing at step {}" + utils::errorurl(5), update->ntimestep); if (neighbor->cluster_check) dihedral_check(neighbor->ndihedrallist,v_dihedrallist); if (lostbond == Thermo::IGNORE) return; @@ -753,7 +754,7 @@ void NeighBondKokkos::dihedral_partial() int all; MPI_Allreduce(&nmissing,&all,1,MPI_INT,MPI_SUM,world); if (all && (me == 0)) - error->warning(FLERR,"Dihedral atoms missing at step {}" + utils::errorurl(30), update->ntimestep); + error->warning(FLERR, "Dihedral atoms missing at step {}" + utils::errorurl(5), update->ntimestep); k_dihedrallist.modify(); } @@ -810,7 +811,7 @@ void NeighBondKokkos::dihedral_check(int nlist, typename AT::t_int_2 int flag_all; MPI_Allreduce(&flag,&flag_all,1,MPI_INT,MPI_SUM,world); if (flag_all) - error->all(FLERR,"Dihedral/improper extent > half of periodic box length"); + error->all(FLERR, Error::NOLASTLINE, "Dihedral/improper extent > half of periodic box length"); } template @@ -892,7 +893,7 @@ void NeighBondKokkos::improper_all() } while (h_fail_flag()); if (nmissing && lostbond == Thermo::ERROR) - error->one(FLERR,"Improper atoms missing at step {}" + utils::errorurl(30), update->ntimestep); + error->one(FLERR, Error::NOLASTLINE, "Improper atoms missing at step {}" + utils::errorurl(5), update->ntimestep); if (neighbor->cluster_check) dihedral_check(neighbor->nimproperlist,v_improperlist); if (lostbond == Thermo::IGNORE) return; @@ -900,7 +901,7 @@ void NeighBondKokkos::improper_all() int all; MPI_Allreduce(&nmissing,&all,1,MPI_INT,MPI_SUM,world); if (all && (me == 0)) - error->warning(FLERR,"Improper atoms missing at step {}" + utils::errorurl(30), update->ntimestep); + error->warning(FLERR, "Improper atoms missing at step {}" + utils::errorurl(5), update->ntimestep); k_improperlist.modify(); } @@ -942,7 +943,7 @@ void NeighBondKokkos::operator()(TagNeighBondImproperAll, const int template void NeighBondKokkos::improper_template() { - error->all(FLERR,"Cannot (yet) use molecular templates with Kokkos"); + error->all(FLERR, Error::NOLASTLINE, "Cannot (yet) use molecular templates with Kokkos"); } /* ---------------------------------------------------------------------- */ @@ -983,7 +984,7 @@ void NeighBondKokkos::improper_partial() } while (h_fail_flag()); if (nmissing && lostbond == Thermo::ERROR) - error->one(FLERR,"Improper atoms missing at step {}" + utils::errorurl(30), update->ntimestep); + error->one(FLERR, Error::NOLASTLINE, "Improper atoms missing at step {}" + utils::errorurl(5), update->ntimestep); if (neighbor->cluster_check) dihedral_check(neighbor->nimproperlist,v_improperlist); if (lostbond == Thermo::IGNORE) return; @@ -991,7 +992,7 @@ void NeighBondKokkos::improper_partial() int all; MPI_Allreduce(&nmissing,&all,1,MPI_INT,MPI_SUM,world); if (all && (me == 0)) - error->warning(FLERR,"Improper atoms missing at step {}" + utils::errorurl(30), update->ntimestep); + error->warning(FLERR, "Improper atoms missing at step {}" + utils::errorurl(5), update->ntimestep); k_improperlist.modify(); } diff --git a/src/ntopo_angle_all.cpp b/src/ntopo_angle_all.cpp index 8e15a5e197..9c855eee36 100644 --- a/src/ntopo_angle_all.cpp +++ b/src/ntopo_angle_all.cpp @@ -59,7 +59,7 @@ void NTopoAngleAll::build() if (atom1 == -1 || atom2 == -1 || atom3 == -1) { nmissing++; if (lostbond == Thermo::ERROR) - error->one(FLERR, "Angle atoms {} {} {} missing on proc {} at step {}" + utils::errorurl(30), angle_atom1[i][m], + error->one(FLERR, Error::NOLASTLINE, "Angle atoms {} {} {} missing on proc {} at step {}" + utils::errorurl(5), angle_atom1[i][m], angle_atom2[i][m], angle_atom3[i][m], me, update->ntimestep); continue; } @@ -84,5 +84,5 @@ void NTopoAngleAll::build() int all; MPI_Allreduce(&nmissing, &all, 1, MPI_INT, MPI_SUM, world); - if (all && (me == 0)) error->warning(FLERR, "Angle atoms missing at step {}" + utils::errorurl(30), update->ntimestep); + if (all && (me == 0)) error->warning(FLERR, "Angle atoms missing at step {}" + utils::errorurl(5), update->ntimestep); } diff --git a/src/ntopo_angle_partial.cpp b/src/ntopo_angle_partial.cpp index 0d3d6d78d8..7d89e81376 100644 --- a/src/ntopo_angle_partial.cpp +++ b/src/ntopo_angle_partial.cpp @@ -60,7 +60,7 @@ void NTopoAnglePartial::build() if (atom1 == -1 || atom2 == -1 || atom3 == -1) { nmissing++; if (lostbond == Thermo::ERROR) - error->one(FLERR, "Angle atoms {} {} {} missing on proc {} at step {}" + utils::errorurl(30), angle_atom1[i][m], + error->one(FLERR, Error::NOLASTLINE, "Angle atoms {} {} {} missing on proc {} at step {}" + utils::errorurl(5), angle_atom1[i][m], angle_atom2[i][m], angle_atom3[i][m], me, update->ntimestep); continue; } @@ -85,5 +85,5 @@ void NTopoAnglePartial::build() int all; MPI_Allreduce(&nmissing, &all, 1, MPI_INT, MPI_SUM, world); - if (all && (me == 0)) error->warning(FLERR, "Angle atoms missing at step {}" + utils::errorurl(30), update->ntimestep); + if (all && (me == 0)) error->warning(FLERR, "Angle atoms missing at step {}" + utils::errorurl(5), update->ntimestep); } diff --git a/src/ntopo_angle_template.cpp b/src/ntopo_angle_template.cpp index 48e5f5eff6..60a6c86f37 100644 --- a/src/ntopo_angle_template.cpp +++ b/src/ntopo_angle_template.cpp @@ -77,7 +77,7 @@ void NTopoAngleTemplate::build() if (atom1 == -1 || atom2 == -1 || atom3 == -1) { nmissing++; if (lostbond == Thermo::ERROR) - error->one(FLERR, "Angle atoms {} {} {} missing on proc {} at step {}" + utils::errorurl(30), + error->one(FLERR, Error::NOLASTLINE, "Angle atoms {} {} {} missing on proc {} at step {}" + utils::errorurl(5), angle_atom1[iatom][m] + tagprev, angle_atom2[iatom][m] + tagprev, angle_atom3[iatom][m] + tagprev, me, update->ntimestep); continue; @@ -104,5 +104,5 @@ void NTopoAngleTemplate::build() int all; MPI_Allreduce(&nmissing, &all, 1, MPI_INT, MPI_SUM, world); - if (all && (me == 0)) error->warning(FLERR, "Angle atoms missing at step {}" + utils::errorurl(30), update->ntimestep); + if (all && (me == 0)) error->warning(FLERR, "Angle atoms missing at step {}" + utils::errorurl(5), update->ntimestep); } diff --git a/src/ntopo_bond_all.cpp b/src/ntopo_bond_all.cpp index c5d511fa1d..d90fe58eab 100644 --- a/src/ntopo_bond_all.cpp +++ b/src/ntopo_bond_all.cpp @@ -56,7 +56,7 @@ void NTopoBondAll::build() if (atom1 == -1) { nmissing++; if (lostbond == Thermo::ERROR) - error->one(FLERR, "Bond atoms {} {} missing on proc {} at step {}" + utils::errorurl(30), tag[i], + error->one(FLERR, Error::NOLASTLINE, "Bond atoms {} {} missing on proc {} at step {}" + utils::errorurl(5), tag[i], bond_atom[i][m], me, update->ntimestep); continue; } @@ -78,5 +78,5 @@ void NTopoBondAll::build() int all; MPI_Allreduce(&nmissing, &all, 1, MPI_INT, MPI_SUM, world); - if (all && (me == 0)) error->warning(FLERR, "Bond atoms missing at step {}" + utils::errorurl(30), update->ntimestep); + if (all && (me == 0)) error->warning(FLERR, "Bond atoms missing at step {}" + utils::errorurl(5), update->ntimestep); } diff --git a/src/ntopo_bond_partial.cpp b/src/ntopo_bond_partial.cpp index 2dc0b3c530..498d9ae3ac 100644 --- a/src/ntopo_bond_partial.cpp +++ b/src/ntopo_bond_partial.cpp @@ -57,7 +57,7 @@ void NTopoBondPartial::build() if (atom1 == -1) { nmissing++; if (lostbond == Thermo::ERROR) - error->one(FLERR, "Bond atoms {} {} missing on proc {} at step {}" + utils::errorurl(30), tag[i], + error->one(FLERR, Error::NOLASTLINE, "Bond atoms {} {} missing on proc {} at step {}" + utils::errorurl(5), tag[i], bond_atom[i][m], me, update->ntimestep); continue; } @@ -79,5 +79,5 @@ void NTopoBondPartial::build() int all; MPI_Allreduce(&nmissing, &all, 1, MPI_INT, MPI_SUM, world); - if (all && (me == 0)) error->warning(FLERR, "Bond atoms missing at step {}" + utils::errorurl(30), update->ntimestep); + if (all && (me == 0)) error->warning(FLERR, "Bond atoms missing at step {}" + utils::errorurl(5), update->ntimestep); } diff --git a/src/ntopo_bond_template.cpp b/src/ntopo_bond_template.cpp index a949fdae8e..5a6b1ad9df 100644 --- a/src/ntopo_bond_template.cpp +++ b/src/ntopo_bond_template.cpp @@ -73,7 +73,7 @@ void NTopoBondTemplate::build() if (atom1 == -1) { nmissing++; if (lostbond == Thermo::ERROR) - error->one(FLERR, "Bond atoms {} {} missing on proc {} at step {}" + utils::errorurl(30), tag[i], + error->one(FLERR, Error::NOLASTLINE, "Bond atoms {} {} missing on proc {} at step {}" + utils::errorurl(5), tag[i], bond_atom[iatom][m] + tagprev, me, update->ntimestep); continue; } @@ -96,5 +96,5 @@ void NTopoBondTemplate::build() int all; MPI_Allreduce(&nmissing, &all, 1, MPI_INT, MPI_SUM, world); - if (all && (me == 0)) error->warning(FLERR, "Bond atoms missing at step {}" + utils::errorurl(30), update->ntimestep); + if (all && (me == 0)) error->warning(FLERR, "Bond atoms missing at step {}" + utils::errorurl(5), update->ntimestep); } diff --git a/src/ntopo_dihedral_all.cpp b/src/ntopo_dihedral_all.cpp index 2d2f2bf289..f0c6f44c79 100644 --- a/src/ntopo_dihedral_all.cpp +++ b/src/ntopo_dihedral_all.cpp @@ -61,7 +61,7 @@ void NTopoDihedralAll::build() if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) { nmissing++; if (lostbond == Thermo::ERROR) - error->one(FLERR, "Dihedral atoms {} {} {} {} missing on proc {} at step {}" + utils::errorurl(30), + error->one(FLERR, Error::NOLASTLINE, "Dihedral atoms {} {} {} {} missing on proc {} at step {}" + utils::errorurl(5), dihedral_atom1[i][m], dihedral_atom2[i][m], dihedral_atom3[i][m], dihedral_atom4[i][m], me, update->ntimestep); continue; @@ -90,5 +90,5 @@ void NTopoDihedralAll::build() int all; MPI_Allreduce(&nmissing, &all, 1, MPI_INT, MPI_SUM, world); if (all && (me == 0)) - error->warning(FLERR, "Dihedral atoms missing at step {}" + utils::errorurl(30), update->ntimestep); + error->warning(FLERR, "Dihedral atoms missing at step {}" + utils::errorurl(5), update->ntimestep); } diff --git a/src/ntopo_dihedral_partial.cpp b/src/ntopo_dihedral_partial.cpp index 5437624b71..7ab254e423 100644 --- a/src/ntopo_dihedral_partial.cpp +++ b/src/ntopo_dihedral_partial.cpp @@ -62,7 +62,7 @@ void NTopoDihedralPartial::build() if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) { nmissing++; if (lostbond == Thermo::ERROR) - error->one(FLERR, "Dihedral atoms {} {} {} {} missing on proc {} at step {}" + utils::errorurl(30), + error->one(FLERR, Error::NOLASTLINE, "Dihedral atoms {} {} {} {} missing on proc {} at step {}" + utils::errorurl(5), dihedral_atom1[i][m], dihedral_atom2[i][m], dihedral_atom3[i][m], dihedral_atom4[i][m], me, update->ntimestep); continue; @@ -91,5 +91,5 @@ void NTopoDihedralPartial::build() int all; MPI_Allreduce(&nmissing, &all, 1, MPI_INT, MPI_SUM, world); if (all && (me == 0)) - error->warning(FLERR, "Dihedral atoms missing at step {}" + utils::errorurl(30), update->ntimestep); + error->warning(FLERR, "Dihedral atoms missing at step {}" + utils::errorurl(5), update->ntimestep); } diff --git a/src/ntopo_dihedral_template.cpp b/src/ntopo_dihedral_template.cpp index 89d4f202f8..5a4ee77ebc 100644 --- a/src/ntopo_dihedral_template.cpp +++ b/src/ntopo_dihedral_template.cpp @@ -78,7 +78,7 @@ void NTopoDihedralTemplate::build() if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) { nmissing++; if (lostbond == Thermo::ERROR) - error->one(FLERR, "Dihedral atoms {} {} {} {} missing on proc {} at step {}" + utils::errorurl(30), + error->one(FLERR, Error::NOLASTLINE, "Dihedral atoms {} {} {} {} missing on proc {} at step {}" + utils::errorurl(5), dihedral_atom1[iatom][m] + tagprev, dihedral_atom2[iatom][m] + tagprev, dihedral_atom3[iatom][m] + tagprev, dihedral_atom4[iatom][m] + tagprev, me, update->ntimestep); @@ -109,5 +109,5 @@ void NTopoDihedralTemplate::build() int all; MPI_Allreduce(&nmissing, &all, 1, MPI_INT, MPI_SUM, world); if (all && (me == 0)) - error->warning(FLERR, "Dihedral atoms missing at step {}" + utils::errorurl(30), update->ntimestep); + error->warning(FLERR, "Dihedral atoms missing at step {}" + utils::errorurl(5), update->ntimestep); } diff --git a/src/ntopo_improper_all.cpp b/src/ntopo_improper_all.cpp index 7e6b4c6e60..56e612a82c 100644 --- a/src/ntopo_improper_all.cpp +++ b/src/ntopo_improper_all.cpp @@ -61,7 +61,7 @@ void NTopoImproperAll::build() if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) { nmissing++; if (lostbond == Thermo::ERROR) - error->one(FLERR, "Improper atoms {} {} {} {} missing on proc {} at step {}" + utils::errorurl(30), + error->one(FLERR, Error::NOLASTLINE, "Improper atoms {} {} {} {} missing on proc {} at step {}" + utils::errorurl(5), improper_atom1[i][m], improper_atom2[i][m], improper_atom3[i][m], improper_atom4[i][m], me, update->ntimestep); continue; @@ -90,5 +90,5 @@ void NTopoImproperAll::build() int all; MPI_Allreduce(&nmissing, &all, 1, MPI_INT, MPI_SUM, world); if (all && (me == 0)) - error->warning(FLERR, "Improper atoms missing at step {}" + utils::errorurl(30), update->ntimestep); + error->warning(FLERR, "Improper atoms missing at step {}" + utils::errorurl(5), update->ntimestep); } diff --git a/src/ntopo_improper_partial.cpp b/src/ntopo_improper_partial.cpp index 7266c5c2a1..fa6f31b005 100644 --- a/src/ntopo_improper_partial.cpp +++ b/src/ntopo_improper_partial.cpp @@ -62,7 +62,7 @@ void NTopoImproperPartial::build() if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) { nmissing++; if (lostbond == Thermo::ERROR) - error->one(FLERR, "Improper atoms {} {} {} {} missing on proc {} at step {}" + utils::errorurl(30), + error->one(FLERR, Error::NOLASTLINE, "Improper atoms {} {} {} {} missing on proc {} at step {}" + utils::errorurl(5), improper_atom1[i][m], improper_atom2[i][m], improper_atom3[i][m], improper_atom4[i][m], me, update->ntimestep); continue; @@ -90,5 +90,5 @@ void NTopoImproperPartial::build() int all; MPI_Allreduce(&nmissing, &all, 1, MPI_INT, MPI_SUM, world); - if (all && me == 0) error->warning(FLERR, "Improper atoms missing at step {}" + utils::errorurl(30), update->ntimestep); + if (all && me == 0) error->warning(FLERR, "Improper atoms missing at step {}" + utils::errorurl(5), update->ntimestep); } diff --git a/src/ntopo_improper_template.cpp b/src/ntopo_improper_template.cpp index bfd097a812..59f0827c89 100644 --- a/src/ntopo_improper_template.cpp +++ b/src/ntopo_improper_template.cpp @@ -78,7 +78,7 @@ void NTopoImproperTemplate::build() if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) { nmissing++; if (lostbond == Thermo::ERROR) - error->one(FLERR, "Improper atoms {} {} {} {} missing on proc {} at step {}" + utils::errorurl(30), + error->one(FLERR, Error::NOLASTLINE, "Improper atoms {} {} {} {} missing on proc {} at step {}" + utils::errorurl(5), improper_atom1[iatom][m] + tagprev, improper_atom2[iatom][m] + tagprev, improper_atom3[iatom][m] + tagprev, improper_atom4[iatom][m] + tagprev, me, update->ntimestep); @@ -109,5 +109,5 @@ void NTopoImproperTemplate::build() int all; MPI_Allreduce(&nmissing, &all, 1, MPI_INT, MPI_SUM, world); if (all && (me == 0)) - error->warning(FLERR, "Improper atoms missing at step {}" + utils::errorurl(30), update->ntimestep); + error->warning(FLERR, "Improper atoms missing at step {}" + utils::errorurl(5), update->ntimestep); } From 2c7e3dddbcfcc6ae6298078c582b3c8b85bb99b7 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 25 Feb 2025 21:37:38 -0500 Subject: [PATCH 024/113] add test to detect if a potential file was incorrectly used with lgvdw yes --- src/REAXFF/reaxff_ffield.cpp | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/src/REAXFF/reaxff_ffield.cpp b/src/REAXFF/reaxff_ffield.cpp index 7dfa2ee1cb..64f860e7b9 100644 --- a/src/REAXFF/reaxff_ffield.cpp +++ b/src/REAXFF/reaxff_ffield.cpp @@ -234,6 +234,12 @@ namespace ReaxFF { if (lgflag) { values = reader.next_values(0); ++lineno; + + // if line does not start with a floating point number, i.e. is the start + // of the data for the next element, the file does not support lgflag != 0 + if (!values.matches("^\\s*\\f+\\s*")) + THROW_ERROR("ReaxFF potential file is not compatible with 'lgvdw yes'"); + CHECK_COLUMNS(2); sbp[i].lgcij = values.next_double(); sbp[i].lgre = values.next_double(); From a99a567f0c38bc48e3540bd1ba196a12cbe971ff Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 26 Feb 2025 11:12:35 -0500 Subject: [PATCH 025/113] add note that dynamic groups are only supported without averaging --- doc/src/fix_reaxff_species.rst | 3 +++ 1 file changed, 3 insertions(+) diff --git a/doc/src/fix_reaxff_species.rst b/doc/src/fix_reaxff_species.rst index 068d1de995..badcf72a56 100644 --- a/doc/src/fix_reaxff_species.rst +++ b/doc/src/fix_reaxff_species.rst @@ -207,6 +207,9 @@ No parameter of this fix can be used with the *start/stop* keywords of the :doc:`run ` command. This fix is not invoked during :doc:`energy minimization `. +This fix supports dynamic groups only if the *Nrepeat* setting is 1, +i.e. there is no averaging. + ---------- .. include:: accel_styles.rst From dc99e204d3b0fb7d55b9eb90ce884c39ff4fab02 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 26 Feb 2025 13:40:19 -0500 Subject: [PATCH 026/113] bugfix from Trung to avoid problems with read_dump when not all MPI ranks have atoms --- src/read_dump.cpp | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/src/read_dump.cpp b/src/read_dump.cpp index 5972b369c8..59fe6c6767 100644 --- a/src/read_dump.cpp +++ b/src/read_dump.cpp @@ -710,12 +710,14 @@ void ReadDump::read_atoms() while (nsend < nread) { lo = MAX(ofirst,rfirst); hi = MIN(olast,rlast); - if (otherproc) // send to otherproc or copy to self - MPI_Send(&buf[nsend][0],(hi-lo)*nfield,MPI_DOUBLE, + int numel = (hi-lo)*nfield; + if (otherproc && numel > 0) { // send to otherproc or copy to self + MPI_Send(&buf[nsend][0],numel,MPI_DOUBLE, otherproc,0,clustercomm); + } else memcpy(&fields[rfirst][0],&buf[nsend][0], - (hi-lo)*nfield*sizeof(double)); + numel*sizeof(double)); nsend += hi-lo; if (hi == olast) { otherproc++; From c6ebb57b4132a1a53c81fb8696f282562898a093 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 27 Feb 2025 23:28:19 -0500 Subject: [PATCH 027/113] make certain that nstyle is always initialized and detect partial variable setups --- src/region.h | 2 +- src/region_plane.cpp | 10 +++++++--- 2 files changed, 8 insertions(+), 4 deletions(-) diff --git a/src/region.h b/src/region.h index 8a51f404a2..b14f966ff1 100644 --- a/src/region.h +++ b/src/region.h @@ -20,7 +20,7 @@ namespace LAMMPS_NS { class Region : protected Pointers { public: - enum { CONSTANT, VARIABLE }; + enum { CONSTANT, VARIABLE, NONE }; char *id, *style; Region **reglist; diff --git a/src/region_plane.cpp b/src/region_plane.cpp index 597f586d8a..c87572864e 100644 --- a/src/region_plane.cpp +++ b/src/region_plane.cpp @@ -25,7 +25,7 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ RegPlane::RegPlane(LAMMPS *lmp, int narg, char **arg) : - Region(lmp, narg, arg), xstr(nullptr), ystr(nullptr), zstr(nullptr), + Region(lmp, narg, arg), xstr(nullptr), ystr(nullptr), zstr(nullptr), nstyle(NONE), nxstr(nullptr), nystr(nullptr), nzstr(nullptr) { xvar = yvar = zvar = 0.0; @@ -83,7 +83,9 @@ RegPlane::RegPlane(LAMMPS *lmp, int narg, char **arg) : nzstr = utils::strdup(arg[7] + 2); varshape = 1; } else { - error->all(FLERR, "The components of the normal vector should be either all variables or all constants"); + error->all( + FLERR, + "The components of the normal vector should be either all variables or all constants"); } if (varshape) { @@ -207,7 +209,9 @@ void RegPlane::shape_update() // enforce unit normal double rsq = normal[0] * normal[0] + normal[1] * normal[1] + normal[2] * normal[2]; - if (rsq == 0.0) error->all(FLERR, "Illegal region plane normal vector: {} {} {}", normal[0], normal[1], normal[2]); + if (rsq == 0.0) + error->all(FLERR, "Illegal region plane normal vector: {} {} {}", normal[0], normal[1], + normal[2]); normal[0] /= sqrt(rsq); normal[1] /= sqrt(rsq); normal[2] /= sqrt(rsq); From f4d2c518e84ec10226ebb003b81fdbfd7b528a0d Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 28 Feb 2025 03:43:58 -0500 Subject: [PATCH 028/113] make certain variable indices are initialized --- src/region_ellipsoid.cpp | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/region_ellipsoid.cpp b/src/region_ellipsoid.cpp index a0b4b9e544..2a4442c0fa 100644 --- a/src/region_ellipsoid.cpp +++ b/src/region_ellipsoid.cpp @@ -38,8 +38,8 @@ static constexpr double EPSILON = std::numeric_limits::epsilon() * 2.0; /* ---------------------------------------------------------------------- */ RegEllipsoid::RegEllipsoid(LAMMPS *lmp, int narg, char **arg) : - Region(lmp, narg, arg), xstr(nullptr), ystr(nullptr), zstr(nullptr), astr(nullptr), - bstr(nullptr), cstr(nullptr) + Region(lmp, narg, arg), xvar(-1), yvar(-1), zvar(-1), avar(-1), bvar(-1), cvar(-1), + xstr(nullptr), ystr(nullptr), zstr(nullptr), astr(nullptr), bstr(nullptr), cstr(nullptr) { options(narg - 8, &arg[8]); From 7fc4ba9628b96d45cb33d5b2ef8ae8cf1eedca98 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 2 Mar 2025 12:40:32 -0500 Subject: [PATCH 029/113] move documentation of sign() function to logical location and add version tag --- doc/src/variable.rst | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/doc/src/variable.rst b/doc/src/variable.rst index 2b59aeb65d..75a13e47e1 100644 --- a/doc/src/variable.rst +++ b/doc/src/variable.rst @@ -51,12 +51,12 @@ Syntax thermo keywords = vol, ke, press, etc from :doc:`thermo_style ` math operators = (), -x, x+y, x-y, x\*y, x/y, x\^y, x%y, x == y, x != y, x < y, x <= y, x > y, x >= y, x && y, x \|\| y, x \|\^ y, !x - math functions = sqrt(x), exp(x), ln(x), log(x), abs(x), + math functions = sqrt(x), exp(x), ln(x), log(x), abs(x), sign(x), sin(x), cos(x), tan(x), asin(x), acos(x), atan(x), atan2(y,x), random(x,y,z), normal(x,y,z), ceil(x), floor(x), round(x), ternary(x,y,z), ramp(x,y), stagger(x,y), logfreq(x,y,z), logfreq2(x,y,z), logfreq3(x,y,z), stride(x,y,z), stride2(x,y,z,a,b,c), - vdisplace(x,y), swiggle(x,y,z), cwiggle(x,y,z), sign(x) + vdisplace(x,y), swiggle(x,y,z), cwiggle(x,y,z) group functions = count(group), mass(group), charge(group), xcm(group,dim), vcm(group,dim), fcm(group,dim), bound(group,dir), gyration(group), ke(group), @@ -541,7 +541,7 @@ variables. +------------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ | Math operators | (), -x, x+y, x-y, x\*y, x/y, x\^y, x%y, x == y, x != y, x < y, x <= y, x > y, x >= y, x && y, x \|\| y, x \|\^ y, !x | +------------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ -| Math functions | sqrt(x), exp(x), ln(x), log(x), abs(x), sin(x), cos(x), tan(x), asin(x), acos(x), atan(x), atan2(y,x), random(x,y,z), normal(x,y,z), ceil(x), floor(x), round(x), ternary(x,y,z), ramp(x,y), stagger(x,y), logfreq(x,y,z), logfreq2(x,y,z), logfreq3(x,y,z), stride(x,y,z), stride2(x,y,z,a,b,c), vdisplace(x,y), swiggle(x,y,z), cwiggle(x,y,z), sign(x) | +| Math functions | sqrt(x), exp(x), ln(x), log(x), abs(x), sign(x), sin(x), cos(x), tan(x), asin(x), acos(x), atan(x), atan2(y,x), random(x,y,z), normal(x,y,z), ceil(x), floor(x), round(x), ternary(x,y,z), ramp(x,y), stagger(x,y), logfreq(x,y,z), logfreq2(x,y,z), logfreq3(x,y,z), stride(x,y,z), stride2(x,y,z,a,b,c), vdisplace(x,y), swiggle(x,y,z), cwiggle(x,y,z) | +------------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ | Group functions | count(ID), mass(ID), charge(ID), xcm(ID,dim), vcm(ID,dim), fcm(ID,dim), bound(ID,dir), gyration(ID), ke(ID), angmom(ID,dim), torque(ID,dim), inertia(ID,dimdim), omega(ID,dim) | +------------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ @@ -692,6 +692,11 @@ sqrt() of the product of one atom's y and z coordinates. Most of the math functions perform obvious operations. The ln() is the natural log; log() is the base 10 log. +.. versionadded:: 4Feb2025 + +The sign(x) function returns 1.0 if the value is greater than or equal +to 0.0, and -1.0 otherwise. + The random(x,y,z) function takes 3 arguments: x = lo, y = hi, and z = seed. It generates a uniform random number between lo and hi. The normal(x,y,z) function also takes 3 arguments: x = mu, y = sigma, and @@ -860,9 +865,6 @@ run, according to one of these formulas, where omega = 2 PI / period: where dt = the timestep size. -The sign(x) function returns 1.0 if the value is greater than or equal -to 0.0, and -1.0 otherwise. - The run begins on startstep. Startstep can span multiple runs, using the *start* keyword of the :doc:`run ` command. See the :doc:`run ` command for details of how to do this. Note that the From 2e3c1dfcc6b135aa398d07efa0fd6f72ca7cddac Mon Sep 17 00:00:00 2001 From: James Michael Goff Date: Mon, 3 Mar 2025 10:59:23 -0700 Subject: [PATCH 030/113] error explanations for net charge warning err_0029 --- doc/src/Errors_details.rst | 36 +++++++++++++++++++++++++ src/DIELECTRIC/pppm_dielectric.cpp | 4 +-- src/DIELECTRIC/pppm_disp_dielectric.cpp | 4 +-- src/KSPACE/ewald_disp.cpp | 2 +- src/MANYBODY/fix_qeq_comb.cpp | 2 +- src/REAXFF/fix_qeq_reaxff.cpp | 2 +- src/REAXFF/fix_qtpie_reaxff.cpp | 2 +- src/kspace.cpp | 4 +-- 8 files changed, 46 insertions(+), 10 deletions(-) diff --git a/doc/src/Errors_details.rst b/doc/src/Errors_details.rst index 32ebafbae2..820721a581 100644 --- a/doc/src/Errors_details.rst +++ b/doc/src/Errors_details.rst @@ -521,3 +521,39 @@ example, are usually not a per-atom property, but defined through the atom type. Thus it would not be required to have a Masses section and the included data would be ignored. LAMMPS prints this warning to inform about this case. + +.. _err0029: + +System is not charge neutral, net charge = ... +-------------------------------------------------- + +the sum of charges in the system is not zero. When a system is not +charge-neutral, methods that evolve/manipulate per-atom charges, evaluate +Coulomb interactions, evaluate Coulomb forces, or evaluate/manipulate other +properties relying on per-atom charges may raise this warning. A non-zero +net charge most commonly arises after setting per-atom charges :doc:`set ` +such that the sum is non-zero or by reading in a system through :doc:`read_data +` where the per-atom charges do not sum to zero. However, a loss of +charge neutrality may occur in other less common ways, like when charge +equilibration methods (e.g., :doc:`fix qeq `) fail. + +A similar warning/error may be raised when using certain charge equilibration +methods: :doc:`fix qeq `, :doc:`fix qeq/comb `, :doc:`fix +qeq/reaxff `, and :doc:`fix qtpie/reaxff `. In +such cases, this warning/error will be raised for the fix :doc:`group ` +when the group has a non-zero net charge. + +When the system is expected to be charge-neutral, this warning often arises due +to an error in the lammps input (e.g., an incorrect :doc:`set ` command, +error in the data file read by :doc:`read_data `, incorrectly +grouping atoms with charge, etc.). If the system is NOT expected to be +charge-neutral, the user should make sure that the method(s) used are +appropriate for systems with a non-zero net charge. Some commonly used fixes for +charge equilibration :doc:`fix qeq `, pair styles that include charge +interactions :doc:`pair_style coul/XXX `, and kspace methods +:doc:`kspace_style ` can, in theory, support systems with non-zero +net charge. However, non-zero net charge can lead to spurious artifacts. The +severity of these artifacts depends on the magnitude of total charge, system +size, and methods used. Before running simulations or calculations for systems +with non-zero net charge, users should test for artifacts and convergence of +properties. diff --git a/src/DIELECTRIC/pppm_dielectric.cpp b/src/DIELECTRIC/pppm_dielectric.cpp index 72d7e908e1..0a24c44bd6 100644 --- a/src/DIELECTRIC/pppm_dielectric.cpp +++ b/src/DIELECTRIC/pppm_dielectric.cpp @@ -308,8 +308,8 @@ void PPPMDielectric::qsum_qsq(int warning_flag) if (fabs(qsum) > SMALL) { std::string message = fmt::format("System is not charge neutral, net " "charge = {:.8}",qsum); - if (!warn_nonneutral) error->all(FLERR,message); - if (warn_nonneutral == 1 && comm->me == 0) error->warning(FLERR,message); + if (!warn_nonneutral) error->all(FLERR,message + utils::errorurl(29)); + if (warn_nonneutral == 1 && comm->me == 0) error->warning(FLERR,message + utils::errorurl(29)); warn_nonneutral = 2; } } diff --git a/src/DIELECTRIC/pppm_disp_dielectric.cpp b/src/DIELECTRIC/pppm_disp_dielectric.cpp index aba8ccf486..252a9386e3 100644 --- a/src/DIELECTRIC/pppm_disp_dielectric.cpp +++ b/src/DIELECTRIC/pppm_disp_dielectric.cpp @@ -582,8 +582,8 @@ void PPPMDispDielectric::qsum_qsq(int warning_flag) if (fabs(qsum) > SMALL) { std::string message = fmt::format("System is not charge neutral, net " "charge = {:.8}",qsum); - if (!warn_nonneutral) error->all(FLERR,message); - if (warn_nonneutral == 1 && comm->me == 0) error->warning(FLERR,message); + if (!warn_nonneutral) error->all(FLERR,message + utils::errorurl(29)); + if (warn_nonneutral == 1 && comm->me == 0) error->warning(FLERR,message + utils::errorurl(29)); warn_nonneutral = 2; } } diff --git a/src/KSPACE/ewald_disp.cpp b/src/KSPACE/ewald_disp.cpp index 9c81b21448..1ba8daa60c 100644 --- a/src/KSPACE/ewald_disp.cpp +++ b/src/KSPACE/ewald_disp.cpp @@ -220,7 +220,7 @@ void EwaldDisp::init() error->all(FLERR,"Cannot use Ewald/disp solver on system without " "charged, dipole, or LJ particles"); if (fabs(qsum) > SMALL && comm->me == 0) - error->warning(FLERR,"System is not charge neutral, net charge = {:.8g}",qsum); + error->warning(FLERR,"System is not charge neutral, net charge = {:.8g}" + utils::errorurl(29),qsum); if (!function[1] && !function[2]) dispersionflag = 0; if (!function[3]) dipoleflag = 0; diff --git a/src/MANYBODY/fix_qeq_comb.cpp b/src/MANYBODY/fix_qeq_comb.cpp index 88c6fb4be4..308a6e17db 100644 --- a/src/MANYBODY/fix_qeq_comb.cpp +++ b/src/MANYBODY/fix_qeq_comb.cpp @@ -143,7 +143,7 @@ void FixQEQComb::init() MPI_Allreduce(&qsum_local,&qsum,1,MPI_DOUBLE,MPI_SUM,world); if ((comm->me == 0) && (fabs(qsum) > QSUMSMALL)) - error->warning(FLERR,"Fix {} group is not charge neutral, net charge = {:.8}", style, qsum); + error->warning(FLERR,"Fix {} group is not charge neutral, net charge = {:.8}" + utils::errorurl(29), style, qsum); } /* ---------------------------------------------------------------------- */ diff --git a/src/REAXFF/fix_qeq_reaxff.cpp b/src/REAXFF/fix_qeq_reaxff.cpp index dc8fbd5afd..ed54ba0cbe 100644 --- a/src/REAXFF/fix_qeq_reaxff.cpp +++ b/src/REAXFF/fix_qeq_reaxff.cpp @@ -412,7 +412,7 @@ void FixQEqReaxFF::init() MPI_Allreduce(&qsum_local,&qsum,1,MPI_DOUBLE,MPI_SUM,world); if ((comm->me == 0) && (fabs(qsum) > QSUMSMALL)) - error->warning(FLERR,"Fix {} group is not charge neutral, net charge = {:.8}", style, qsum); + error->warning(FLERR,"Fix {} group is not charge neutral, net charge = {:.8}" + utils::errorurl(29), style, qsum); // get pointer to fix efield if present. there may be at most one instance of fix efield in use. diff --git a/src/REAXFF/fix_qtpie_reaxff.cpp b/src/REAXFF/fix_qtpie_reaxff.cpp index 22866fc363..6e4924eb1b 100644 --- a/src/REAXFF/fix_qtpie_reaxff.cpp +++ b/src/REAXFF/fix_qtpie_reaxff.cpp @@ -439,7 +439,7 @@ void FixQtpieReaxFF::init() MPI_Allreduce(&qsum_local,&qsum,1,MPI_DOUBLE,MPI_SUM,world); if ((comm->me == 0) && (fabs(qsum) > QSUMSMALL)) - error->warning(FLERR,"Fix {} group is not charge neutral, net charge = {:.8}", style, qsum); + error->warning(FLERR,"Fix {} group is not charge neutral, net charge = {:.8}" + utils::errorurl(29), style, qsum); // get pointer to fix efield if present. there may be at most one instance of fix efield in use. efield = nullptr; diff --git a/src/kspace.cpp b/src/kspace.cpp index 7d51c46ea8..bf5fdf8378 100644 --- a/src/kspace.cpp +++ b/src/kspace.cpp @@ -323,8 +323,8 @@ void KSpace::qsum_qsq(int warning_flag) if (fabs(qsum) > SMALL) { std::string message = fmt::format("System is not charge neutral, net " "charge = {:.8}",qsum); - if (!warn_nonneutral) error->all(FLERR,message); - if (warn_nonneutral == 1 && comm->me == 0) error->warning(FLERR,message); + if (!warn_nonneutral) error->all(FLERR,message + utils::errorurl(29)); + if (warn_nonneutral == 1 && comm->me == 0) error->warning(FLERR,message + utils::errorurl(29)); warn_nonneutral = 2; } } From 71b86b102d462e46ef7a9424273eda905cbf00ca Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 3 Mar 2025 21:08:45 -0500 Subject: [PATCH 031/113] enable use of Sphinx 8.2.x --- doc/utils/requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/utils/requirements.txt b/doc/utils/requirements.txt index d842f47c11..fbb161baa5 100644 --- a/doc/utils/requirements.txt +++ b/doc/utils/requirements.txt @@ -1,4 +1,4 @@ -Sphinx >= 5.3.0, <8.2.0 +Sphinx >= 5.3.0, <8.3.0 sphinxcontrib-spelling sphinxcontrib-jquery sphinx-design From cc70b5bb892e0cd1a94834afba49f2d6b23acf92 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 4 Mar 2025 23:15:41 -0500 Subject: [PATCH 032/113] document some internal styles --- doc/src/Developer.rst | 1 + doc/src/Developer_internal.rst | 113 ++++++++++++++++++++ doc/utils/sphinx-config/false_positives.txt | 2 + 3 files changed, 116 insertions(+) create mode 100644 doc/src/Developer_internal.rst diff --git a/doc/src/Developer.rst b/doc/src/Developer.rst index b0cfcc14fc..d4afd6f298 100644 --- a/doc/src/Developer.rst +++ b/doc/src/Developer.rst @@ -24,4 +24,5 @@ of time and requests from the LAMMPS user community. Classes Developer_platform Developer_utils + Developer_internal Developer_grid diff --git a/doc/src/Developer_internal.rst b/doc/src/Developer_internal.rst new file mode 100644 index 0000000000..5a134a8b32 --- /dev/null +++ b/doc/src/Developer_internal.rst @@ -0,0 +1,113 @@ + +Internal Styles +--------------- + +LAMMPS has a number of styles that are not meant to be used in an input +file and thus are not documented in the :doc:`LAMMPS command +documentation `. The differentiation between user +commands and internal commands is through the case of the command name: +user commands and styles are all lower case, internal styles are all +upper case. Internal styles are not called from the input file, but +their classes are instantiated by other styles. Often they are +created by other styles to store internal data or to perform actions +regularly at specific steps of the simulation. + +The paragraphs below document some of those styles that have general +utility and may be used to avoid redundant implementation. + +DEPRECATED Styles +^^^^^^^^^^^^^^^^^ + +The styles called DEPRECATED (e.g. pair, bond, fix, compute, region, etc.) +have the purpose to inform users that a specific style has been removed +or renamed. This is achieved by creating an alias for the deprecated +style to the corresponding class. For example, the fix style DEPRECATED +is aliased to fix style ave/spatial and fix style ave/spatial/sphere with +the following code: + +.. code-block:: c++ + + FixStyle(DEPRECATED,FixDeprecated); + FixStyle(ave/spatial,FixDeprecated); + FixStyle(ave/spatial/sphere,FixDeprecated); + +The individual class will then determine based on the style name +what action to perform: + +- inform that the style has been removed and what style replaces it, if any, and then error out +- inform that the style has been renamed and then either execute the replacement or error out +- inform that the style is no longer required, and it is thus ignored and continue + +There is also a section in the user's guide for :doc:`removed commands +and packages ` with additional explanations. + +Internal fix styles +^^^^^^^^^^^^^^^^^^^ + +fix DUMMY +""""""""" + +Most fix classes cannot be instantiated before the simulation box has +been created since they access data that is only available then. +However, in some cases it is required that a fix must be at or close to +the top of the list of all fixes. In those cases an instance of the +DUMMY fix style may be created by calling ``Modify::add_fix()`` and then +later replaced by calling ``Modify::replace_fix()``. + +fix STORE/ATOM +"""""""""""""" + +Fix STORE/ATOM can be used as persistent storage of per-atom data. + +**Syntax** + +.. code-block:: LAMMPS + + fix ID group-ID STORE/ATOM N1 N2 gflag rflag + +* ID, group-ID are documented in :doc:`fix ` command +* STORE/ATOM = style name of this fix command +* N1 = 1, N2 = 0 : data is per-atom vector = single value per atom +* N1 > 1, N2 = 0 : data is per-atom array = N1 values per atom +* N1 > 0, N2 > 0 : data is per-atom tensor = N1xN2 values per atom +* gflag = 1 communicate per-atom values with ghost atoms, 0 update ghost atoms +* rflag = 1 store per-atom value in restart file, 0 do not store data in restart + +Similar functionality is also available through using custom per-atom +properties with :doc:`fix property/atom `. The +choice between the two fixes should be based on whether the user should +be able to access this per-atom data: if yes, then fix property/atom is +preferred, otherwise fix STORE/ATOM. + +fix STORE/GLOBAL +"""""""""""""""" + +Fix STORE/GLOBAL can be used as persistent storage of global data with support for restarts + +**Syntax** + +.. code-block:: LAMMPS + + fix ID group-ID STORE/GLOBAL N1 N2 + +* ID, group-ID are documented in :doc:`fix ` command +* STORE/GLOBAL = style name of this fix command +* N1 >=1 : number of global items to store +* N2 = 1 : data is global vector of length N1 +* N2 > 1 : data is global N1xN2 array + +fix STORE/LOCAL +""""""""""""""" + +Fix STORE/LOCAL can be used as persistent storage for local data + +**Syntax** + +.. code-block:: LAMMPS + + fix ID group-ID STORE/LOCAL Nreset Nvalues + +* ID, group-ID are documented in :doc:`fix ` command +* STORE/LOCAL = style name of this fix command +* Nreset = frequency at which local data is available +* Nvalues = number of values per local item, that is the number of columns diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index f94d528cfe..517748825c 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -1321,6 +1321,7 @@ geturl gewald Gezelter gfile +gflag Gflop gfortran ghostneigh @@ -3250,6 +3251,7 @@ rewrap rezwanur rfac rfile +rflag rg Rg Rhaphson From 505d295d16fc8a16ca427123c8bd017b0096707c Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 4 Mar 2025 23:34:24 -0500 Subject: [PATCH 033/113] small correction --- doc/src/Developer_internal.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/src/Developer_internal.rst b/doc/src/Developer_internal.rst index 5a134a8b32..739422d8b7 100644 --- a/doc/src/Developer_internal.rst +++ b/doc/src/Developer_internal.rst @@ -70,7 +70,7 @@ Fix STORE/ATOM can be used as persistent storage of per-atom data. * N1 = 1, N2 = 0 : data is per-atom vector = single value per atom * N1 > 1, N2 = 0 : data is per-atom array = N1 values per atom * N1 > 0, N2 > 0 : data is per-atom tensor = N1xN2 values per atom -* gflag = 1 communicate per-atom values with ghost atoms, 0 update ghost atoms +* gflag = 1 communicate per-atom values with ghost atoms, 0 do not update ghost atom data * rflag = 1 store per-atom value in restart file, 0 do not store data in restart Similar functionality is also available through using custom per-atom From b433c8cb772aee80cc5523193118dcdd46c8ef91 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 5 Mar 2025 04:16:13 -0500 Subject: [PATCH 034/113] only trim if neighbor list request has a custom cutoff --- src/npair_skip_size_off2on.cpp | 2 +- src/npair_skip_size_off2on_oneside.cpp | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/src/npair_skip_size_off2on.cpp b/src/npair_skip_size_off2on.cpp index 89e633b238..46bc90a1ed 100644 --- a/src/npair_skip_size_off2on.cpp +++ b/src/npair_skip_size_off2on.cpp @@ -102,7 +102,7 @@ void NPairSkipSizeOff2onTemp::build(NeighList *list) dely = ytmp - x[j][1]; delz = ztmp - x[j][2]; rsq = delx * delx + dely * dely + delz * delz; - if (rsq > cutsq_custom) continue; + if ((cutsq_custom > 0.0) && (rsq > cutsq_custom)) continue; } neighptr[n++] = joriginal; diff --git a/src/npair_skip_size_off2on_oneside.cpp b/src/npair_skip_size_off2on_oneside.cpp index 7682b90d95..20a2f11cd1 100644 --- a/src/npair_skip_size_off2on_oneside.cpp +++ b/src/npair_skip_size_off2on_oneside.cpp @@ -104,7 +104,7 @@ void NPairSkipSizeOff2onOnesideTemp::build(NeighList *list) dely = ytmp - x[j][1]; delz = ztmp - x[j][2]; rsq = delx * delx + dely * dely + delz * delz; - if (rsq > cutsq_custom) continue; + if ((cutsq_custom > 0.0) && (rsq > cutsq_custom)) continue; } // flip I,J if necessary to satisfy onesided constraint @@ -163,7 +163,7 @@ void NPairSkipSizeOff2onOnesideTemp::build(NeighList *list) dely = ytmp - x[j][1]; delz = ztmp - x[j][2]; rsq = delx * delx + dely * dely + delz * delz; - if (rsq > cutsq_custom) continue; + if ((cutsq_custom > 0.0) && (rsq > cutsq_custom)) continue; } // flip I,J if necessary to satisfy onesided constraint From 47cea8e1ba5ea09445ea903ff068d4e84311a7f7 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 5 Mar 2025 04:17:38 -0500 Subject: [PATCH 035/113] use pairwise cutoff for trimming unless a custom cutoff if given --- src/npair.cpp | 21 +++++++++++---------- src/npair_halffull.cpp | 11 ++++++++--- src/npair_skip.cpp | 9 ++++++--- src/npair_skip_respa.cpp | 23 ++++++++++++++++------- src/npair_trim.cpp | 8 ++++++-- 5 files changed, 47 insertions(+), 25 deletions(-) diff --git a/src/npair.cpp b/src/npair.cpp index d98d5716dd..fb34120b83 100644 --- a/src/npair.cpp +++ b/src/npair.cpp @@ -13,27 +13,29 @@ ------------------------------------------------------------------------- */ #include "npair.h" -#include -#include "neighbor.h" -#include "neigh_request.h" -#include "nbin.h" -#include "nstencil.h" + #include "atom.h" -#include "update.h" -#include "memory.h" #include "error.h" +#include "memory.h" +#include "nbin.h" +#include "neigh_request.h" +#include "neighbor.h" +#include "nstencil.h" +#include "update.h" + +#include using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NPair::NPair(LAMMPS *lmp) - : Pointers(lmp), nb(nullptr), ns(nullptr), bins(nullptr), stencil(nullptr) +NPair::NPair(LAMMPS *lmp) : Pointers(lmp), nb(nullptr), ns(nullptr), bins(nullptr), stencil(nullptr) { last_build = -1; mycutneighsq = nullptr; molecular = atom->molecular; copymode = 0; + cutoff_custom = 0.0; execution_space = Host; } @@ -50,7 +52,6 @@ NPair::~NPair() void NPair::post_constructor(NeighRequest *nrq) { - cutoff_custom = 0.0; if (nrq->cut) cutoff_custom = nrq->cutoff; } diff --git a/src/npair_halffull.cpp b/src/npair_halffull.cpp index aa560b5731..7a815a5137 100644 --- a/src/npair_halffull.cpp +++ b/src/npair_halffull.cpp @@ -50,7 +50,7 @@ NPairHalffull::NPairHalffull(LAMMPS *lmp) : NPair(lmp) {} template void NPairHalffull::build(NeighList *list) { - int i, j, ii, jj, n, jnum, joriginal; + int i, j, ii, jj, n, jnum, joriginal, itype, jtype; int *neighptr, *jlist; double xtmp, ytmp, ztmp, delx, dely, delz, rsq; @@ -58,6 +58,7 @@ void NPairHalffull::build(NeighList *list) double **x = atom->x; int nlocal = atom->nlocal; + int *type = atom->type; int *ilist = list->ilist; int *numneigh = list->numneigh; @@ -85,6 +86,7 @@ void NPairHalffull::build(NeighList *list) // loop over parent full list i = ilist_full[ii]; + itype = type[i]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; @@ -95,6 +97,7 @@ void NPairHalffull::build(NeighList *list) for (jj = 0; jj < jnum; jj++) { joriginal = jlist[jj]; j = joriginal & NEIGHMASK; + jtype = type[j]; if (NEWTON) { if (j < nlocal) { @@ -121,7 +124,8 @@ void NPairHalffull::build(NeighList *list) delz = ztmp - x[j][2]; rsq = delx * delx + dely * dely + delz * delz; - if (rsq > cutsq_custom) continue; + double cutsq_trim = (cutsq_custom > 0.0) ? cutsq_custom : cutneighsq[itype][jtype]; + if (rsq > cutsq_trim) continue; } neighptr[n++] = joriginal; @@ -133,7 +137,8 @@ void NPairHalffull::build(NeighList *list) delz = ztmp - x[j][2]; rsq = delx * delx + dely * dely + delz * delz; - if (rsq > cutsq_custom) continue; + double cutsq_trim = (cutsq_custom > 0.0) ? cutsq_custom : cutneighsq[itype][jtype]; + if (rsq > cutsq_trim) continue; } neighptr[n++] = joriginal; diff --git a/src/npair_skip.cpp b/src/npair_skip.cpp index 75802567b7..ab23a4fe5f 100644 --- a/src/npair_skip.cpp +++ b/src/npair_skip.cpp @@ -37,7 +37,7 @@ NPairSkipTemp::NPairSkipTemp(LAMMPS *lmp) : NPair(lmp) {} template void NPairSkipTemp::build(NeighList *list) { - int i, j, ii, jj, n, itype, jnum, joriginal; + int i, j, ii, jj, n, itype, jtype, jnum, joriginal; int *neighptr, *jlist; int *type = atom->type; @@ -94,7 +94,8 @@ void NPairSkipTemp::build(NeighList *list) for (jj = 0; jj < jnum; jj++) { joriginal = jlist[jj]; j = joriginal & NEIGHMASK; - if (!molskip && ijskip[itype][type[j]]) continue; + jtype = type[j]; + if (!molskip && ijskip[itype][jtype]) continue; if ((molskip == NeighRequest::INTRA) && (molecule[i] != molecule[j])) continue; if ((molskip == NeighRequest::INTER) && (molecule[i] == molecule[j])) continue; @@ -103,7 +104,9 @@ void NPairSkipTemp::build(NeighList *list) dely = ytmp - x[j][1]; delz = ztmp - x[j][2]; rsq = delx * delx + dely * dely + delz * delz; - if (rsq > cutsq_custom) continue; + + double cutsq_trim = (cutsq_custom > 0.0) ? cutsq_custom : cutneighsq[itype][jtype]; + if (rsq > cutsq_trim) continue; } neighptr[n++] = joriginal; diff --git a/src/npair_skip_respa.cpp b/src/npair_skip_respa.cpp index 211aa6142a..90566e8786 100644 --- a/src/npair_skip_respa.cpp +++ b/src/npair_skip_respa.cpp @@ -36,7 +36,7 @@ NPairSkipRespaTemp::NPairSkipRespaTemp(LAMMPS *lmp) : NPair(lmp) {} template void NPairSkipRespaTemp::build(NeighList *list) { - int i, j, ii, jj, n, itype, jnum, joriginal, n_inner, n_middle; + int i, j, ii, jj, n, itype, jtype, jnum, joriginal, n_inner, n_middle; int *neighptr, *jlist, *neighptr_inner, *neighptr_middle; int *type = atom->type; @@ -117,7 +117,8 @@ void NPairSkipRespaTemp::build(NeighList *list) for (jj = 0; jj < jnum; jj++) { joriginal = jlist[jj]; j = joriginal & NEIGHMASK; - if (!molskip && ijskip[itype][type[j]]) continue; + jtype = type[j]; + if (!molskip && ijskip[itype][jtype]) continue; if ((molskip == NeighRequest::INTRA) && (molecule[i] != molecule[j])) continue; if ((molskip == NeighRequest::INTER) && (molecule[i] == molecule[j])) continue; @@ -126,7 +127,9 @@ void NPairSkipRespaTemp::build(NeighList *list) dely = ytmp - x[j][1]; delz = ztmp - x[j][2]; rsq = delx * delx + dely * dely + delz * delz; - if (rsq > cutsq_custom) continue; + + double cutsq_trim = (cutsq_custom > 0.0) ? cutsq_custom : cutneighsq[itype][jtype]; + if (rsq > cutsq_trim) continue; } neighptr[n++] = joriginal; @@ -140,7 +143,8 @@ void NPairSkipRespaTemp::build(NeighList *list) for (jj = 0; jj < jnum; jj++) { joriginal = jlist[jj]; j = joriginal & NEIGHMASK; - if (!molskip && ijskip[itype][type[j]]) continue; + jtype = type[j]; + if (!molskip && ijskip[itype][jtype]) continue; if ((molskip == NeighRequest::INTRA) && (molecule[i] != molecule[j])) continue; if ((molskip == NeighRequest::INTER) && (molecule[i] == molecule[j])) continue; @@ -149,7 +153,9 @@ void NPairSkipRespaTemp::build(NeighList *list) dely = ytmp - x[j][1]; delz = ztmp - x[j][2]; rsq = delx * delx + dely * dely + delz * delz; - if (rsq > cutsq_custom) continue; + + double cutsq_trim = (cutsq_custom > 0.0) ? cutsq_custom : cut_inner_sq; + if (rsq > cutsq_trim) continue; } neighptr_inner[n_inner++] = joriginal; @@ -164,7 +170,8 @@ void NPairSkipRespaTemp::build(NeighList *list) for (jj = 0; jj < jnum; jj++) { joriginal = jlist[jj]; j = joriginal & NEIGHMASK; - if (!molskip && ijskip[itype][type[j]]) continue; + jtype = type[j]; + if (!molskip && ijskip[itype][jtype]) continue; if ((molskip == NeighRequest::INTRA) && (molecule[i] != molecule[j])) continue; if ((molskip == NeighRequest::INTER) && (molecule[i] == molecule[j])) continue; @@ -173,7 +180,9 @@ void NPairSkipRespaTemp::build(NeighList *list) dely = ytmp - x[j][1]; delz = ztmp - x[j][2]; rsq = delx * delx + dely * dely + delz * delz; - if (rsq > cutsq_custom) continue; + + double cutsq_trim = (cutsq_custom > 0.0) ? cutsq_custom : cut_middle_sq; + if (rsq > cutsq_trim) continue; } neighptr_middle[n_middle++] = joriginal; diff --git a/src/npair_trim.cpp b/src/npair_trim.cpp index 1b25646185..c89445cea0 100644 --- a/src/npair_trim.cpp +++ b/src/npair_trim.cpp @@ -34,12 +34,13 @@ void NPairTrim::build(NeighList *list) double cutsq_custom = cutoff_custom * cutoff_custom; - int ii, jj, n, jnum, joriginal; + int ii, jj, n, jnum, joriginal, itype, jtype; int *neighptr, *jlist; double xtmp, ytmp, ztmp; double delx, dely, delz, rsq; double **x = atom->x; + int *type = atom->type; int *ilist = list->ilist; int *numneigh = list->numneigh; @@ -64,6 +65,7 @@ void NPairTrim::build(NeighList *list) neighptr = ipage->vget(); const int i = ilist_copy[ii]; + itype = type[i]; ilist[ii] = i; xtmp = x[i][0]; ytmp = x[i][1]; @@ -77,13 +79,15 @@ void NPairTrim::build(NeighList *list) for (jj = 0; jj < jnum; jj++) { joriginal = jlist[jj]; const int j = joriginal & NEIGHMASK; + jtype = type[j]; delx = xtmp - x[j][0]; dely = ytmp - x[j][1]; delz = ztmp - x[j][2]; rsq = delx * delx + dely * dely + delz * delz; - if (rsq > cutsq_custom) continue; + double cutsq_trim = (cutsq_custom > 0.0) ? cutsq_custom : cutneighsq[itype][jtype]; + if (rsq > cutsq_trim) continue; neighptr[n++] = joriginal; } From abc14c00a0202dd6142a37a10e37c809fa47579e Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 5 Mar 2025 17:40:36 -0500 Subject: [PATCH 036/113] use different method to enforce the C locale in LAMMPS GUI --- tools/lammps-gui/main.cpp | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/tools/lammps-gui/main.cpp b/tools/lammps-gui/main.cpp index 53bdaca8fd..5f2599c3df 100644 --- a/tools/lammps-gui/main.cpp +++ b/tools/lammps-gui/main.cpp @@ -20,6 +20,7 @@ #include #include #include +#include #include #include @@ -35,9 +36,10 @@ int main(int argc, char *argv[]) qRegisterMetaTypeStreamOperators>("QList"); #endif + // enforce using the plain ASCII C locale with UTF-8 encoding within the GUI. + qputenv("LC_ALL", "C.UTF-8"); + QApplication app(argc, argv); - // enforce using the plain ASCII C locale within the GUI. - QLocale::setDefault(QLocale::c()); QCoreApplication::setOrganizationName("The LAMMPS Developers"); QCoreApplication::setOrganizationDomain("lammps.org"); QCoreApplication::setApplicationName("LAMMPS-GUI - QT" stringify(QT_VERSION_MAJOR)); From 09c8dc07d8cd3de3ac815a51452b3faab6ffcf6e Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 6 Mar 2025 11:08:22 -0500 Subject: [PATCH 037/113] update statements about what packages support and what not --- doc/src/Speed_compare.rst | 13 ++++--------- 1 file changed, 4 insertions(+), 9 deletions(-) diff --git a/doc/src/Speed_compare.rst b/doc/src/Speed_compare.rst index 7821214c83..3f72e5d715 100644 --- a/doc/src/Speed_compare.rst +++ b/doc/src/Speed_compare.rst @@ -44,11 +44,6 @@ section below for examples where this has been done. system the crossover (in single precision) is often about 50K-100K atoms per GPU. When performing double precision calculations the crossover point can be significantly smaller. -* Both KOKKOS and GPU package compute bonded interactions (bonds, angles, - etc) on the CPU. If the GPU package is running with several MPI processes - assigned to one GPU, the cost of computing the bonded interactions is - spread across more CPUs and hence the GPU package can run faster in these - cases. * When using LAMMPS with multiple MPI ranks assigned to the same GPU, its performance depends to some extent on the available bandwidth between the CPUs and the GPU. This can differ significantly based on the @@ -85,10 +80,10 @@ section below for examples where this has been done. code (with a performance penalty due to having data transfers between host and GPU). * The GPU package requires neighbor lists to be built on the CPU when using - exclusion lists, or a triclinic simulation box. -* The GPU package can be compiled for CUDA or OpenCL and thus supports - both, NVIDIA and AMD GPUs well. On NVIDIA hardware, using CUDA is typically - resulting in equal or better performance over OpenCL. + hybrid pair styles, exclusion lists, or a triclinic simulation box. +* The GPU package can be compiled for CUDA, HIP, or OpenCL and thus supports + NVIDIA, AMD, and Intel GPUs well. On NVIDIA hardware, using CUDA is + typically resulting in equal or better performance over OpenCL. * OpenCL in the GPU package does theoretically also support Intel CPUs or Intel Xeon Phi, but the native support for those in KOKKOS (or INTEL) is superior. From 916ab55a31f67e5b58d72b6455d6d50243ce2883 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 6 Mar 2025 13:15:09 -0500 Subject: [PATCH 038/113] reverse normalization between type pairs if the types were swapped on input --- src/compute_rdf.cpp | 33 +++++++++++++++++++++++---------- src/compute_rdf.h | 2 +- 2 files changed, 24 insertions(+), 11 deletions(-) diff --git a/src/compute_rdf.cpp b/src/compute_rdf.cpp index 0dc7da3460..50f075760f 100644 --- a/src/compute_rdf.cpp +++ b/src/compute_rdf.cpp @@ -43,8 +43,8 @@ using namespace MathConst; ComputeRDF::ComputeRDF(LAMMPS *lmp, int narg, char **arg) : Compute(lmp, narg, arg), rdfpair(nullptr), nrdfpair(nullptr), ilo(nullptr), ihi(nullptr), jlo(nullptr), jhi(nullptr), - hist(nullptr), histall(nullptr), typecount(nullptr), icount(nullptr), jcount(nullptr), - duplicates(nullptr) + rev(nullptr), hist(nullptr), histall(nullptr), typecount(nullptr), + icount(nullptr), jcount(nullptr), duplicates(nullptr) { if (narg < 4) utils::missing_cmd_args(FLERR,"compute rdf", error); @@ -95,10 +95,12 @@ ComputeRDF::ComputeRDF(LAMMPS *lmp, int narg, char **arg) : ihi = new int[npairs]; jlo = new int[npairs]; jhi = new int[npairs]; + rev = new int[npairs]; if (!nargpair) { ilo[0] = 1; ihi[0] = ntypes; jlo[0] = 1; jhi[0] = ntypes; + rev[0] = 0; } else { iarg = 4; for (int ipair = 0; ipair < npairs; ipair++) { @@ -110,11 +112,12 @@ ComputeRDF::ComputeRDF(LAMMPS *lmp, int narg, char **arg) : if ( (ilo[ipair] == ihi[ipair]) && (jlo[ipair] == jhi[ipair]) && (ilo[ipair] > jlo[ipair]) ) { + rev[ipair] = 1; jlo[ipair] = ihi[ipair]; ilo[ipair] = jhi[ipair]; ihi[ipair] = ilo[ipair]; jhi[ipair] = jlo[ipair]; - } + } else rev[ipair] = 0; iarg += 2; } @@ -381,18 +384,28 @@ void ComputeRDF::compute_array() constant = 4.0*MY_PI / (3.0*domain->xprd*domain->yprd*domain->zprd); for (m = 0; m < npairs; m++) { - normfac = (icount[m] > 0) ? static_cast(jcount[m]) - - static_cast(duplicates[m])/icount[m] : 0.0; + if (rev[m]) { // swap i and j because they were entered in different order + normfac = (jcount[m] > 0) ? static_cast(icount[m]) + - static_cast(duplicates[m])/jcount[m] : 0.0; + } else { + normfac = (icount[m] > 0) ? static_cast(jcount[m]) + - static_cast(duplicates[m])/icount[m] : 0.0; + } ncoord = 0.0; for (ibin = 0; ibin < nbin; ibin++) { rlower = ibin*delr; rupper = (ibin+1)*delr; vfrac = constant * (rupper*rupper*rupper - rlower*rlower*rlower); - if (vfrac * normfac != 0.0) - gr = histall[m][ibin] / (vfrac * normfac * icount[m]); - else gr = 0.0; - if (icount[m] != 0) - ncoord += gr * vfrac * normfac; + gr = 0.0; + if (vfrac * normfac != 0.0) { + if (rev[m]) { // swap i and j because they were entered in different order + gr = histall[m][ibin] / (vfrac * normfac * jcount[m]); + if (jcount[m] != 0) ncoord += gr * vfrac * normfac; + } else { + gr = histall[m][ibin] / (vfrac * normfac * icount[m]); + if (icount[m] != 0) ncoord += gr * vfrac * normfac; + } + } array[ibin][1+2*m] = gr; array[ibin][2+2*m] = ncoord; } diff --git a/src/compute_rdf.h b/src/compute_rdf.h index d2914ca6c6..5cceb0ee4b 100644 --- a/src/compute_rdf.h +++ b/src/compute_rdf.h @@ -41,7 +41,7 @@ class ComputeRDF : public Compute { double mycutneigh; // user-specified cutoff + neighbor skin int ***rdfpair; // map 2 type pair to rdf pair for each histo int **nrdfpair; // # of histograms for each type pair - int *ilo, *ihi, *jlo, *jhi; + int *ilo, *ihi, *jlo, *jhi, *rev; double **hist; // histogram bins double **histall; // summed histogram bins across all procs From 46393cc93022e7d34d2bb0b0056fad2f4d96b87b Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 6 Mar 2025 13:15:24 -0500 Subject: [PATCH 039/113] modernize error messages --- src/compute_rdf.cpp | 22 ++++++++++++---------- 1 file changed, 12 insertions(+), 10 deletions(-) diff --git a/src/compute_rdf.cpp b/src/compute_rdf.cpp index 50f075760f..c1e7dda2bb 100644 --- a/src/compute_rdf.cpp +++ b/src/compute_rdf.cpp @@ -52,7 +52,7 @@ ComputeRDF::ComputeRDF(LAMMPS *lmp, int narg, char **arg) : extarray = 0; nbin = utils::inumeric(FLERR,arg[3],false,lmp); - if (nbin < 1) error->all(FLERR,"Illegal compute rdf command"); + if (nbin < 1) error->all(FLERR, 3, "Number of bins for compute rdf must be > 0"); // optional args // nargpair = # of pairwise args, starting at iarg = 4 @@ -69,19 +69,20 @@ ComputeRDF::ComputeRDF(LAMMPS *lmp, int narg, char **arg) : if (strcmp(arg[iarg],"cutoff") == 0) { if (iarg+2 > narg) utils::missing_cmd_args(FLERR,"compute rdf cutoff", error); if ((neighbor->style == Neighbor::MULTI) || (neighbor->style == Neighbor::MULTI_OLD)) - error->all(FLERR, "Compute rdf with custom cutoff requires neighbor style 'bin' or 'nsq'"); + error->all(FLERR, iarg, "Compute rdf with custom cutoff requires neighbor style 'bin' or 'nsq'"); cutoff_user = utils::numeric(FLERR,arg[iarg+1],false,lmp); if (cutoff_user <= 0.0) cutflag = 0; else cutflag = 1; iarg += 2; - } else error->all(FLERR,"Unknown compute rdf keyword {}", arg[iarg]); + } else error->all(FLERR, iarg, "Unknown compute rdf keyword {}", arg[iarg]); } // pairwise args - if (nargpair == 0) npairs = 1; - else { - if (nargpair % 2) error->all(FLERR,"Illegal compute rdf command"); + if (nargpair == 0) { + npairs = 1; + } else { + if (nargpair % 2) error->all(FLERR, 4, "Must provide atom types in pairs for compute rdf command"); npairs = nargpair/2; } @@ -174,7 +175,7 @@ void ComputeRDF::init() const double skin = neighbor->skin; if (!force->pair && !cutflag) - error->all(FLERR,"Compute rdf requires a pair style or an explicit cutoff"); + error->all(FLERR, Error::NOLASTLINE, "Compute rdf requires a pair style or an explicit cutoff"); if (cutflag) { mycutneigh = cutoff_user + skin; @@ -184,8 +185,8 @@ void ComputeRDF::init() else cutghost = comm->cutghostuser; if (mycutneigh > cutghost) - error->all(FLERR,"Compute rdf cutoff plus skin {} exceeds ghost atom range {} - " - "use comm_modify cutoff command to increase it", mycutneigh, cutghost); + error->all(FLERR, Error::NOLASTLINE, "Compute rdf cutoff plus skin {} exceeds ghost atom " + "range {} - use comm_modify cutoff command to increase it", mycutneigh, cutghost); delr = cutoff_user / nbin; } delr = force->pair->cutforce / nbin; @@ -215,7 +216,8 @@ void ComputeRDF::init() auto req = neighbor->add_request(this, NeighConst::REQ_OCCASIONAL); if (cutflag) { if ((neighbor->style == Neighbor::MULTI) || (neighbor->style == Neighbor::MULTI_OLD)) - error->all(FLERR, "Compute rdf with custom cutoff requires neighbor style 'bin' or 'nsq'"); + error->all(FLERR, Error::NOLASTLINE, + "Compute rdf with custom cutoff requires neighbor style 'bin' or 'nsq'"); req->set_cutoff(mycutneigh); } } From 9b1dca201ffee322c10c2ed7d6d8b8ca9d1aa01b Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 6 Mar 2025 15:45:24 -0500 Subject: [PATCH 040/113] rewrite incorrect statement --- cmake/presets/kokkos-cuda.cmake | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/cmake/presets/kokkos-cuda.cmake b/cmake/presets/kokkos-cuda.cmake index 878ce0c566..31942b8fae 100644 --- a/cmake/presets/kokkos-cuda.cmake +++ b/cmake/presets/kokkos-cuda.cmake @@ -1,6 +1,5 @@ # preset that enables KOKKOS and selects CUDA compilation with OpenMP -# enabled as well. This preselects CC 5.0 as default GPU arch, since -# that is compatible with all higher CC, but not the default CC 3.5 +# enabled as well. The GPU architecture *must* match your hardware set(PKG_KOKKOS ON CACHE BOOL "" FORCE) set(Kokkos_ENABLE_SERIAL ON CACHE BOOL "" FORCE) set(Kokkos_ENABLE_CUDA ON CACHE BOOL "" FORCE) From 22fa86a1b7d13da3b15cd50d718845b3faa28b05 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 6 Mar 2025 20:44:05 -0500 Subject: [PATCH 041/113] add "condense" keyword to delete_atoms what will compact the atom IDs while preserving their order --- doc/src/delete_atoms.rst | 28 ++++++++++---- src/delete_atoms.cpp | 80 +++++++++++++++++++++++++++++++++------- src/delete_atoms.h | 2 +- 3 files changed, 87 insertions(+), 23 deletions(-) diff --git a/doc/src/delete_atoms.rst b/doc/src/delete_atoms.rst index 296a12dc5c..7ce3c1b58d 100644 --- a/doc/src/delete_atoms.rst +++ b/doc/src/delete_atoms.rst @@ -35,11 +35,12 @@ Syntax *variable* args = variable-name * zero or more keyword/value pairs may be appended -* keyword = *compress* or *bond* or *mol* +* keyword = *compress* or *condense* or *bond* or *mol* .. parsed-literal:: *compress* value = *no* or *yes* + *condense* value = *no* or *yes* *bond* value = *no* or *yes* *mol* value = *no* or *yes* @@ -50,6 +51,7 @@ Examples delete_atoms group edge delete_atoms region sphere compress no + delete_atoms region sphere condense yes delete_atoms overlap 0.3 all all delete_atoms overlap 0.5 solvent colloid delete_atoms random fraction 0.1 yes all cube 482793 bond yes @@ -129,21 +131,31 @@ other options listed above. Here is the meaning of the optional keywords. -If the *compress* keyword is set to *yes*, then after atoms are -deleted, then atom IDs are re-assigned so that they run from 1 to the -number of atoms in the system. Note that this is not done for -molecular systems (see the :doc:`atom_style ` command), -regardless of the *compress* setting, since it would foul up the bond -connectivity that has already been assigned. However, the +If the *compress* keyword is set to *yes* (which is the default), then +after atoms are deleted, the atom IDs are re-assigned so that they run +from 1 to the number of atoms in the system. Note that this is not done +for molecular systems (see the :doc:`atom_style ` command), +regardless of the *compress* setting, since it would corrupt the bond +connectivity information that has already been assigned. However, the :doc:`reset_atoms id ` command can be used after this command to accomplish the same thing. -Note that the re-assignment of IDs is not really a compression, where +Note that this re-assignment of IDs is not really a compression, where gaps in atom IDs are removed by decrementing atom IDs that are larger. Instead the IDs for all atoms are erased, and new IDs are assigned so that the atoms owned by individual processors have consecutive IDs, as the :doc:`create_atoms ` command explains. +.. versionadded:: TBD + +If the *condense* keyword set to *yes*, then after atoms are deleted, +the atom IDs are re-assigned in a way such that the order of atom-IDs is +preserved. This process is not efficient and cannot be used for very +large systems and requires local storage that scales with the number of +total atoms in the system. Also, the *compress* and the *condense* +keywords cannot be used at the same time. Whichever of the two is used +last will be applied. + A molecular system with fixed bonds, angles, dihedrals, or improper interactions, is one where the topology of the interactions is typically defined in the data file read by the :doc:`read_data diff --git a/src/delete_atoms.cpp b/src/delete_atoms.cpp index 35f608461b..65b74df50e 100644 --- a/src/delete_atoms.cpp +++ b/src/delete_atoms.cpp @@ -35,6 +35,7 @@ #include "region.h" #include "variable.h" +#include #include #include #include @@ -52,9 +53,9 @@ DeleteAtoms::DeleteAtoms(LAMMPS *lmp) : Command(lmp) {} void DeleteAtoms::command(int narg, char **arg) { if (domain->box_exist == 0) - error->all(FLERR, "Delete_atoms command before simulation box is defined"); + error->all(FLERR, -1, "Delete_atoms command before simulation box is defined"); if (narg < 1) utils::missing_cmd_args(FLERR, "delete_atoms", error); - if (atom->tag_enable == 0) error->all(FLERR, "Cannot use delete_atoms unless atoms have IDs"); + if (atom->tag_enable == 0) error->all(FLERR, -1, "Cannot use delete_atoms unless atoms have IDs"); // store state before delete @@ -78,21 +79,21 @@ void DeleteAtoms::command(int narg, char **arg) delete_random(narg, arg); // deprecated porosity option, now included in new partial option else if (strcmp(arg[0], "porosity") == 0) { - error->all(FLERR, + error->all(FLERR, Error::ARGZERO, "The delete_atoms 'porosity' keyword has been removed.\n" "Please use: delete_atoms random fraction frac exact group-ID region-ID seed\n"); } else if (strcmp(arg[0], "variable") == 0) delete_variable(narg, arg); else - error->all(FLERR, "Unknown delete_atoms sub-command: {}", arg[0]); + error->all(FLERR, Error::ARGZERO, "Unknown delete_atoms sub-command: {}", arg[0]); if (allflag) { int igroup = group->find("all"); if ((igroup >= 0) && modify->check_rigid_group_overlap(group->bitmask[igroup])) - error->warning(FLERR, "Attempting to delete atoms in rigid bodies"); + if (comm->me == 0) error->warning(FLERR, "Attempting to delete atoms in rigid bodies"); } else { if (modify->check_rigid_list_overlap(dlist)) - error->warning(FLERR, "Attempting to delete atoms in rigid bodies"); + if (comm->me == 0) error->warning(FLERR, "Attempting to delete atoms in rigid bodies"); } // if allflag = 1, just reset atom->nlocal @@ -130,6 +131,9 @@ void DeleteAtoms::command(int narg, char **arg) // if non-molecular system and compress flag set: // reset atom tags to be contiguous // set all atom IDs to 0, call tag_extend() + // if condense flag set, collect atom IDs for all atoms in replicated global array. + // sort array according to tag value, skip over tags that are zero and determine new tag. + // build new array with tags for all local atoms. if (compress_flag) { if (atom->molecular == Atom::ATOMIC) { @@ -139,6 +143,47 @@ void DeleteAtoms::command(int narg, char **arg) atom->tag_extend(); } else if (comm->me == 0) error->warning(FLERR, "Ignoring 'compress yes' for molecular system"); + } else if (condense_flag) { + if (atom->molecular == Atom::ATOMIC) { + if (atom->map_style == Atom::MAP_NONE) + error->all(FLERR, Error::NOLASTLINE, "Using 'condense yes' option requires an atom map"); + if (atom->map_tag_max + 1 > MAXSMALLINT) + error->all(FLERR, Error::NOLASTLINE, "Too many atoms for using 'condense yes' option"); + tagint *tag = atom->tag; + int nlocal = atom->nlocal; + int nall = nlocal + atom->nghost; + tagint maxtag = atom->map_tag_max + 1; + auto mytags = std::vector(maxtag, 0); + auto alltags = std::vector(maxtag, 0); + for (int i = 0; i < nlocal; i++) mytags[tag[i]] = tag[i]; + MPI_Allreduce(mytags.data(), alltags.data(), maxtag, MPI_LMP_TAGINT, MPI_SUM, world); + std::sort(alltags.begin(), alltags.end()); + tagint newtag = 0; + int localidx; + mytags.resize(nall); + for (int i = 0; i < nall; ++i) mytags[i] = 0; + // update atom map + atom->map_init(0); + atom->nghost = 0; + atom->map_set(); + for (auto t : alltags) { + // skip over unset tags + if (!t) continue; + ++newtag; + localidx = atom->map(t); + if ((localidx < 0)) continue; + mytags[localidx] = newtag; + } + for (int i = 0; i < nall; ++i) tag[i] = mytags[i]; + + // recreate atom map again + atom->map_tag_max = -1; + atom->map_style_set(); + atom->map_init(0); + atom->nghost = 0; + atom->map_set(); + } else if (comm->me == 0) + error->warning(FLERR, "Ignoring 'condense yes' for molecular system"); } // reset atom->natoms and also topology counts @@ -309,7 +354,7 @@ void DeleteAtoms::delete_overlap(int narg, char **arg) if (force->pair == nullptr) error->all(FLERR, "Delete_atoms requires a pair style be defined"); if (cut > neighbor->cutneighmax) error->all(FLERR, "Delete_atoms cutoff > max neighbor cutoff"); - if (cut > neighbor->cutneighmin && comm->me == 0) + if ((cut > neighbor->cutneighmin) && comm->me == 0) error->warning(FLERR, "Delete_atoms cutoff > minimum neighbor cutoff"); // setup domain, communication and neighboring @@ -880,28 +925,35 @@ void DeleteAtoms::options(int narg, char **arg) { compress_flag = 1; bond_flag = mol_flag = 0; + condense_flag = 0; int iarg = 0; while (iarg < narg) { if (strcmp(arg[iarg], "compress") == 0) { if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "delete_atoms compress", error); compress_flag = utils::logical(FLERR, arg[iarg + 1], false, lmp); + if (condense_flag && compress_flag) condense_flag = 0; + iarg += 2; + } else if (strcmp(arg[iarg], "condense") == 0) { + if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "delete_atoms condense", error); + condense_flag = utils::logical(FLERR, arg[iarg + 1], false, lmp); + if (compress_flag && condense_flag) compress_flag = 0; iarg += 2; } else if (strcmp(arg[iarg], "bond") == 0) { if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "delete_atoms bond", error); - if (atom->molecular == Atom::ATOMIC) - error->all(FLERR, "Cannot use delete_atoms bond yes for non-molecular systems"); - if (atom->molecular == Atom::TEMPLATE) - error->all(FLERR, "Cannot use delete_atoms bond yes with atom_style template"); bond_flag = utils::logical(FLERR, arg[iarg + 1], false, lmp); + if (bond_flag && (atom->molecular == Atom::ATOMIC)) + error->all(FLERR, iarg, "Cannot use delete_atoms bond yes for non-molecular systems"); + if (bond_flag && (atom->molecular == Atom::TEMPLATE)) + error->all(FLERR, iarg, "Cannot use delete_atoms bond yes with atom_style template"); iarg += 2; } else if (strcmp(arg[iarg], "mol") == 0) { if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "delete_atoms mol", error); - if (atom->molecule_flag == 0) - error->all(FLERR, "Delete_atoms mol yes requires atom attribute molecule"); mol_flag = utils::logical(FLERR, arg[iarg + 1], false, lmp); + if (mol_flag && (atom->molecule_flag == 0)) + error->all(FLERR, iarg, "Delete_atoms mol yes requires atom attribute molecule"); iarg += 2; } else - error->all(FLERR, "Unknown delete_atoms option: {}", arg[iarg]); + error->all(FLERR, iarg, "Unknown delete_atoms option: {}", arg[iarg]); } } diff --git a/src/delete_atoms.h b/src/delete_atoms.h index a1825dab93..23eb3139ba 100644 --- a/src/delete_atoms.h +++ b/src/delete_atoms.h @@ -32,7 +32,7 @@ class DeleteAtoms : public Command { protected: int *dlist; - int allflag, compress_flag, bond_flag, mol_flag; + int allflag, compress_flag, condense_flag, bond_flag, mol_flag; std::map *hash; void delete_group(int, char **); From 7bd7be8f8693a4538d9c2f65878f7ffdddd8a8cd Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 7 Mar 2025 01:59:41 -0500 Subject: [PATCH 042/113] error out when trying unsupported pimd method with multiple processors per bead --- src/REPLICA/fix_pimd_langevin.cpp | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/src/REPLICA/fix_pimd_langevin.cpp b/src/REPLICA/fix_pimd_langevin.cpp index 4e530bd97e..271725e238 100644 --- a/src/REPLICA/fix_pimd_langevin.cpp +++ b/src/REPLICA/fix_pimd_langevin.cpp @@ -523,7 +523,10 @@ void FixPIMDLangevin::setup(int vflag) nmpimd_transform(bufbeads, x, M_x2xp[universe->iworld]); } else if (method == PIMD) { inter_replica_comm(x); - spring_force(); + if (cmode == SINGLE_PROC) + spring_force(); + else if (cmode == MULTI_PROC) + error->universe_all(FLERR, "Method pimd only supports a single processor per bead"); } else { error->universe_all( FLERR, From 2ff078f9730cf092e0c88580b707555182559e64 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 7 Mar 2025 02:24:12 -0500 Subject: [PATCH 043/113] add some more tests for delete_atom --- unittest/commands/test_delete_atoms.cpp | 55 ++++++++++++++++++++++++- 1 file changed, 54 insertions(+), 1 deletion(-) diff --git a/unittest/commands/test_delete_atoms.cpp b/unittest/commands/test_delete_atoms.cpp index 7c09e7497e..0caefce465 100644 --- a/unittest/commands/test_delete_atoms.cpp +++ b/unittest/commands/test_delete_atoms.cpp @@ -94,18 +94,25 @@ protected: TEST_F(DeleteAtomsTest, Simple) { + ASSERT_EQ(atom->map_tag_max, -1); + HIDE_OUTPUT([&] { + command("atom_modify map yes"); + }); atomic_system(); ASSERT_EQ(atom->natoms, 512); + ASSERT_EQ(atom->map_tag_max, 512); HIDE_OUTPUT([&] { - command("delete_atoms group top"); + command("delete_atoms group top compress no"); }); ASSERT_EQ(atom->natoms, 448); + ASSERT_EQ(atom->map_tag_max, 512); HIDE_OUTPUT([&] { command("delete_atoms region left"); }); ASSERT_EQ(atom->natoms, 392); + ASSERT_EQ(atom->map_tag_max, 392); HIDE_OUTPUT([&] { command("delete_atoms random fraction 0.5 yes all right 43252"); @@ -154,6 +161,52 @@ TEST_F(DeleteAtomsTest, Simple) TEST_FAILURE(".*ERROR: Delete_atoms random fraction has invalid value: -0.4.*", command("delete_atoms random fraction -0.4 no bottom right 77325");); } + +TEST_F(DeleteAtomsTest, Condense) +{ + HIDE_OUTPUT([&] { + command("atom_modify id yes map yes "); + command("region box block -4 4 -4 4 -4 4"); + command("create_box 1 box"); + command("fix oldid all property/atom i_oldid ghost yes"); + command("create_atoms 1 random 8 9648523 box"); + command("variable oldid atom id"); + command("set atom * i_oldid v_oldid"); + command("group odd id 1:8:2"); + }); + ASSERT_EQ(atom->natoms, 8); + ASSERT_EQ(atom->map_tag_max, 8); + int flag = -1, cols = -1; + auto index_custom = atom->find_custom("oldid", flag, cols); + ASSERT_TRUE(index_custom >= 0); + ASSERT_EQ(flag, 0); + ASSERT_EQ(cols, 0); + + HIDE_OUTPUT([&] { + command("delete_atoms group odd compress no"); + }); + ASSERT_EQ(atom->natoms, 4); + ASSERT_EQ(atom->map_tag_max, 8); + for (int i = 0; i < 4; ++i) + ASSERT_EQ(atom->ivector[index_custom][i], atom->tag[i]); + + HIDE_OUTPUT([&] { + command("delete_atoms group all"); + command("create_atoms 1 random 8 9648523 box"); + command("variable oldid atom id"); + command("set atom * i_oldid v_oldid"); + command("group odd delete"); + command("group odd id 1:8:2"); + }); + + HIDE_OUTPUT([&] { + command("delete_atoms group odd condense yes"); + }); + ASSERT_EQ(atom->natoms, 4); + ASSERT_EQ(atom->map_tag_max, 4); + for (int i = 0; i < 4; ++i) + ASSERT_EQ(atom->ivector[index_custom][i]/2, atom->tag[i]); +} } // namespace LAMMPS_NS int main(int argc, char **argv) From 6e94d83cffac6c6e4b26538d08370d6be6fc3f8c Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 7 Mar 2025 11:40:27 -0500 Subject: [PATCH 044/113] add option to synchronize fix halt stop requests across multi-partition runs --- doc/src/fix_halt.rst | 24 +++++++++---- src/fix_halt.cpp | 80 ++++++++++++++++++++++++++++++++++++++++---- src/fix_halt.h | 2 +- 3 files changed, 93 insertions(+), 13 deletions(-) diff --git a/doc/src/fix_halt.rst b/doc/src/fix_halt.rst index 0bcf2fb5ea..f17cafc58c 100644 --- a/doc/src/fix_halt.rst +++ b/doc/src/fix_halt.rst @@ -25,13 +25,14 @@ Syntax * operator = "<" or "<=" or ">" or ">=" or "==" or "!=" or "\|\^" * avalue = numeric value to compare attribute to * zero or more keyword/value pairs may be appended -* keyword = *error* or *message* or *path* +* keyword = *error* or *message* or *path* or *universe* .. parsed-literal:: *error* value = *hard* or *soft* or *continue* *message* value = *yes* or *no* *path* value = path to check for free space (may be in quotes) + *universe* value = *yes* or *no* Examples @@ -40,8 +41,10 @@ Examples .. code-block:: LAMMPS fix 10 all halt 1 bondmax > 1.5 - fix 10 all halt 10 v_myCheck != 0 error soft + fix 10 all halt 10 v_myCheck != 0 error soft message no fix 10 all halt 100 diskfree < 100000.0 path "dump storage/." + fix 2 all halt 100 v_curtime > ${maxtime} universe yes + Description """"""""""" @@ -162,12 +165,21 @@ is printed; the run simply exits. The latter may be desirable for post-processing tools that extract thermodynamic information from log files. +The optional *universe* keyword determines whether the halt request +should be synchronized across the partitions of a :doc:`multi-partition +run `. If *universe* is set to yes, fix halt will check if +there is a specific message received from any of the other partitions +requesting to stop the run on this partition as well. Consequently, if +fix halt determines to halt the simulation, the fix will send messages +to all other partitions so they stop their runs, too. + Restart, fix_modify, output, run start/stop, minimize info """"""""""""""""""""""""""""""""""""""""""""""""""""""""""" -No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options -are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various :doc:`output commands `. +No information about this fix is written to :doc:`binary restart files +`. None of the :doc:`fix_modify ` options are +relevant to this fix. No global or per-atom quantities are stored by +this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of the :doc:`run ` command. @@ -183,4 +195,4 @@ Related commands Default """"""" -The option defaults are error = soft, message = yes, and path = ".". +The option defaults are error = soft, message = yes, path = ".", and universe = no. diff --git a/src/fix_halt.cpp b/src/fix_halt.cpp index b34c79867f..a0047a3f7a 100644 --- a/src/fix_halt.cpp +++ b/src/fix_halt.cpp @@ -22,6 +22,7 @@ #include "neighbor.h" #include "timer.h" #include "update.h" +#include "universe.h" #include "variable.h" #include @@ -34,6 +35,7 @@ enum { BONDMAX, TLIMIT, DISKFREE, VARIABLE }; enum { LT, LE, GT, GE, EQ, NEQ, XOR }; enum { HARD, SOFT, CONTINUE }; enum { NOMSG = 0, YESMSG = 1 }; +static constexpr int UTAG = 999; /* ---------------------------------------------------------------------- */ @@ -42,11 +44,10 @@ FixHalt::FixHalt(LAMMPS *lmp, int narg, char **arg) : { if (narg < 7) utils::missing_cmd_args(FLERR, "fix halt", error); nevery = utils::inumeric(FLERR, arg[3], false, lmp); - if (nevery <= 0) error->all(FLERR, "Illegal fix halt command: nevery must be > 0"); + if (nevery <= 0) error->all(FLERR, 3, "Illegal fix halt command: nevery must be > 0"); // comparison args - idvar = nullptr; int iarg = 4; if (strcmp(arg[iarg], "tlimit") == 0) { @@ -56,20 +57,22 @@ FixHalt::FixHalt(LAMMPS *lmp, int narg, char **arg) : dlimit_path = utils::strdup("."); } else if (strcmp(arg[iarg], "bondmax") == 0) { attribute = BONDMAX; - } else { + } else if (utils::strmatch(arg[iarg], "^v_")) { ArgInfo argi(arg[iarg], ArgInfo::VARIABLE); if ((argi.get_type() == ArgInfo::UNKNOWN) || (argi.get_type() == ArgInfo::NONE) || (argi.get_dim() != 0)) - error->all(FLERR, "Invalid fix halt attribute {}", arg[iarg]); + error->all(FLERR, iarg, "Invalid fix halt attribute {}", arg[iarg]); attribute = VARIABLE; idvar = argi.copy_name(); ivar = input->variable->find(idvar); - if (ivar < 0) error->all(FLERR, "Could not find fix halt variable name"); + if (ivar < 0) error->all(FLERR, iarg, "Could not find fix halt variable name {}", idvar); if (input->variable->equalstyle(ivar) == 0) - error->all(FLERR, "Fix halt variable is not equal-style variable"); + error->all(FLERR, iarg, "Fix halt variable is not equal-style variable"); + } else { + error->all(FLERR, iarg, "Unknown fix halt keyword {}", arg[iarg]); } // clang-format off @@ -90,6 +93,7 @@ FixHalt::FixHalt(LAMMPS *lmp, int narg, char **arg) : eflag = SOFT; msgflag = YESMSG; + uflag = NOMSG; ++iarg; while (iarg < narg) { if (strcmp(arg[iarg], "error") == 0) { @@ -103,6 +107,10 @@ FixHalt::FixHalt(LAMMPS *lmp, int narg, char **arg) : if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "fix halt message", error); msgflag = utils::logical(FLERR, arg[iarg + 1], false, lmp); iarg += 2; + } else if (strcmp(arg[iarg], "universe") == 0) { + if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "fix halt universe", error); + uflag = utils::logical(FLERR, arg[iarg + 1], false, lmp); + iarg += 2; } else if (strcmp(arg[iarg], "path") == 0) { if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "fix halt error", error); ++iarg; @@ -189,6 +197,50 @@ void FixHalt::min_post_force(int /* vflag */) void FixHalt::end_of_step() { + // check if another partition has exited and we need to exit, too. + + if (uflag) { + MPI_Status status; + int partition = -1; + int flag = 0; + if (comm->me == 0) { + + // probe if any stop request from another partition is pending + + MPI_Iprobe(MPI_ANY_SOURCE, UTAG, universe->uworld, &flag, &status); + + if (flag) { + // determine which partition sent the stop request and receive the message + for (int i = 0; i < universe->nworlds; ++i) + if (universe->root_proc[i] == status.MPI_SOURCE) partition = i + 1; + + MPI_Recv(&flag, 1, MPI_INT, status.MPI_SOURCE, UTAG, universe->uworld, MPI_STATUS_IGNORE); + } + } + + // broadcast stop request partition to all processes in our partition + + MPI_Bcast(&partition, 1, MPI_INT, 0, world); + + // exit request pending handle the same as below + + if (partition > 0) { + + // hard halt -> exit LAMMPS + // soft/continue halt -> trigger timer to break from run loop + // print message with ID of fix halt in case multiple instances + + auto message = fmt::format("Received universe halt request from partition {} for fix-id {} on step {}", + partition, id, update->ntimestep); + if (eflag == HARD) { + error->all(FLERR, message); + } else if ((eflag == SOFT) || (eflag == CONTINUE)) { + if ((comm->me == 0) && (msgflag == YESMSG)) error->message(FLERR, message); + timer->force_timeout(); + } + } + } + // variable evaluation may invoke computes so wrap with clear/add double attvalue; @@ -228,6 +280,22 @@ void FixHalt::end_of_step() if ((attvalue == 0.0 && value == 0.0) || (attvalue != 0.0 && value != 0.0)) return; } + // send message to all other root processes to trigger exit across universe, if requested + + if (uflag && (comm->me == 0)) { + MPI_Request *req = new MPI_Request[universe->nworlds]; + for (int i = 0; i < universe->nworlds; ++i) { + if (universe->me == universe->root_proc[i]) continue; + MPI_Isend(&eflag, 1, MPI_INT, universe->root_proc[i], UTAG, universe->uworld, req + i); + } + + // wait for all sends to complete, so MPI_Finalize() will be happy + for (int i = 0; i < universe->nworlds; ++i) { + if (universe->me == universe->root_proc[i]) continue; + MPI_Wait(req + i, MPI_STATUS_IGNORE); + } + } + // hard halt -> exit LAMMPS // soft/continue halt -> trigger timer to break from run loop // print message with ID of fix halt in case multiple instances diff --git a/src/fix_halt.h b/src/fix_halt.h index d6c46778e4..1fe789e9fa 100644 --- a/src/fix_halt.h +++ b/src/fix_halt.h @@ -35,7 +35,7 @@ class FixHalt : public Fix { void post_run() override; private: - int attribute, operation, eflag, msgflag, ivar; + int attribute, operation, eflag, msgflag, ivar, uflag; bigint nextstep, thisstep; double value, tratio; char *idvar; From 24fc6eb10a2b1ff13b3707f7fb4e0a63ebdb7552 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 7 Mar 2025 11:40:41 -0500 Subject: [PATCH 045/113] modernize error messages --- src/fix_halt.cpp | 15 ++++++++------- 1 file changed, 8 insertions(+), 7 deletions(-) diff --git a/src/fix_halt.cpp b/src/fix_halt.cpp index a0047a3f7a..2139242169 100644 --- a/src/fix_halt.cpp +++ b/src/fix_halt.cpp @@ -21,8 +21,8 @@ #include "modify.h" #include "neighbor.h" #include "timer.h" -#include "update.h" #include "universe.h" +#include "update.h" #include "variable.h" #include @@ -84,7 +84,7 @@ FixHalt::FixHalt(LAMMPS *lmp, int narg, char **arg) : else if (strcmp(arg[iarg],"==") == 0) operation = EQ; else if (strcmp(arg[iarg],"!=") == 0) operation = NEQ; else if (strcmp(arg[iarg],"|^") == 0) operation = XOR; - else error->all(FLERR,"Invalid fix halt operator"); + else error->all(FLERR, iarg, "Invalid fix halt operator {}", arg[iarg]); ++iarg; value = utils::numeric(FLERR, arg[iarg], false, lmp); @@ -101,7 +101,7 @@ FixHalt::FixHalt(LAMMPS *lmp, int narg, char **arg) : if (strcmp(arg[iarg + 1], "hard") == 0) eflag = HARD; else if (strcmp(arg[iarg + 1], "soft") == 0) eflag = SOFT; else if (strcmp(arg[iarg + 1], "continue") == 0) eflag = CONTINUE; - else error->all(FLERR, "Unknown fix halt error condition {}", arg[iarg]); + else error->all(FLERR, iarg + 1, "Unknown fix halt error condition {}", arg[iarg]); iarg += 2; } else if (strcmp(arg[iarg], "message") == 0) { if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "fix halt message", error); @@ -112,7 +112,7 @@ FixHalt::FixHalt(LAMMPS *lmp, int narg, char **arg) : uflag = utils::logical(FLERR, arg[iarg + 1], false, lmp); iarg += 2; } else if (strcmp(arg[iarg], "path") == 0) { - if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "fix halt error", error); + if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "fix halt path", error); ++iarg; delete[] dlimit_path; // strip off outer quotes, if present @@ -165,9 +165,10 @@ void FixHalt::init() if (attribute == VARIABLE) { ivar = input->variable->find(idvar); - if (ivar < 0) error->all(FLERR, "Could not find fix halt variable {}", idvar); + if (ivar < 0) + error->all(FLERR, Error::NOLASTLINE, "Could not find fix halt variable {}", idvar); if (input->variable->equalstyle(ivar) == 0) - error->all(FLERR, "Fix halt variable {} is not equal-style variable", idvar); + error->all(FLERR, Error::NOLASTLINE, "Fix halt variable {} is not equal-style", idvar); } // settings used by TLIMIT @@ -180,7 +181,7 @@ void FixHalt::init() if (attribute == DISKFREE) { if (!dlimit_path || platform::disk_free(dlimit_path) < 0.0) - error->all(FLERR, "Disk limit not supported by OS or illegal path"); + error->all(FLERR, Error::NOLASTLINE, "Disk limit not supported by OS or illegal path"); } } From 9af8fdc91e925b08a5a424176af1147f3ea35930 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 7 Mar 2025 11:50:53 -0500 Subject: [PATCH 046/113] add MPI stub for MPI_Iprobe() --- src/STUBS/mpi.cpp | 8 ++++++++ src/STUBS/mpi.h | 1 + 2 files changed, 9 insertions(+) diff --git a/src/STUBS/mpi.cpp b/src/STUBS/mpi.cpp index 53b83236ba..f938c26f21 100644 --- a/src/STUBS/mpi.cpp +++ b/src/STUBS/mpi.cpp @@ -300,6 +300,14 @@ int MPI_Irecv(void *buf, int count, MPI_Datatype datatype, int source, int tag, /* ---------------------------------------------------------------------- */ +int MPI_Iprobe(int, int, MPI_Comm, int *flag, MPI_Status *); +{ + if (flag) *flag = 0; + return 0; +} + +/* ---------------------------------------------------------------------- */ + int MPI_Wait(MPI_Request *request, MPI_Status *status) { static int callcount = 0; diff --git a/src/STUBS/mpi.h b/src/STUBS/mpi.h index 71da393642..b89c098bad 100644 --- a/src/STUBS/mpi.h +++ b/src/STUBS/mpi.h @@ -105,6 +105,7 @@ int MPI_Recv(void *buf, int count, MPI_Datatype datatype, int source, int tag, M MPI_Status *status); int MPI_Irecv(void *buf, int count, MPI_Datatype datatype, int source, int tag, MPI_Comm comm, MPI_Request *request); +int MPI_Iprobe(int source, int tag, MPI_Comm comm, int *flag, MPI_Status *status); int MPI_Wait(MPI_Request *request, MPI_Status *status); int MPI_Waitall(int n, MPI_Request *request, MPI_Status *status); int MPI_Waitany(int count, MPI_Request *request, int *index, MPI_Status *status); From 976b73a2f2ab7c7ad15227aa97feb2f8dc8fece8 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 7 Mar 2025 12:05:38 -0500 Subject: [PATCH 047/113] fix typo --- src/STUBS/mpi.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/STUBS/mpi.cpp b/src/STUBS/mpi.cpp index f938c26f21..22cbc9af17 100644 --- a/src/STUBS/mpi.cpp +++ b/src/STUBS/mpi.cpp @@ -300,7 +300,7 @@ int MPI_Irecv(void *buf, int count, MPI_Datatype datatype, int source, int tag, /* ---------------------------------------------------------------------- */ -int MPI_Iprobe(int, int, MPI_Comm, int *flag, MPI_Status *); +int MPI_Iprobe(int, int, MPI_Comm, int *flag, MPI_Status *) { if (flag) *flag = 0; return 0; From 388f279633a7f8c9161ed575d3f61b333fdf96a3 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 7 Mar 2025 12:43:32 -0500 Subject: [PATCH 048/113] set stores_ids flag for some fixes as suggested by @sjplimp --- src/AMOEBA/fix_amoeba_bitorsion.cpp | 1 + src/AMOEBA/fix_amoeba_pitorsion.cpp | 1 + src/MACHDYN/fix_smd_tlsph_reference_configuration.cpp | 1 + src/MOLECULE/fix_cmap.cpp | 1 + src/PERI/fix_peri_neigh.cpp | 1 + 5 files changed, 5 insertions(+) diff --git a/src/AMOEBA/fix_amoeba_bitorsion.cpp b/src/AMOEBA/fix_amoeba_bitorsion.cpp index f814f4109a..9e2decd5c9 100644 --- a/src/AMOEBA/fix_amoeba_bitorsion.cpp +++ b/src/AMOEBA/fix_amoeba_bitorsion.cpp @@ -82,6 +82,7 @@ FixAmoebaBiTorsion::FixAmoebaBiTorsion(LAMMPS *lmp, int narg, char **arg) : wd_section = 1; respa_level_support = 1; ilevel_respa = 0; + stores_ids = 1; MPI_Comm_rank(world,&me); MPI_Comm_size(world,&nprocs); diff --git a/src/AMOEBA/fix_amoeba_pitorsion.cpp b/src/AMOEBA/fix_amoeba_pitorsion.cpp index 352e559d6b..e341771b15 100644 --- a/src/AMOEBA/fix_amoeba_pitorsion.cpp +++ b/src/AMOEBA/fix_amoeba_pitorsion.cpp @@ -62,6 +62,7 @@ FixAmoebaPiTorsion::FixAmoebaPiTorsion(LAMMPS *lmp, int narg, char **arg) : wd_section = 1; respa_level_support = 1; ilevel_respa = 0; + stores_ids = 1; MPI_Comm_rank(world,&me); MPI_Comm_size(world,&nprocs); diff --git a/src/MACHDYN/fix_smd_tlsph_reference_configuration.cpp b/src/MACHDYN/fix_smd_tlsph_reference_configuration.cpp index 72ad76eccd..f15af121a2 100644 --- a/src/MACHDYN/fix_smd_tlsph_reference_configuration.cpp +++ b/src/MACHDYN/fix_smd_tlsph_reference_configuration.cpp @@ -60,6 +60,7 @@ FixSMD_TLSPH_ReferenceConfiguration::FixSMD_TLSPH_ReferenceConfiguration(LAMMPS if (atom->map_style == Atom::MAP_NONE) error->all(FLERR, "Pair tlsph with partner list requires an atom map, see atom_modify"); + stores_ids = 1; maxpartner = 1; npartner = nullptr; partner = nullptr; diff --git a/src/MOLECULE/fix_cmap.cpp b/src/MOLECULE/fix_cmap.cpp index 29fa8e4072..a3b0bee9c8 100644 --- a/src/MOLECULE/fix_cmap.cpp +++ b/src/MOLECULE/fix_cmap.cpp @@ -87,6 +87,7 @@ FixCMAP::FixCMAP(LAMMPS *lmp, int narg, char **arg) : respa_level_support = 1; ilevel_respa = 0; eflag_caller = 1; + stores_ids = 1; // allocate memory for CMAP data diff --git a/src/PERI/fix_peri_neigh.cpp b/src/PERI/fix_peri_neigh.cpp index 3d965b7280..6adfc96f3f 100644 --- a/src/PERI/fix_peri_neigh.cpp +++ b/src/PERI/fix_peri_neigh.cpp @@ -52,6 +52,7 @@ FixPeriNeigh::FixPeriNeigh(LAMMPS *lmp,int narg, char **arg) : restart_global = 1; restart_peratom = 1; first = 1; + stores_ids = 1; // perform initial allocation of atom-based arrays // register with atom class From e3cf1dec279579ffaf5eea8613bb7d45185f1f3c Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 8 Mar 2025 17:52:26 -0500 Subject: [PATCH 049/113] restore original delete_atoms implementation. new version spun off as PR #4492 --- doc/src/delete_atoms.rst | 28 ++++---------- src/delete_atoms.cpp | 80 +++++++--------------------------------- src/delete_atoms.h | 2 +- 3 files changed, 23 insertions(+), 87 deletions(-) diff --git a/doc/src/delete_atoms.rst b/doc/src/delete_atoms.rst index 7ce3c1b58d..296a12dc5c 100644 --- a/doc/src/delete_atoms.rst +++ b/doc/src/delete_atoms.rst @@ -35,12 +35,11 @@ Syntax *variable* args = variable-name * zero or more keyword/value pairs may be appended -* keyword = *compress* or *condense* or *bond* or *mol* +* keyword = *compress* or *bond* or *mol* .. parsed-literal:: *compress* value = *no* or *yes* - *condense* value = *no* or *yes* *bond* value = *no* or *yes* *mol* value = *no* or *yes* @@ -51,7 +50,6 @@ Examples delete_atoms group edge delete_atoms region sphere compress no - delete_atoms region sphere condense yes delete_atoms overlap 0.3 all all delete_atoms overlap 0.5 solvent colloid delete_atoms random fraction 0.1 yes all cube 482793 bond yes @@ -131,31 +129,21 @@ other options listed above. Here is the meaning of the optional keywords. -If the *compress* keyword is set to *yes* (which is the default), then -after atoms are deleted, the atom IDs are re-assigned so that they run -from 1 to the number of atoms in the system. Note that this is not done -for molecular systems (see the :doc:`atom_style ` command), -regardless of the *compress* setting, since it would corrupt the bond -connectivity information that has already been assigned. However, the +If the *compress* keyword is set to *yes*, then after atoms are +deleted, then atom IDs are re-assigned so that they run from 1 to the +number of atoms in the system. Note that this is not done for +molecular systems (see the :doc:`atom_style ` command), +regardless of the *compress* setting, since it would foul up the bond +connectivity that has already been assigned. However, the :doc:`reset_atoms id ` command can be used after this command to accomplish the same thing. -Note that this re-assignment of IDs is not really a compression, where +Note that the re-assignment of IDs is not really a compression, where gaps in atom IDs are removed by decrementing atom IDs that are larger. Instead the IDs for all atoms are erased, and new IDs are assigned so that the atoms owned by individual processors have consecutive IDs, as the :doc:`create_atoms ` command explains. -.. versionadded:: TBD - -If the *condense* keyword set to *yes*, then after atoms are deleted, -the atom IDs are re-assigned in a way such that the order of atom-IDs is -preserved. This process is not efficient and cannot be used for very -large systems and requires local storage that scales with the number of -total atoms in the system. Also, the *compress* and the *condense* -keywords cannot be used at the same time. Whichever of the two is used -last will be applied. - A molecular system with fixed bonds, angles, dihedrals, or improper interactions, is one where the topology of the interactions is typically defined in the data file read by the :doc:`read_data diff --git a/src/delete_atoms.cpp b/src/delete_atoms.cpp index 65b74df50e..35f608461b 100644 --- a/src/delete_atoms.cpp +++ b/src/delete_atoms.cpp @@ -35,7 +35,6 @@ #include "region.h" #include "variable.h" -#include #include #include #include @@ -53,9 +52,9 @@ DeleteAtoms::DeleteAtoms(LAMMPS *lmp) : Command(lmp) {} void DeleteAtoms::command(int narg, char **arg) { if (domain->box_exist == 0) - error->all(FLERR, -1, "Delete_atoms command before simulation box is defined"); + error->all(FLERR, "Delete_atoms command before simulation box is defined"); if (narg < 1) utils::missing_cmd_args(FLERR, "delete_atoms", error); - if (atom->tag_enable == 0) error->all(FLERR, -1, "Cannot use delete_atoms unless atoms have IDs"); + if (atom->tag_enable == 0) error->all(FLERR, "Cannot use delete_atoms unless atoms have IDs"); // store state before delete @@ -79,21 +78,21 @@ void DeleteAtoms::command(int narg, char **arg) delete_random(narg, arg); // deprecated porosity option, now included in new partial option else if (strcmp(arg[0], "porosity") == 0) { - error->all(FLERR, Error::ARGZERO, + error->all(FLERR, "The delete_atoms 'porosity' keyword has been removed.\n" "Please use: delete_atoms random fraction frac exact group-ID region-ID seed\n"); } else if (strcmp(arg[0], "variable") == 0) delete_variable(narg, arg); else - error->all(FLERR, Error::ARGZERO, "Unknown delete_atoms sub-command: {}", arg[0]); + error->all(FLERR, "Unknown delete_atoms sub-command: {}", arg[0]); if (allflag) { int igroup = group->find("all"); if ((igroup >= 0) && modify->check_rigid_group_overlap(group->bitmask[igroup])) - if (comm->me == 0) error->warning(FLERR, "Attempting to delete atoms in rigid bodies"); + error->warning(FLERR, "Attempting to delete atoms in rigid bodies"); } else { if (modify->check_rigid_list_overlap(dlist)) - if (comm->me == 0) error->warning(FLERR, "Attempting to delete atoms in rigid bodies"); + error->warning(FLERR, "Attempting to delete atoms in rigid bodies"); } // if allflag = 1, just reset atom->nlocal @@ -131,9 +130,6 @@ void DeleteAtoms::command(int narg, char **arg) // if non-molecular system and compress flag set: // reset atom tags to be contiguous // set all atom IDs to 0, call tag_extend() - // if condense flag set, collect atom IDs for all atoms in replicated global array. - // sort array according to tag value, skip over tags that are zero and determine new tag. - // build new array with tags for all local atoms. if (compress_flag) { if (atom->molecular == Atom::ATOMIC) { @@ -143,47 +139,6 @@ void DeleteAtoms::command(int narg, char **arg) atom->tag_extend(); } else if (comm->me == 0) error->warning(FLERR, "Ignoring 'compress yes' for molecular system"); - } else if (condense_flag) { - if (atom->molecular == Atom::ATOMIC) { - if (atom->map_style == Atom::MAP_NONE) - error->all(FLERR, Error::NOLASTLINE, "Using 'condense yes' option requires an atom map"); - if (atom->map_tag_max + 1 > MAXSMALLINT) - error->all(FLERR, Error::NOLASTLINE, "Too many atoms for using 'condense yes' option"); - tagint *tag = atom->tag; - int nlocal = atom->nlocal; - int nall = nlocal + atom->nghost; - tagint maxtag = atom->map_tag_max + 1; - auto mytags = std::vector(maxtag, 0); - auto alltags = std::vector(maxtag, 0); - for (int i = 0; i < nlocal; i++) mytags[tag[i]] = tag[i]; - MPI_Allreduce(mytags.data(), alltags.data(), maxtag, MPI_LMP_TAGINT, MPI_SUM, world); - std::sort(alltags.begin(), alltags.end()); - tagint newtag = 0; - int localidx; - mytags.resize(nall); - for (int i = 0; i < nall; ++i) mytags[i] = 0; - // update atom map - atom->map_init(0); - atom->nghost = 0; - atom->map_set(); - for (auto t : alltags) { - // skip over unset tags - if (!t) continue; - ++newtag; - localidx = atom->map(t); - if ((localidx < 0)) continue; - mytags[localidx] = newtag; - } - for (int i = 0; i < nall; ++i) tag[i] = mytags[i]; - - // recreate atom map again - atom->map_tag_max = -1; - atom->map_style_set(); - atom->map_init(0); - atom->nghost = 0; - atom->map_set(); - } else if (comm->me == 0) - error->warning(FLERR, "Ignoring 'condense yes' for molecular system"); } // reset atom->natoms and also topology counts @@ -354,7 +309,7 @@ void DeleteAtoms::delete_overlap(int narg, char **arg) if (force->pair == nullptr) error->all(FLERR, "Delete_atoms requires a pair style be defined"); if (cut > neighbor->cutneighmax) error->all(FLERR, "Delete_atoms cutoff > max neighbor cutoff"); - if ((cut > neighbor->cutneighmin) && comm->me == 0) + if (cut > neighbor->cutneighmin && comm->me == 0) error->warning(FLERR, "Delete_atoms cutoff > minimum neighbor cutoff"); // setup domain, communication and neighboring @@ -925,35 +880,28 @@ void DeleteAtoms::options(int narg, char **arg) { compress_flag = 1; bond_flag = mol_flag = 0; - condense_flag = 0; int iarg = 0; while (iarg < narg) { if (strcmp(arg[iarg], "compress") == 0) { if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "delete_atoms compress", error); compress_flag = utils::logical(FLERR, arg[iarg + 1], false, lmp); - if (condense_flag && compress_flag) condense_flag = 0; - iarg += 2; - } else if (strcmp(arg[iarg], "condense") == 0) { - if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "delete_atoms condense", error); - condense_flag = utils::logical(FLERR, arg[iarg + 1], false, lmp); - if (compress_flag && condense_flag) compress_flag = 0; iarg += 2; } else if (strcmp(arg[iarg], "bond") == 0) { if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "delete_atoms bond", error); + if (atom->molecular == Atom::ATOMIC) + error->all(FLERR, "Cannot use delete_atoms bond yes for non-molecular systems"); + if (atom->molecular == Atom::TEMPLATE) + error->all(FLERR, "Cannot use delete_atoms bond yes with atom_style template"); bond_flag = utils::logical(FLERR, arg[iarg + 1], false, lmp); - if (bond_flag && (atom->molecular == Atom::ATOMIC)) - error->all(FLERR, iarg, "Cannot use delete_atoms bond yes for non-molecular systems"); - if (bond_flag && (atom->molecular == Atom::TEMPLATE)) - error->all(FLERR, iarg, "Cannot use delete_atoms bond yes with atom_style template"); iarg += 2; } else if (strcmp(arg[iarg], "mol") == 0) { if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "delete_atoms mol", error); + if (atom->molecule_flag == 0) + error->all(FLERR, "Delete_atoms mol yes requires atom attribute molecule"); mol_flag = utils::logical(FLERR, arg[iarg + 1], false, lmp); - if (mol_flag && (atom->molecule_flag == 0)) - error->all(FLERR, iarg, "Delete_atoms mol yes requires atom attribute molecule"); iarg += 2; } else - error->all(FLERR, iarg, "Unknown delete_atoms option: {}", arg[iarg]); + error->all(FLERR, "Unknown delete_atoms option: {}", arg[iarg]); } } diff --git a/src/delete_atoms.h b/src/delete_atoms.h index 23eb3139ba..a1825dab93 100644 --- a/src/delete_atoms.h +++ b/src/delete_atoms.h @@ -32,7 +32,7 @@ class DeleteAtoms : public Command { protected: int *dlist; - int allflag, compress_flag, condense_flag, bond_flag, mol_flag; + int allflag, compress_flag, bond_flag, mol_flag; std::map *hash; void delete_group(int, char **); From 15b7dd78f02998b7615b2b2996822a03a2b93ab0 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 8 Mar 2025 18:00:57 -0500 Subject: [PATCH 050/113] Revert "add some more tests for delete_atom" This reverts commit 2ff078f9730cf092e0c88580b707555182559e64. --- unittest/commands/test_delete_atoms.cpp | 55 +------------------------ 1 file changed, 1 insertion(+), 54 deletions(-) diff --git a/unittest/commands/test_delete_atoms.cpp b/unittest/commands/test_delete_atoms.cpp index 0caefce465..7c09e7497e 100644 --- a/unittest/commands/test_delete_atoms.cpp +++ b/unittest/commands/test_delete_atoms.cpp @@ -94,25 +94,18 @@ protected: TEST_F(DeleteAtomsTest, Simple) { - ASSERT_EQ(atom->map_tag_max, -1); - HIDE_OUTPUT([&] { - command("atom_modify map yes"); - }); atomic_system(); ASSERT_EQ(atom->natoms, 512); - ASSERT_EQ(atom->map_tag_max, 512); HIDE_OUTPUT([&] { - command("delete_atoms group top compress no"); + command("delete_atoms group top"); }); ASSERT_EQ(atom->natoms, 448); - ASSERT_EQ(atom->map_tag_max, 512); HIDE_OUTPUT([&] { command("delete_atoms region left"); }); ASSERT_EQ(atom->natoms, 392); - ASSERT_EQ(atom->map_tag_max, 392); HIDE_OUTPUT([&] { command("delete_atoms random fraction 0.5 yes all right 43252"); @@ -161,52 +154,6 @@ TEST_F(DeleteAtomsTest, Simple) TEST_FAILURE(".*ERROR: Delete_atoms random fraction has invalid value: -0.4.*", command("delete_atoms random fraction -0.4 no bottom right 77325");); } - -TEST_F(DeleteAtomsTest, Condense) -{ - HIDE_OUTPUT([&] { - command("atom_modify id yes map yes "); - command("region box block -4 4 -4 4 -4 4"); - command("create_box 1 box"); - command("fix oldid all property/atom i_oldid ghost yes"); - command("create_atoms 1 random 8 9648523 box"); - command("variable oldid atom id"); - command("set atom * i_oldid v_oldid"); - command("group odd id 1:8:2"); - }); - ASSERT_EQ(atom->natoms, 8); - ASSERT_EQ(atom->map_tag_max, 8); - int flag = -1, cols = -1; - auto index_custom = atom->find_custom("oldid", flag, cols); - ASSERT_TRUE(index_custom >= 0); - ASSERT_EQ(flag, 0); - ASSERT_EQ(cols, 0); - - HIDE_OUTPUT([&] { - command("delete_atoms group odd compress no"); - }); - ASSERT_EQ(atom->natoms, 4); - ASSERT_EQ(atom->map_tag_max, 8); - for (int i = 0; i < 4; ++i) - ASSERT_EQ(atom->ivector[index_custom][i], atom->tag[i]); - - HIDE_OUTPUT([&] { - command("delete_atoms group all"); - command("create_atoms 1 random 8 9648523 box"); - command("variable oldid atom id"); - command("set atom * i_oldid v_oldid"); - command("group odd delete"); - command("group odd id 1:8:2"); - }); - - HIDE_OUTPUT([&] { - command("delete_atoms group odd condense yes"); - }); - ASSERT_EQ(atom->natoms, 4); - ASSERT_EQ(atom->map_tag_max, 4); - for (int i = 0; i < 4; ++i) - ASSERT_EQ(atom->ivector[index_custom][i]/2, atom->tag[i]); -} } // namespace LAMMPS_NS int main(int argc, char **argv) From ca3d2de44bc2fbd5605a5cfdc5bfaf34f4bd40b5 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 9 Mar 2025 22:10:52 -0400 Subject: [PATCH 051/113] fix broken URL due to typo --- doc/src/region2vmd.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/src/region2vmd.rst b/doc/src/region2vmd.rst index 54216bb925..760facf06f 100644 --- a/doc/src/region2vmd.rst +++ b/doc/src/region2vmd.rst @@ -35,7 +35,7 @@ Description .. versionadded:: TBD -Write a `VMD `_ Tcl script file with +Write a `VMD `_ Tcl script file with commands that aim to create a visualization of :doc:`regions `. There may be multiple region visualizations stored in a single file. From 9ee1648af2f6cf993ac587e8e2ff6c9d880f259f Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 9 Mar 2025 22:21:51 -0400 Subject: [PATCH 052/113] document removed compute atom/molecule and its equivalent using chunks --- doc/src/Commands_removed.rst | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/doc/src/Commands_removed.rst b/doc/src/Commands_removed.rst index de60d6636c..cb67a3d07d 100644 --- a/doc/src/Commands_removed.rst +++ b/doc/src/Commands_removed.rst @@ -170,6 +170,18 @@ performance characteristics on NVIDIA GPUs. Both, the KOKKOS and the :ref:`GPU package ` are maintained and allow running LAMMPS with GPU acceleration. +Compute atom/molecule +_____________________ + +.. deprecated:: 11 Dec2015 + +The atom/molecule command has been removed from LAMMPS since it was superseded +by the more general and extensible "chunk infrastructure". Here the system is +partitioned in one of many possible ways - including using molecule IDs - +through the :doc:`compute chunk/atom ` command and then +summing is done using :doc:`compute reduce/chunk ` Please +refer to the :doc:`chunk HOWTO ` section for an overview. + Fix ave/spatial and fix ave/spatial/sphere ------------------------------------------ From 4be39d6d2be3df9644237332fd416fec4cc0c5a3 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 9 Mar 2025 22:46:03 -0400 Subject: [PATCH 053/113] fix typos --- doc/src/bond_bpm_spring.rst | 2 +- doc/src/bond_bpm_spring_plastic.rst | 4 ++-- doc/src/bond_rheo_shell.rst | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/doc/src/bond_bpm_spring.rst b/doc/src/bond_bpm_spring.rst index 69d8e2d491..ac83ad4543 100644 --- a/doc/src/bond_bpm_spring.rst +++ b/doc/src/bond_bpm_spring.rst @@ -153,7 +153,7 @@ the data file or restart files read by the :doc:`read_data ` or :doc:`read_restart ` commands: * :math:`k` (force/distance units) -* :math:`\epsilon_c` (unit less) +* :math:`\epsilon_c` (unitless) * :math:`\gamma` (force/velocity units) Additionally, if *volume/factor* is set to *yes*, a fourth coefficient diff --git a/doc/src/bond_bpm_spring_plastic.rst b/doc/src/bond_bpm_spring_plastic.rst index fb0c50e9d3..8597501f6f 100644 --- a/doc/src/bond_bpm_spring_plastic.rst +++ b/doc/src/bond_bpm_spring_plastic.rst @@ -108,9 +108,9 @@ the data file or restart files read by the :doc:`read_data ` or :doc:`read_restart ` commands: * :math:`k` (force/distance units) -* :math:`\epsilon_c` (unit less) +* :math:`\epsilon_c` (unitless) * :math:`\gamma` (force/velocity units) -* :math:`\epsilon_p (unit less) +* :math:`\epsilon_p` (unitless) See the :doc:`bpm/spring doc page ` for information on the *smooth*, *normalize*, *break*, *overlay/pair*, and *store/local* diff --git a/doc/src/bond_rheo_shell.rst b/doc/src/bond_rheo_shell.rst index 090f5ab7aa..ef8d7d4249 100644 --- a/doc/src/bond_rheo_shell.rst +++ b/doc/src/bond_rheo_shell.rst @@ -94,7 +94,7 @@ the data file or restart files read by the :doc:`read_data ` or :doc:`read_restart ` commands: * :math:`k` (force/distance units) -* :math:`\epsilon_c` (unit less) +* :math:`\epsilon_c` (unitless) * :math:`\gamma` (force/velocity units) Unlike other BPM-style bonds, this bond style does not update special From 79d2346eaa6a4f2957c311d08cc54c854777a5c1 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 10 Mar 2025 06:25:11 -0400 Subject: [PATCH 054/113] resolve spelling and formatting issues --- doc/src/bond_bpm_spring.rst | 2 +- doc/src/bond_bpm_spring_plastic.rst | 19 ++++++++++--------- doc/utils/sphinx-config/false_positives.txt | 1 + 3 files changed, 12 insertions(+), 10 deletions(-) diff --git a/doc/src/bond_bpm_spring.rst b/doc/src/bond_bpm_spring.rst index ac83ad4543..27962c81a1 100644 --- a/doc/src/bond_bpm_spring.rst +++ b/doc/src/bond_bpm_spring.rst @@ -142,7 +142,7 @@ is accordingly replaced with a square root. This approximation assumes bonds are evenly distributed on a spherical surface and neglects constant prefactors which are irrelevant since only the ratio of volumes matters. This term may be used to adjust the Poisson's ratio. See the simulation in the -examples/bpm/poissons_ratio directory for a demonstration of this effect. +``examples/bpm/poissons_ratio`` directory for a demonstration of this effect. If a bond is broken (or created), :math:`V_{0,i}` is updated by subtracting (or adding) that bond's contribution. diff --git a/doc/src/bond_bpm_spring_plastic.rst b/doc/src/bond_bpm_spring_plastic.rst index 8597501f6f..3bc2c4ee46 100644 --- a/doc/src/bond_bpm_spring_plastic.rst +++ b/doc/src/bond_bpm_spring_plastic.rst @@ -133,16 +133,17 @@ Restart and other info """"""""""""""""""""""""""""""""""""""""""""""""""""""""""" This bond style writes the reference state and plastic history of each -bond to :doc:`binary restart files `. Loading a restart -file will properly restore bonds. However, the reference state is NOT -written to data files. Therefore reading a data file will not -restore bonds and will cause their reference states to be redefined. +bond to :doc:`binary restart files `. Loading a restart file +will properly restore bonds. However, the reference state is NOT written +to data files. Therefore reading a data file will not restore bonds and +will cause their reference states to be redefined. -The potential energy and the single() function of this bond style returns zero. -The single() function also calculates two extra bond quantities, the initial -distance :math:`r_0` and the current equilbrium length :math:`r_eq`. These extra -quantities can be accessed by the :doc:`compute bond/local ` -command as *b1* and *b2*, respectively. +The potential energy and the single() function of this bond style +returns zero. The single() function also calculates two extra bond +quantities, the initial distance :math:`r_0` and the current equilibrium +length :math:`r_eq`. These extra quantities can be accessed by the +:doc:`compute bond/local ` command as *b1* and *b2*, +respectively. Restrictions """""""""""" diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index a9490a1e3b..a6548dbbcd 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -2951,6 +2951,7 @@ pKa pKb pKs planeforce +plastically Plathe Plimpton plog From 312bdcbddd0c25297598c679cb427277aa991679 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 10 Mar 2025 06:26:37 -0400 Subject: [PATCH 055/113] correct and clarify statements about the potentials and their relations to each other --- doc/src/bond_harmonic.rst | 2 ++ doc/src/bond_harmonic_shift.rst | 17 +++++++++++------ doc/src/bond_harmonic_shift_cut.rst | 11 ++++++++--- 3 files changed, 21 insertions(+), 9 deletions(-) diff --git a/doc/src/bond_harmonic.rst b/doc/src/bond_harmonic.rst index a76cc54746..70e652bb4a 100644 --- a/doc/src/bond_harmonic.rst +++ b/doc/src/bond_harmonic.rst @@ -60,6 +60,8 @@ Related commands """""""""""""""" :doc:`bond_coeff `, :doc:`delete_bonds ` +:doc:`bond style harmonic/shift `, +:doc:`bond style harmonic/shift/cut ` Default """"""" diff --git a/doc/src/bond_harmonic_shift.rst b/doc/src/bond_harmonic_shift.rst index 43e10bde00..e57d464af8 100644 --- a/doc/src/bond_harmonic_shift.rst +++ b/doc/src/bond_harmonic_shift.rst @@ -31,9 +31,15 @@ the potential E = \frac{U_{\text{min}}}{(r_0-r_c)^2} \left[ (r-r_0)^2-(r_c-r_0)^2 \right] -where :math:`r_0` is the equilibrium bond distance, and :math:`r_c` the critical distance. -The potential is :math:`-U_{\text{min}}` at :math:`r0` and zero at :math:`r_c`. The spring constant is -:math:`k = U_{\text{min}} / [ 2 (r_0-r_c)^2]`. +where :math:`r_0` is the equilibrium bond distance, and :math:`r_c` the +critical distance. The potential energy has the value +:math:`-U_{\text{min}}` at :math:`r_0` and zero at :math:`r_c`. This +bond style differs from :doc:`bond_style harmonic ` +by the value of the potential energy. + +The equivalent spring constant value *K* for use with :doc:`bond_style +harmonic ` can be computed using :math:`K = +U_{\text{min}} / [(r_0-r_c)^2]`. The following coefficients must be defined for each bond type via the :doc:`bond_coeff ` command as in the example above, or in @@ -41,9 +47,7 @@ the data file or restart files read by the :doc:`read_data ` or :doc:`read_restart ` commands: * :math:`U_{\text{min}}` (energy) - * :math:`r_0` (distance) - * :math:`r_c` (distance) ---------- @@ -63,7 +67,8 @@ Related commands """""""""""""""" :doc:`bond_coeff `, :doc:`delete_bonds `, -:doc:`bond_harmonic ` +:doc:`bond style harmonic `, +:doc:`bond style harmonic/shift/cut ` Default """"""" diff --git a/doc/src/bond_harmonic_shift_cut.rst b/doc/src/bond_harmonic_shift_cut.rst index d8d4a792b7..964ae4b9ba 100644 --- a/doc/src/bond_harmonic_shift_cut.rst +++ b/doc/src/bond_harmonic_shift_cut.rst @@ -31,9 +31,14 @@ uses the potential E = \frac{U_{\text{min}}}{(r_0-r_c)^2} \left[ (r-r_0)^2-(r_c-r_0)^2 \right] -where :math:`r_0` is the equilibrium bond distance, and rc the critical distance. -The bond potential is zero for distances :math:`r > r_c`. The potential is :math:`-U_{\text{min}}` -at :math:`r_0` and zero at :math:`r_c`. The spring constant is :math:`k = U_{\text{min}} / [ 2 (r_0-r_c)^2]`. +where :math:`r_0` is the equilibrium bond distance, and :math:`r_c` the +critical distance. The bond potential is zero and thus its force also +zero for distances :math:`r > r_c`. The potential energy has the value +:math:`-U_{\text{min}}` at :math:`r_0` and zero at :math:`r_c`. + +The equivalent spring constant value *K* for use with :doc:`bond_style +harmonic ` for :math:`r <= r_c`, can be computed using +:math:`K = U_{\text{min}} / [(r_0-r_c)^2]` The following coefficients must be defined for each bond type via the :doc:`bond_coeff ` command as in the example above, or in From 4cafb49c34f24dc0941311e91271ecf99a4e8f1e Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 10 Mar 2025 06:28:28 -0400 Subject: [PATCH 056/113] report which variable name was incorrect --- src/input.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/input.cpp b/src/input.cpp index 814f900fbd..377df97e87 100644 --- a/src/input.cpp +++ b/src/input.cpp @@ -610,7 +610,7 @@ void Input::substitute(char *&str, char *&str2, int &max, int &max2, int flag) while (var[i] != '\0' && var[i] != '}') i++; - if (var[i] == '\0') error->one(FLERR,"Invalid variable name"); + if (var[i] == '\0') error->one(FLERR,"Invalid variable name {}", var); var[i] = '\0'; beyond = ptr + strlen(var) + 3; value = variable->retrieve(var); From 6ff0f645e06c4ad269fe2a0cba542fbd206753b7 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 10 Mar 2025 06:28:45 -0400 Subject: [PATCH 057/113] formatting --- doc/utils/sphinx-config/conf.py.in | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/doc/utils/sphinx-config/conf.py.in b/doc/utils/sphinx-config/conf.py.in index e4b461397d..073143a7e9 100644 --- a/doc/utils/sphinx-config/conf.py.in +++ b/doc/utils/sphinx-config/conf.py.in @@ -208,13 +208,11 @@ html_favicon = '_static/lammps.ico' # Add any paths that contain custom static files (such as style sheets) here, # relative to this directory. They are copied after the builtin static files, # so a file named "default.css" will overwrite the builtin "default.css". -html_static_path = ['_static'] +html_static_path = ['_static',] # These paths are either relative to html_static_path # or fully qualified paths (eg. https://...) -html_css_files = [ - 'css/lammps.css', -] +html_css_files = ['css/lammps.css',] # Add any extra paths that contain custom files (such as robots.txt or # .htaccess) here, relative to this directory. These files are copied From 5a1aed7957a5703759415b34e0644029c07d4185 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 10 Mar 2025 12:16:51 -0400 Subject: [PATCH 058/113] properly tally the SYNC time contributions to the ALL time entry this way its contribution is not double counted when determining the "Other" time data. --- src/timer.cpp | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/src/timer.cpp b/src/timer.cpp index e448e73f2c..dea008a3c9 100644 --- a/src/timer.cpp +++ b/src/timer.cpp @@ -79,8 +79,12 @@ void Timer::_stamp(enum ttype which) if (_level > NORMAL) current_cpu = platform::cputime(); current_wall = platform::walltime(); - cpu_array[SYNC] += current_cpu - previous_cpu; - wall_array[SYNC] += current_wall - previous_wall; + const double delta_cpu = current_cpu - previous_cpu; + const double delta_wall = current_wall - previous_wall; + cpu_array[SYNC] += delta_cpu; + wall_array[SYNC] += delta_wall; + cpu_array[ALL] += delta_cpu; + wall_array[ALL] += delta_wall; previous_cpu = current_cpu; previous_wall = current_wall; } From 9c494d0a2562aace5c76d22510ee8c9ecb22e426 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 10 Mar 2025 13:30:08 -0400 Subject: [PATCH 059/113] include space in custom formats to show how spaces can be used to separate columns --- doc/src/fix_ave_chunk.rst | 4 ++-- doc/src/fix_ave_time.rst | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/doc/src/fix_ave_chunk.rst b/doc/src/fix_ave_chunk.rst index 76c7ec4cfc..704019d46a 100644 --- a/doc/src/fix_ave_chunk.rst +++ b/doc/src/fix_ave_chunk.rst @@ -459,8 +459,8 @@ output. This option can only be used with the *ave running* setting. The *format* keyword sets the numeric format of each value when it is printed to a file via the *file* keyword. Note that all values are -floating point quantities. The default format is %g. You can specify -a higher precision if desired (e.g., %20.16g). +floating point quantities. The default format is " %g". You can specify +a higher precision if desired (e.g., " %20.16g"). The *title1* and *title2* and *title3* keywords allow specification of the strings that will be printed as the first three lines of the output diff --git a/doc/src/fix_ave_time.rst b/doc/src/fix_ave_time.rst index 00771a1422..661ea2d466 100644 --- a/doc/src/fix_ave_time.rst +++ b/doc/src/fix_ave_time.rst @@ -304,8 +304,8 @@ output. This option can only be used with the *ave running* setting. The *format* keyword sets the numeric format of each value when it is printed to a file via the *file* keyword. Note that all values are -floating point quantities. The default format is %g. You can specify -a higher precision if desired (e.g., %20.16g). +floating point quantities. The default format is " %g". You can specify +a higher precision if desired (e.g., " %20.16g"). The *title1* and *title2* and *title3* keywords allow specification of the strings that will be printed as the first 2 or 3 lines of the From 8af31ca28cf666ccae731f4993df5f6924d5eff0 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 10 Mar 2025 16:04:35 -0400 Subject: [PATCH 060/113] fix minor memory leaks --- src/SPIN/compute_spin.cpp | 2 ++ src/SPIN/fix_nve_spin.cpp | 2 ++ 2 files changed, 4 insertions(+) diff --git a/src/SPIN/compute_spin.cpp b/src/SPIN/compute_spin.cpp index fc5e223e75..745b4ffa0a 100644 --- a/src/SPIN/compute_spin.cpp +++ b/src/SPIN/compute_spin.cpp @@ -105,6 +105,7 @@ void ComputeSpin::init() // init length of vector of ptrs to Pair/Spin styles if (npairspin > 0) { + delete[] spin_pairs; spin_pairs = new PairSpin*[npairspin]; } @@ -142,6 +143,7 @@ void ComputeSpin::init() nprecspin = precfixes.size(); if (nprecspin > 0) { + delete[] lockprecessionspin; lockprecessionspin = new FixPrecessionSpin *[nprecspin]; precession_spin_flag = 1; diff --git a/src/SPIN/fix_nve_spin.cpp b/src/SPIN/fix_nve_spin.cpp index bfc1543eed..1a08e2cf00 100644 --- a/src/SPIN/fix_nve_spin.cpp +++ b/src/SPIN/fix_nve_spin.cpp @@ -185,6 +185,7 @@ void FixNVESpin::init() // init length of vector of ptrs to Pair/Spin styles if (npairspin > 0) { + delete[] spin_pairs; spin_pairs = new PairSpin*[npairspin]; } @@ -231,6 +232,7 @@ void FixNVESpin::init() // init length of vector of ptrs to precession/spin styles if (nprecspin > 0) { + delete[] lockprecessionspin; lockprecessionspin = new FixPrecessionSpin*[nprecspin]; } From 08f8be18e521303e725530936d51c0b08c2e5196 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 10 Mar 2025 17:03:51 -0400 Subject: [PATCH 061/113] rework SPIN restart/data file examples --- .../SPIN/read_restart/Norm_randXY_8x8x32.data | 10255 ++++------------ examples/SPIN/read_restart/in.spin.read_data | 57 +- examples/SPIN/read_restart/in.spin.restart | 54 +- .../SPIN/read_restart/in.spin.write_restart | 64 +- .../log.10Mar25.spin.read_data.g++.1 | 136 + .../log.10Mar25.spin.read_data.g++.4 | 136 + .../log.10Mar25.spin.restart.g++.1 | 136 + .../log.10Mar25.spin.restart.g++.4 | 135 + .../log.10Mar25.spin.write_restart.g++.1 | 142 + .../log.10Mar25.spin.write_restart.g++.4 | 142 + .../log.14Apr20.spin.read_data.g++.1 | 110 - .../log.14Apr20.spin.read_data.g++.4 | 110 - .../log.14Apr20.spin.restart.g++.1 | 116 - .../log.14Apr20.spin.restart.g++.4 | 115 - .../log.14Apr20.spin.write_restart.g++.1 | 120 - .../log.14Apr20.spin.write_restart.g++.4 | 120 - .../read_restart/restart_hcp_cobalt.equil | Bin 60909 -> 60984 bytes 17 files changed, 2972 insertions(+), 8976 deletions(-) create mode 100644 examples/SPIN/read_restart/log.10Mar25.spin.read_data.g++.1 create mode 100644 examples/SPIN/read_restart/log.10Mar25.spin.read_data.g++.4 create mode 100644 examples/SPIN/read_restart/log.10Mar25.spin.restart.g++.1 create mode 100644 examples/SPIN/read_restart/log.10Mar25.spin.restart.g++.4 create mode 100644 examples/SPIN/read_restart/log.10Mar25.spin.write_restart.g++.1 create mode 100644 examples/SPIN/read_restart/log.10Mar25.spin.write_restart.g++.4 delete mode 100644 examples/SPIN/read_restart/log.14Apr20.spin.read_data.g++.1 delete mode 100644 examples/SPIN/read_restart/log.14Apr20.spin.read_data.g++.4 delete mode 100644 examples/SPIN/read_restart/log.14Apr20.spin.restart.g++.1 delete mode 100644 examples/SPIN/read_restart/log.14Apr20.spin.restart.g++.4 delete mode 100644 examples/SPIN/read_restart/log.14Apr20.spin.write_restart.g++.1 delete mode 100644 examples/SPIN/read_restart/log.14Apr20.spin.write_restart.g++.4 diff --git a/examples/SPIN/read_restart/Norm_randXY_8x8x32.data b/examples/SPIN/read_restart/Norm_randXY_8x8x32.data index d239bb6ca0..cc3dc7998c 100644 --- a/examples/SPIN/read_restart/Norm_randXY_8x8x32.data +++ b/examples/SPIN/read_restart/Norm_randXY_8x8x32.data @@ -1,8207 +1,2066 @@ -LAMMPS data file via write_data, version 4 May 2017, timestep = 0 +LAMMPS data file via write_data, version 4 Feb 2025, timestep = 0, units = metal -8192 atoms +1024 atoms 1 atom types -0.0000000000000000e+00 2.8320000000000000e+01 xlo xhi -0.0000000000000000e+00 2.8320000000000000e+01 ylo yhi -0.0000000000000000e+00 1.1328000000000000e+02 zlo zhi +0 15 xlo xhi +0 28.32 ylo yhi +0 13.68 zlo zhi Masses -1 58.93 +1 58.9332 Atoms # spin -1 1 1.72 0.0 0.0 0.0 0.52887 -0.848703 1.0 -2 1 1.72 1.77 1.77 0.0 -0.745115 -0.666936 1.0 -3 1 1.72 1.77 0.0 1.77 -0.989437 -0.144964 1.0 -4 1 1.72 0.0 1.77 1.77 0.999926 -0.0121449 1.0 -5 1 1.72 3.54 0.0 0.0 0.377063 -0.926188 1.0 -6 1 1.72 5.31 1.77 0.0 0.412944 0.910756 1.0 -7 1 1.72 5.31 0.0 1.77 -0.999979 0.00650985 1.0 -8 1 1.72 3.54 1.77 1.77 0.535453 -0.844565 1.0 -9 1 1.72 7.0799999 0.0 0.0 -0.986135 0.165942 1.0 -10 1 1.72 8.8500004 1.77 0.0 -0.37352 -0.927622 1.0 -11 1 1.72 8.8500004 0.0 1.77 -0.926878 0.375363 1.0 -12 1 1.72 7.0799999 1.77 1.77 -0.690063 -0.72375 1.0 -13 1 1.72 10.6199999 0.0 0.0 -0.7204 -0.693559 1.0 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0 +1013 0 0 0 +1014 0 0 0 +1015 0 0 0 +1016 0 0 0 +1017 0 0 0 +1018 0 0 0 +1019 0 0 0 +1020 0 0 0 +1021 0 0 0 +1022 0 0 0 +1023 0 0 0 +1024 0 0 0 diff --git a/examples/SPIN/read_restart/in.spin.read_data b/examples/SPIN/read_restart/in.spin.read_data index b2b55a9fcb..0875ad0f9d 100644 --- a/examples/SPIN/read_restart/in.spin.read_data +++ b/examples/SPIN/read_restart/in.spin.read_data @@ -1,45 +1,46 @@ -units metal -dimension 3 -boundary p p p +units metal +dimension 3 +boundary p p p -atom_style spin +atom_style spin # necessary for the serial algorithm (sametag) -atom_modify map array -read_data Norm_randXY_8x8x32.data +atom_modify map array +read_data Norm_randXY_8x8x32.data +replicate 1 1 2 -mass 1 58.93 +mass 1 58.93 -pair_style hybrid/overlay eam/alloy spin/exchange 4.0 -pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co -pair_coeff * * spin/exchange exchange 4.0 0.0446928 0.003496 1.4885 +pair_style hybrid/overlay eam/alloy spin/exchange 4.0 +pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co +pair_coeff * * spin/exchange exchange 4.0 0.0446928 0.003496 1.4885 -neighbor 1.0 bin -neigh_modify every 1 check no delay 0 +neighbor 1.0 bin +neigh_modify every 1 check no delay 0 -fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 -fix 2 all langevin/spin 0.0 0.0 21 +fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 +fix 2 all langevin/spin 0.0 0.0 21 -fix 3 all nve/spin lattice moving -timestep 0.0001 +fix 3 all nve/spin lattice moving +timestep 0.0001 # define outputs and computes -compute out_mag all spin -compute out_pe all pe -compute out_ke all ke -compute out_temp all temp +compute out_mag all spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp -variable magz equal c_out_mag[3] -variable magnorm equal c_out_mag[4] -variable emag equal c_out_mag[5] -variable tmag equal c_out_mag[6] +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] thermo 20 thermo_style custom step time v_magnorm pe v_emag v_tmag temp etotal thermo_modify format float %20.15g -compute outsp all property/atom spx spy spz sp fmx fmy fmz -dump 1 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7] - -run 100 +compute outsp all property/atom spx spy spz sp fmx fmy fmz +#dump 1 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7] +#dump_modify 1 sort id +run 100 diff --git a/examples/SPIN/read_restart/in.spin.restart b/examples/SPIN/read_restart/in.spin.restart index 985da65eb4..72ed6b1b09 100644 --- a/examples/SPIN/read_restart/in.spin.restart +++ b/examples/SPIN/read_restart/in.spin.restart @@ -1,49 +1,49 @@ # start a spin-lattice simulation from a data file -units metal -atom_style spin +units metal +atom_style spin -dimension 3 -boundary p p p +dimension 3 +boundary p p p # necessary for the serial algorithm (sametag) -atom_modify map array +atom_modify map array -read_restart restart_hcp_cobalt.equil +read_restart restart_hcp_cobalt.equil # setting mass, mag. moments, and interactions -mass 1 58.93 +mass 1 58.93 -pair_style hybrid/overlay eam/alloy spin/exchange 4.0 -pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co -pair_coeff * * spin/exchange exchange 4.0 0.3593 1.135028015e-05 1.064568567 +pair_style hybrid/overlay eam/alloy spin/exchange 4.0 +pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co +pair_coeff * * spin/exchange exchange 4.0 0.3593 1.135028015e-05 1.064568567 -neighbor 1.0 bin -neigh_modify every 1 check no delay 0 +neighbor 1.0 bin +neigh_modify every 1 check no delay 0 -fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 -fix 2 all langevin/spin 0.0 0.0 21 +fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 +fix 2 all langevin/spin 0.0 0.0 21 -fix 3 all nve/spin lattice moving -timestep 0.0001 +fix 3 all nve/spin lattice moving +timestep 0.0001 # define outputs -compute out_mag all spin -compute out_pe all pe -compute out_ke all ke -compute out_temp all temp +compute out_mag all spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp -variable magz equal c_out_mag[3] -variable magnorm equal c_out_mag[4] -variable emag equal c_out_mag[5] -variable tmag equal c_out_mag[6] +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] thermo 20 thermo_style custom step time v_magnorm pe v_emag v_tmag temp etotal thermo_modify format float %20.15g -compute outsp all property/atom spx spy spz sp fmx fmy fmz -dump 100 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7] +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 100 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7] -run 100 +run 100 diff --git a/examples/SPIN/read_restart/in.spin.write_restart b/examples/SPIN/read_restart/in.spin.write_restart index 19ab8e6b30..d0e8f79e1b 100644 --- a/examples/SPIN/read_restart/in.spin.write_restart +++ b/examples/SPIN/read_restart/in.spin.write_restart @@ -1,54 +1,54 @@ # fcc cobalt in a 3d periodic box -units metal -atom_style spin +units metal +atom_style spin -dimension 3 -boundary p p p +dimension 3 +boundary p p p # necessary for the serial algorithm (sametag) -atom_modify map array +atom_modify map array -lattice hcp 2.5071 -region box block 0.0 5.0 0.0 5.0 0.0 5.0 -create_box 1 box -create_atoms 1 box +lattice hcp 2.5071 +region box block 0.0 5.0 0.0 5.0 0.0 5.0 +create_box 1 box +create_atoms 1 box # setting mass, mag. moments, and interactions for cobalt -mass 1 58.93 +mass 1 58.93 -set group all spin/random 31 1.72 +set group all spin/atom/random 31 1.72 -pair_style spin/exchange 4.0 -pair_coeff * * exchange 4.0 0.3593 1.135028015e-05 1.064568567 +pair_style spin/exchange 4.0 +pair_coeff * * exchange 4.0 0.3593 1.135028015e-05 1.064568567 -neighbor 0.1 bin -neigh_modify every 10 check yes delay 20 +neighbor 0.1 bin +neigh_modify every 10 check yes delay 20 -fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 -fix 2 all langevin/spin 100.0 0.01 21 +fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 +fix 2 all langevin/spin 100.0 0.01 21 -fix 3 all nve/spin lattice frozen -timestep 0.0001 +fix 3 all nve/spin lattice frozen +timestep 0.0001 # compute and output options -compute out_mag all spin -compute out_pe all pe -compute out_ke all ke -compute out_temp all temp +compute out_mag all spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp -variable magz equal c_out_mag[3] -variable magnorm equal c_out_mag[4] -variable emag equal c_out_mag[5] -variable tmag equal c_out_mag[6] +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] thermo_style custom step time v_magnorm pe v_emag temp etotal thermo 100 -compute outsp all property/atom spx spy spz sp fmx fmy fmz -dump 100 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7] - -run 1000 -write_restart restart_hcp_cobalt.equil +compute outsp all property/atom spx spy spz sp fmx fmy fmz +#dump 100 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7] +#dump_modify 100 sort id +run 1000 +write_restart restart_hcp_cobalt.equil diff --git a/examples/SPIN/read_restart/log.10Mar25.spin.read_data.g++.1 b/examples/SPIN/read_restart/log.10Mar25.spin.read_data.g++.1 new file mode 100644 index 0000000000..6cc2175cbb --- /dev/null +++ b/examples/SPIN/read_restart/log.10Mar25.spin.read_data.g++.1 @@ -0,0 +1,136 @@ +LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-210-g8af31ca28c-modified) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99) + using 1 OpenMP thread(s) per MPI task +units metal +dimension 3 +boundary p p p + +atom_style spin + +# necessary for the serial algorithm (sametag) +atom_modify map array +read_data Norm_randXY_8x8x32.data +Reading data file ... + orthogonal box = (0 0 0) to (15 28.32 13.68) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 1024 atoms + reading velocities ... + 1024 velocities + read_data CPU = 0.004 seconds +replicate 1 1 2 +Replication is creating a 1x1x2 = 2 times larger system... + orthogonal box = (0 0 0) to (15 28.32 27.36) + 1 by 1 by 1 MPI processor grid + 2048 atoms + replicate CPU = 0.001 seconds + +mass 1 58.93 + +pair_style hybrid/overlay eam/alloy spin/exchange 4.0 +pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co +pair_coeff * * spin/exchange exchange 4.0 0.0446928 0.003496 1.4885 + +neighbor 1.0 bin +neigh_modify every 1 check no delay 0 + +fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 +fix 2 all langevin/spin 0.0 0.0 21 + +fix 3 all nve/spin lattice moving +timestep 0.0001 + +# define outputs and computes + +compute out_mag all spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo 20 +thermo_style custom step time v_magnorm pe v_emag v_tmag temp etotal +thermo_modify format float %20.15g + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +#dump 1 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7] +#dump_modify 1 sort id +run 100 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- fix nve/spin command: doi:10.1016/j.jcp.2018.06.042 + +@article{tranchida2018massively, +title={Massively Parallel Symplectic Algorithm for Coupled Magnetic Spin Dynamics and Molecular Dynamics}, +author={Tranchida, J and Plimpton, S J and Thibaudeau, P and Thompson, A P}, +journal={Journal of Computational Physics}, +volume={372}, +pages={406--425}, +year={2018}, +publisher={Elsevier} +doi={10.1016/j.jcp.2018.06.042} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7.499539 + ghost atom cutoff = 7.499539 + binsize = 3.7497695, bins = 5 8 8 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair eam/alloy, perpetual, half/full from (2) + attributes: half, newton on, cut 7.499539 + pair build: halffull/newton + stencil: none + bin: none + (2) pair spin/exchange, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 9.082 | 9.082 | 9.082 Mbytes + Step Time v_magnorm PotEng v_emag v_tmag Temp TotEng + 0 0 0.99566943155533 116726.359107918 -852.392312873949 34.9207785637842 0 116726.359107918 + 20 0.002 0.995669416541629 70905.5692189811 -849.222504107045 34.647400481739 172820.122486868 116632.998844426 + 40 0.004 0.995669401356638 71221.2391274615 -848.368415908416 34.9759984641547 171555.103338675 116613.950357609 + 60 0.006 0.995669394598344 69647.7523345612 -845.585158124559 36.100016238044 177502.681559427 116614.166097826 + 80 0.008 0.995669395756676 107415.560454437 -846.200871523815 37.9775024824566 35031.4099604677 116684.714477685 + 100 0.01 0.995669403283478 63849.6798250643 -836.341677782106 39.680777051272 199492.565587335 116634.518317396 +Loop time of 2.9685 on 1 procs for 100 steps with 2048 atoms + +Performance: 0.291 ns/day, 82.458 hours/ns, 33.687 timesteps/s, 68.991 katom-step/s +99.6% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.0382 | 1.0382 | 1.0382 | 0.0 | 34.97 +Neigh | 0.78323 | 0.78323 | 0.78323 | 0.0 | 26.38 +Comm | 0.013266 | 0.013266 | 0.013266 | 0.0 | 0.45 +Output | 0.00021367 | 0.00021367 | 0.00021367 | 0.0 | 0.01 +Modify | 1.1318 | 1.1318 | 1.1318 | 0.0 | 38.13 +Other | | 0.00176 | | | 0.06 + +Nlocal: 2048 ave 2048 max 2048 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 7952 ave 7952 max 7952 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 314944 ave 314944 max 314944 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 629888 ave 629888 max 629888 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 629888 +Ave neighs/atom = 307.5625 +Neighbor list builds = 100 +Dangerous builds not checked +Total wall time: 0:00:03 diff --git a/examples/SPIN/read_restart/log.10Mar25.spin.read_data.g++.4 b/examples/SPIN/read_restart/log.10Mar25.spin.read_data.g++.4 new file mode 100644 index 0000000000..cd15387170 --- /dev/null +++ b/examples/SPIN/read_restart/log.10Mar25.spin.read_data.g++.4 @@ -0,0 +1,136 @@ +LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-210-g8af31ca28c-modified) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99) + using 1 OpenMP thread(s) per MPI task +units metal +dimension 3 +boundary p p p + +atom_style spin + +# necessary for the serial algorithm (sametag) +atom_modify map array +read_data Norm_randXY_8x8x32.data +Reading data file ... + orthogonal box = (0 0 0) to (15 28.32 13.68) + 2 by 2 by 1 MPI processor grid + reading atoms ... + 1024 atoms + reading velocities ... + 1024 velocities + read_data CPU = 0.004 seconds +replicate 1 1 2 +Replication is creating a 1x1x2 = 2 times larger system... + orthogonal box = (0 0 0) to (15 28.32 27.36) + 1 by 2 by 2 MPI processor grid + 2048 atoms + replicate CPU = 0.002 seconds + +mass 1 58.93 + +pair_style hybrid/overlay eam/alloy spin/exchange 4.0 +pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co +pair_coeff * * spin/exchange exchange 4.0 0.0446928 0.003496 1.4885 + +neighbor 1.0 bin +neigh_modify every 1 check no delay 0 + +fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 +fix 2 all langevin/spin 0.0 0.0 21 + +fix 3 all nve/spin lattice moving +timestep 0.0001 + +# define outputs and computes + +compute out_mag all spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo 20 +thermo_style custom step time v_magnorm pe v_emag v_tmag temp etotal +thermo_modify format float %20.15g + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +#dump 1 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7] +#dump_modify 1 sort id +run 100 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- fix nve/spin command: doi:10.1016/j.jcp.2018.06.042 + +@article{tranchida2018massively, +title={Massively Parallel Symplectic Algorithm for Coupled Magnetic Spin Dynamics and Molecular Dynamics}, +author={Tranchida, J and Plimpton, S J and Thibaudeau, P and Thompson, A P}, +journal={Journal of Computational Physics}, +volume={372}, +pages={406--425}, +year={2018}, +publisher={Elsevier} +doi={10.1016/j.jcp.2018.06.042} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7.499539 + ghost atom cutoff = 7.499539 + binsize = 3.7497695, bins = 5 8 8 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair eam/alloy, perpetual, half/full from (2) + attributes: half, newton on, cut 7.499539 + pair build: halffull/newton + stencil: none + bin: none + (2) pair spin/exchange, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.812 | 5.812 | 5.812 Mbytes + Step Time v_magnorm PotEng v_emag v_tmag Temp TotEng + 0 0 0.995669431555328 116726.359107923 -852.39231287395 34.9207785637843 0 116726.359107923 + 20 0.002 0.995669419512638 70905.5692199804 -849.222502855646 34.6474282239503 172820.122483292 116632.998844479 + 40 0.004 0.995669419108591 71221.2391285209 -848.368412494784 34.97611050919 171555.103335676 116613.950357875 + 60 0.006 0.99566940895435 69647.7523345112 -845.585157291247 36.1001312564486 177502.681560664 116614.166098104 + 80 0.008 0.995669417344697 107415.560454912 -846.200874451992 37.9776090859263 35031.4099596403 116684.714477941 + 100 0.01 0.995669427709463 63849.6798245944 -836.341678212079 39.6809090980074 199492.565591024 116634.518317902 +Loop time of 0.981181 on 4 procs for 100 steps with 2048 atoms + +Performance: 0.881 ns/day, 27.255 hours/ns, 101.918 timesteps/s, 208.728 katom-step/s +99.0% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.3068 | 0.31135 | 0.31472 | 0.5 | 31.73 +Neigh | 0.21997 | 0.22967 | 0.23853 | 1.6 | 23.41 +Comm | 0.013651 | 0.026146 | 0.03694 | 6.4 | 2.66 +Output | 0.00010966 | 0.0001265 | 0.00017442 | 0.0 | 0.01 +Modify | 0.41246 | 0.41281 | 0.41313 | 0.0 | 42.07 +Other | | 0.001083 | | | 0.11 + +Nlocal: 512 ave 521 max 503 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 4112 ave 4121 max 4103 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 78736 ave 80265 max 77207 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +FullNghs: 157472 ave 160276 max 154668 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 629888 +Ave neighs/atom = 307.5625 +Neighbor list builds = 100 +Dangerous builds not checked +Total wall time: 0:00:01 diff --git a/examples/SPIN/read_restart/log.10Mar25.spin.restart.g++.1 b/examples/SPIN/read_restart/log.10Mar25.spin.restart.g++.1 new file mode 100644 index 0000000000..2d80452e77 --- /dev/null +++ b/examples/SPIN/read_restart/log.10Mar25.spin.restart.g++.1 @@ -0,0 +1,136 @@ +LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-209-g9c494d0a25-modified) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99) + using 1 OpenMP thread(s) per MPI task +# start a spin-lattice simulation from a data file +units metal +atom_style spin + +dimension 3 +boundary p p p + +# necessary for the serial algorithm (sametag) +atom_modify map array + +read_restart restart_hcp_cobalt.equil +Reading restart file ... + restart file = 4 Feb 2025, LAMMPS = 4 Feb 2025 +WARNING: Restart file used different # of processors: 4 vs. 1 (src/read_restart.cpp:628) + restoring atom style spin from restart + orthogonal box = (0 0 0) to (12.5355 21.712123 20.470386) + 1 by 1 by 1 MPI processor grid + restoring pair style spin/exchange from restart + 500 atoms + read_restart CPU = 0.001 seconds + +# setting mass, mag. moments, and interactions + +mass 1 58.93 + +pair_style hybrid/overlay eam/alloy spin/exchange 4.0 +pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co +pair_coeff * * spin/exchange exchange 4.0 0.3593 1.135028015e-05 1.064568567 + +neighbor 1.0 bin +neigh_modify every 1 check no delay 0 + +fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 +fix 2 all langevin/spin 0.0 0.0 21 + +fix 3 all nve/spin lattice moving +timestep 0.0001 + +# define outputs + +compute out_mag all spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo 20 +thermo_style custom step time v_magnorm pe v_emag v_tmag temp etotal +thermo_modify format float %20.15g + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 100 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7] + +run 100 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- fix nve/spin command: doi:10.1016/j.jcp.2018.06.042 + +@article{tranchida2018massively, +title={Massively Parallel Symplectic Algorithm for Coupled Magnetic Spin Dynamics and Molecular Dynamics}, +author={Tranchida, J and Plimpton, S J and Thibaudeau, P and Thompson, A P}, +journal={Journal of Computational Physics}, +volume={372}, +pages={406--425}, +year={2018}, +publisher={Elsevier} +doi={10.1016/j.jcp.2018.06.042} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7.499539 + ghost atom cutoff = 7.499539 + binsize = 3.7497695, bins = 4 6 6 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair eam/alloy, perpetual, half/full from (2) + attributes: half, newton on, cut 7.499539 + pair build: halffull/newton + stencil: none + bin: none + (2) pair spin/exchange, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +WARNING: Dump 100 includes no atom IDs and is not sorted by ID. This may complicate post-processing tasks or visualization (src/dump.cpp:220) +Per MPI rank memory allocation (min/avg/max) = 5.255 | 5.255 | 5.255 Mbytes + Step Time v_magnorm PotEng v_emag v_tmag Temp TotEng + 1000 0.1 0.108329626151838 -2200.38234464056 -5.38239240501934 2538.4004919406 0 -2200.38234464056 + 1020 0.102 0.108329682386499 -2200.39166154869 -5.39173355873446 2513.35505416838 0.14443948124536 -2200.38234508481 + 1040 0.104 0.108329779277802 -2200.41807807023 -5.41850411117855 2478.80774498816 0.553977603827987 -2200.38234606476 + 1060 0.106 0.10832983679925 -2200.45800593865 -5.45989595459997 2449.72742607971 1.1729875955989 -2200.38234728585 + 1080 0.108 0.108329813608032 -2200.50691109393 -5.5124931569671 2427.22111176668 1.93117695188971 -2200.38234861173 + 1100 0.11 0.108329744840252 -2200.5598219415 -5.57257298837707 2400.88858161056 2.75147127466091 -2200.38234980911 +Loop time of 0.469378 on 1 procs for 100 steps with 500 atoms + +Performance: 1.841 ns/day, 13.038 hours/ns, 213.048 timesteps/s, 106.524 katom-step/s +99.2% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.12016 | 0.12016 | 0.12016 | 0.0 | 25.60 +Neigh | 0.1469 | 0.1469 | 0.1469 | 0.0 | 31.30 +Comm | 0.0045348 | 0.0045348 | 0.0045348 | 0.0 | 0.97 +Output | 0.071711 | 0.071711 | 0.071711 | 0.0 | 15.28 +Modify | 0.12549 | 0.12549 | 0.12549 | 0.0 | 26.74 +Other | | 0.0005849 | | | 0.12 + +Nlocal: 500 ave 500 max 500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 2534 ave 2534 max 2534 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 36500 ave 36500 max 36500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 73000 ave 73000 max 73000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 73000 +Ave neighs/atom = 146 +Neighbor list builds = 100 +Dangerous builds not checked +Total wall time: 0:00:00 diff --git a/examples/SPIN/read_restart/log.10Mar25.spin.restart.g++.4 b/examples/SPIN/read_restart/log.10Mar25.spin.restart.g++.4 new file mode 100644 index 0000000000..a6509783e9 --- /dev/null +++ b/examples/SPIN/read_restart/log.10Mar25.spin.restart.g++.4 @@ -0,0 +1,135 @@ +LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-209-g9c494d0a25-modified) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99) + using 1 OpenMP thread(s) per MPI task +# start a spin-lattice simulation from a data file +units metal +atom_style spin + +dimension 3 +boundary p p p + +# necessary for the serial algorithm (sametag) +atom_modify map array + +read_restart restart_hcp_cobalt.equil +Reading restart file ... + restart file = 4 Feb 2025, LAMMPS = 4 Feb 2025 + restoring atom style spin from restart + orthogonal box = (0 0 0) to (12.5355 21.712123 20.470386) + 1 by 2 by 2 MPI processor grid + restoring pair style spin/exchange from restart + 500 atoms + read_restart CPU = 0.001 seconds + +# setting mass, mag. moments, and interactions + +mass 1 58.93 + +pair_style hybrid/overlay eam/alloy spin/exchange 4.0 +pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co +pair_coeff * * spin/exchange exchange 4.0 0.3593 1.135028015e-05 1.064568567 + +neighbor 1.0 bin +neigh_modify every 1 check no delay 0 + +fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 +fix 2 all langevin/spin 0.0 0.0 21 + +fix 3 all nve/spin lattice moving +timestep 0.0001 + +# define outputs + +compute out_mag all spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo 20 +thermo_style custom step time v_magnorm pe v_emag v_tmag temp etotal +thermo_modify format float %20.15g + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 100 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7] + +run 100 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- fix nve/spin command: doi:10.1016/j.jcp.2018.06.042 + +@article{tranchida2018massively, +title={Massively Parallel Symplectic Algorithm for Coupled Magnetic Spin Dynamics and Molecular Dynamics}, +author={Tranchida, J and Plimpton, S J and Thibaudeau, P and Thompson, A P}, +journal={Journal of Computational Physics}, +volume={372}, +pages={406--425}, +year={2018}, +publisher={Elsevier} +doi={10.1016/j.jcp.2018.06.042} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7.499539 + ghost atom cutoff = 7.499539 + binsize = 3.7497695, bins = 4 6 6 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair eam/alloy, perpetual, half/full from (2) + attributes: half, newton on, cut 7.499539 + pair build: halffull/newton + stencil: none + bin: none + (2) pair spin/exchange, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +WARNING: Dump 100 includes no atom IDs and is not sorted by ID. This may complicate post-processing tasks or visualization (src/dump.cpp:220) +Per MPI rank memory allocation (min/avg/max) = 5.188 | 5.188 | 5.188 Mbytes + Step Time v_magnorm PotEng v_emag v_tmag Temp TotEng + 1000 0.1 0.108329626151837 -2200.38234464016 -5.38239240501934 2538.4004919406 0 -2200.38234464016 + 1020 0.102 0.108329679130501 -2200.39166154883 -5.39173355888088 2513.35482198786 0.144439483520248 -2200.3823450848 + 1040 0.104 0.108329711621363 -2200.41807807205 -5.41850411300556 2478.80746282814 0.553977632037396 -2200.38234606475 + 1060 0.106 0.108329705919754 -2200.4580059451 -5.45989596110734 2449.72703106051 1.17298769526935 -2200.38234728587 + 1080 0.108 0.108329685101234 -2200.50691110405 -5.51249316740617 2427.22060141747 1.93117710885529 -2200.38234861172 + 1100 0.11 0.108329648174842 -2200.55982193806 -5.57257298547573 2400.88784946371 2.75147122140813 -2200.38234980911 +Loop time of 0.170658 on 4 procs for 100 steps with 500 atoms + +Performance: 5.063 ns/day, 4.740 hours/ns, 585.968 timesteps/s, 292.984 katom-step/s +97.6% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.031046 | 0.031556 | 0.031914 | 0.2 | 18.49 +Neigh | 0.036174 | 0.036592 | 0.037219 | 0.2 | 21.44 +Comm | 0.0051867 | 0.0053356 | 0.0055157 | 0.2 | 3.13 +Output | 0.020206 | 0.022625 | 0.025235 | 1.2 | 13.26 +Modify | 0.071608 | 0.074173 | 0.076565 | 0.7 | 43.46 +Other | | 0.0003758 | | | 0.22 + +Nlocal: 125 ave 127 max 122 min +Histogram: 1 0 0 0 1 0 0 0 0 2 +Nghost: 1387 ave 1390 max 1385 min +Histogram: 2 0 0 0 0 0 1 0 0 1 +Neighs: 9125 ave 9271 max 8945 min +Histogram: 1 0 0 1 0 0 0 0 1 1 +FullNghs: 18250 ave 18542 max 17812 min +Histogram: 1 0 0 0 1 0 0 0 0 2 + +Total # of neighbors = 73000 +Ave neighs/atom = 146 +Neighbor list builds = 100 +Dangerous builds not checked +Total wall time: 0:00:00 diff --git a/examples/SPIN/read_restart/log.10Mar25.spin.write_restart.g++.1 b/examples/SPIN/read_restart/log.10Mar25.spin.write_restart.g++.1 new file mode 100644 index 0000000000..f5eca88e4a --- /dev/null +++ b/examples/SPIN/read_restart/log.10Mar25.spin.write_restart.g++.1 @@ -0,0 +1,142 @@ +LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-209-g9c494d0a25-modified) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99) + using 1 OpenMP thread(s) per MPI task +# fcc cobalt in a 3d periodic box + +units metal +atom_style spin + +dimension 3 +boundary p p p + +# necessary for the serial algorithm (sametag) +atom_modify map array + +lattice hcp 2.5071 +Lattice spacing in x,y,z = 2.5071 4.3424246 4.0940772 +region box block 0.0 5.0 0.0 5.0 0.0 5.0 +create_box 1 box +Created orthogonal box = (0 0 0) to (12.5355 21.712123 20.470386) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 500 atoms + using lattice units in orthogonal box = (0 0 0) to (12.5355 21.712123 20.470386) + create_atoms CPU = 0.000 seconds + +# setting mass, mag. moments, and interactions for cobalt + +mass 1 58.93 + +set group all spin/atom/random 31 1.72 +Setting atom values ... + 500 settings made for spin/atom/random + +pair_style spin/exchange 4.0 +pair_coeff * * exchange 4.0 0.3593 1.135028015e-05 1.064568567 + +neighbor 0.1 bin +neigh_modify every 10 check yes delay 20 + +fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 +fix 2 all langevin/spin 100.0 0.01 21 + +fix 3 all nve/spin lattice frozen +timestep 0.0001 + +# compute and output options + +compute out_mag all spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo_style custom step time v_magnorm pe v_emag temp etotal +thermo 100 + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +#dump 100 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7] +#dump_modify 100 sort id +run 1000 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- fix nve/spin command: doi:10.1016/j.jcp.2018.06.042 + +@article{tranchida2018massively, +title={Massively Parallel Symplectic Algorithm for Coupled Magnetic Spin Dynamics and Molecular Dynamics}, +author={Tranchida, J and Plimpton, S J and Thibaudeau, P and Thompson, A P}, +journal={Journal of Computational Physics}, +volume={372}, +pages={406--425}, +year={2018}, +publisher={Elsevier} +doi={10.1016/j.jcp.2018.06.042} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 10 steps, delay = 20 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 4.1 + ghost atom cutoff = 4.1 + binsize = 2.05, bins = 7 11 10 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair spin/exchange, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.78 | 4.78 | 4.78 Mbytes + Step Time v_magnorm PotEng v_emag Temp TotEng + 0 0 0.076558814 0.89911794 0.89911794 0 0.89911794 + 100 0.01 0.077627966 0.36694275 0.36694275 0 0.36694275 + 200 0.02 0.076678387 -0.20241504 -0.20241504 0 -0.20241504 + 300 0.03 0.079174207 -0.67593525 -0.67593525 0 -0.67593525 + 400 0.04 0.085031074 -1.5172826 -1.5172826 0 -1.5172826 + 500 0.05 0.087026279 -2.042653 -2.042653 0 -2.042653 + 600 0.06 0.087064628 -2.6297295 -2.6297295 0 -2.6297295 + 700 0.07 0.089787949 -3.3144767 -3.3144767 0 -3.3144767 + 800 0.08 0.091698615 -4.028707 -4.028707 0 -4.028707 + 900 0.09 0.090031988 -4.6007241 -4.6007241 0 -4.6007241 + 1000 0.1 0.093256399 -5.2351082 -5.2351082 0 -5.2351082 +Loop time of 0.710237 on 1 procs for 1000 steps with 500 atoms + +Performance: 12.165 ns/day, 1.973 hours/ns, 1407.980 timesteps/s, 703.990 katom-step/s +99.5% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.12753 | 0.12753 | 0.12753 | 0.0 | 17.96 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.012846 | 0.012846 | 0.012846 | 0.0 | 1.81 +Output | 0.00014416 | 0.00014416 | 0.00014416 | 0.0 | 0.02 +Modify | 0.56854 | 0.56854 | 0.56854 | 0.0 | 80.05 +Other | | 0.001178 | | | 0.17 + +Nlocal: 500 ave 500 max 500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1221 ave 1221 max 1221 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 10000 ave 10000 max 10000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 10000 +Ave neighs/atom = 20 +Neighbor list builds = 0 +Dangerous builds = 0 +write_restart restart_hcp_cobalt.equil +System init for write_restart ... +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Total wall time: 0:00:00 diff --git a/examples/SPIN/read_restart/log.10Mar25.spin.write_restart.g++.4 b/examples/SPIN/read_restart/log.10Mar25.spin.write_restart.g++.4 new file mode 100644 index 0000000000..38dbc7abd8 --- /dev/null +++ b/examples/SPIN/read_restart/log.10Mar25.spin.write_restart.g++.4 @@ -0,0 +1,142 @@ +LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-209-g9c494d0a25-modified) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99) + using 1 OpenMP thread(s) per MPI task +# fcc cobalt in a 3d periodic box + +units metal +atom_style spin + +dimension 3 +boundary p p p + +# necessary for the serial algorithm (sametag) +atom_modify map array + +lattice hcp 2.5071 +Lattice spacing in x,y,z = 2.5071 4.3424246 4.0940772 +region box block 0.0 5.0 0.0 5.0 0.0 5.0 +create_box 1 box +Created orthogonal box = (0 0 0) to (12.5355 21.712123 20.470386) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 500 atoms + using lattice units in orthogonal box = (0 0 0) to (12.5355 21.712123 20.470386) + create_atoms CPU = 0.001 seconds + +# setting mass, mag. moments, and interactions for cobalt + +mass 1 58.93 + +set group all spin/atom/random 31 1.72 +Setting atom values ... + 500 settings made for spin/atom/random + +pair_style spin/exchange 4.0 +pair_coeff * * exchange 4.0 0.3593 1.135028015e-05 1.064568567 + +neighbor 0.1 bin +neigh_modify every 10 check yes delay 20 + +fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 +fix 2 all langevin/spin 100.0 0.01 21 + +fix 3 all nve/spin lattice frozen +timestep 0.0001 + +# compute and output options + +compute out_mag all spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo_style custom step time v_magnorm pe v_emag temp etotal +thermo 100 + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +#dump 100 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7] +#dump_modify 100 sort id +run 1000 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- fix nve/spin command: doi:10.1016/j.jcp.2018.06.042 + +@article{tranchida2018massively, +title={Massively Parallel Symplectic Algorithm for Coupled Magnetic Spin Dynamics and Molecular Dynamics}, +author={Tranchida, J and Plimpton, S J and Thibaudeau, P and Thompson, A P}, +journal={Journal of Computational Physics}, +volume={372}, +pages={406--425}, +year={2018}, +publisher={Elsevier} +doi={10.1016/j.jcp.2018.06.042} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 10 steps, delay = 20 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 4.1 + ghost atom cutoff = 4.1 + binsize = 2.05, bins = 7 11 10 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair spin/exchange, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.732 | 4.732 | 4.733 Mbytes + Step Time v_magnorm PotEng v_emag Temp TotEng + 0 0 0.076558814 0.89911794 0.89911794 0 0.89911794 + 100 0.01 0.078299852 0.44131103 0.44131103 0 0.44131103 + 200 0.02 0.081260369 -0.2174146 -0.2174146 0 -0.2174146 + 300 0.03 0.081195064 -0.87039697 -0.87039697 0 -0.87039697 + 400 0.04 0.087298284 -1.7069593 -1.7069593 0 -1.7069593 + 500 0.05 0.087663192 -2.1882865 -2.1882865 0 -2.1882865 + 600 0.06 0.091713114 -2.926766 -2.926766 0 -2.926766 + 700 0.07 0.093779218 -3.3532704 -3.3532704 0 -3.3532704 + 800 0.08 0.097960251 -3.9343481 -3.9343481 0 -3.9343481 + 900 0.09 0.10193598 -4.7944099 -4.7944099 0 -4.7944099 + 1000 0.1 0.10832963 -5.3823924 -5.3823924 0 -5.3823924 +Loop time of 0.391762 on 4 procs for 1000 steps with 500 atoms + +Performance: 22.054 ns/day, 1.088 hours/ns, 2552.571 timesteps/s, 1.276 Matom-step/s +98.1% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.031554 | 0.032024 | 0.032587 | 0.2 | 8.17 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.014944 | 0.015944 | 0.016873 | 0.6 | 4.07 +Output | 0.00010694 | 0.00012063 | 0.00015425 | 0.0 | 0.03 +Modify | 0.34232 | 0.34279 | 0.34327 | 0.1 | 87.50 +Other | | 0.0008836 | | | 0.23 + +Nlocal: 125 ave 125 max 125 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 597.5 ave 600 max 595 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 2500 ave 2500 max 2500 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 10000 +Ave neighs/atom = 20 +Neighbor list builds = 0 +Dangerous builds = 0 +write_restart restart_hcp_cobalt.equil +System init for write_restart ... +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Total wall time: 0:00:00 diff --git a/examples/SPIN/read_restart/log.14Apr20.spin.read_data.g++.1 b/examples/SPIN/read_restart/log.14Apr20.spin.read_data.g++.1 deleted file mode 100644 index 4a744700f9..0000000000 --- a/examples/SPIN/read_restart/log.14Apr20.spin.read_data.g++.1 +++ /dev/null @@ -1,110 +0,0 @@ -LAMMPS (19 Mar 2020) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:94) - using 1 OpenMP thread(s) per MPI task -units metal -dimension 3 -boundary p p p - -atom_style spin - -# necessary for the serial algorithm (sametag) -atom_modify map array -read_data Norm_randXY_8x8x32.data - orthogonal box = (0 0 0) to (28.32 28.32 113.28) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 8192 atoms - read_data CPU = 0.022048 secs - -mass 1 58.93 - -pair_style hybrid/overlay eam/alloy spin/exchange 4.0 -pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co -pair_coeff * * spin/exchange exchange 4.0 0.0446928 0.003496 1.4885 - -neighbor 1.0 bin -neigh_modify every 1 check no delay 0 - -fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 -fix 2 all langevin/spin 0.0 0.0 21 - -fix 3 all nve/spin lattice moving -timestep 0.0001 - -# define outputs and computes - -compute out_mag all spin -compute out_pe all pe -compute out_ke all ke -compute out_temp all temp - -variable magz equal c_out_mag[3] -variable magnorm equal c_out_mag[4] -variable emag equal c_out_mag[5] -variable tmag equal c_out_mag[6] - -thermo 20 -thermo_style custom step time v_magnorm pe v_emag v_tmag temp etotal -thermo_modify format float %20.15g - -compute outsp all property/atom spx spy spz sp fmx fmy fmz -dump 1 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7] - -run 100 -Neighbor list info ... - update every 1 steps, delay 0 steps, check no - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 7.49954 - ghost atom cutoff = 7.49954 - binsize = 3.74977, bins = 8 8 31 - 2 neighbor lists, perpetual/occasional/extra = 2 0 0 - (1) pair eam/alloy, perpetual, half/full from (2) - attributes: half, newton on - pair build: halffull/newton - stencil: none - bin: none - (2) pair spin/exchange, perpetual - attributes: full, newton on - pair build: full/bin/atomonly - stencil: full/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 19.99 | 19.99 | 19.99 Mbytes -Step Time v_magnorm PotEng v_emag v_tmag Temp TotEng - 0 0 0.0177864461018737 -36558.7284872918 -661.829206399896 1274.398774669 0 -36558.7284872918 - 20 0.002 0.0177864377256184 -36558.7389378387 -661.839683504936 1259.94171978912 0.00986992693139795 -36558.7284878577 - 40 0.004 0.017786472977471 -36558.7684525639 -661.869582914286 1224.05894016152 0.0377451568363827 -36558.7284891299 - 60 0.006 0.0177865119543331 -36558.8126238543 -661.915330492427 1184.24369688088 0.0794631076347515 -36558.728490712 - 80 0.008 0.0177865172048059 -36558.8659242367 -661.972562482488 1152.05459929593 0.129803482511904 -36558.7284922233 - 100 0.01 0.0177865063752424 -36558.9229549739 -662.037138807935 1129.51470280479 0.183667498513087 -36558.7284933644 -Loop time of 14.3276 on 1 procs for 100 steps with 8192 atoms - -Performance: 0.060 ns/day, 397.988 hours/ns, 6.980 timesteps/s -99.7% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 4.0409 | 4.0409 | 4.0409 | 0.0 | 28.20 -Neigh | 3.6219 | 3.6219 | 3.6219 | 0.0 | 25.28 -Comm | 0.055327 | 0.055327 | 0.055327 | 0.0 | 0.39 -Output | 2.4259 | 2.4259 | 2.4259 | 0.0 | 16.93 -Modify | 4.1688 | 4.1688 | 4.1688 | 0.0 | 29.10 -Other | | 0.01477 | | | 0.10 - -Nlocal: 8192 ave 8192 max 8192 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 14621 ave 14621 max 14621 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 573440 ave 573440 max 573440 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 1.14688e+06 ave 1.14688e+06 max 1.14688e+06 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 1146880 -Ave neighs/atom = 140 -Neighbor list builds = 100 -Dangerous builds not checked - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:14 diff --git a/examples/SPIN/read_restart/log.14Apr20.spin.read_data.g++.4 b/examples/SPIN/read_restart/log.14Apr20.spin.read_data.g++.4 deleted file mode 100644 index 6ce648abf3..0000000000 --- a/examples/SPIN/read_restart/log.14Apr20.spin.read_data.g++.4 +++ /dev/null @@ -1,110 +0,0 @@ -LAMMPS (19 Mar 2020) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:94) - using 1 OpenMP thread(s) per MPI task -units metal -dimension 3 -boundary p p p - -atom_style spin - -# necessary for the serial algorithm (sametag) -atom_modify map array -read_data Norm_randXY_8x8x32.data - orthogonal box = (0 0 0) to (28.32 28.32 113.28) - 1 by 1 by 4 MPI processor grid - reading atoms ... - 8192 atoms - read_data CPU = 0.013634 secs - -mass 1 58.93 - -pair_style hybrid/overlay eam/alloy spin/exchange 4.0 -pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co -pair_coeff * * spin/exchange exchange 4.0 0.0446928 0.003496 1.4885 - -neighbor 1.0 bin -neigh_modify every 1 check no delay 0 - -fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 -fix 2 all langevin/spin 0.0 0.0 21 - -fix 3 all nve/spin lattice moving -timestep 0.0001 - -# define outputs and computes - -compute out_mag all spin -compute out_pe all pe -compute out_ke all ke -compute out_temp all temp - -variable magz equal c_out_mag[3] -variable magnorm equal c_out_mag[4] -variable emag equal c_out_mag[5] -variable tmag equal c_out_mag[6] - -thermo 20 -thermo_style custom step time v_magnorm pe v_emag v_tmag temp etotal -thermo_modify format float %20.15g - -compute outsp all property/atom spx spy spz sp fmx fmy fmz -dump 1 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7] - -run 100 -Neighbor list info ... - update every 1 steps, delay 0 steps, check no - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 7.49954 - ghost atom cutoff = 7.49954 - binsize = 3.74977, bins = 8 8 31 - 2 neighbor lists, perpetual/occasional/extra = 2 0 0 - (1) pair eam/alloy, perpetual, half/full from (2) - attributes: half, newton on - pair build: halffull/newton - stencil: none - bin: none - (2) pair spin/exchange, perpetual - attributes: full, newton on - pair build: full/bin/atomonly - stencil: full/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 8.961 | 9.047 | 9.29 Mbytes -Step Time v_magnorm PotEng v_emag v_tmag Temp TotEng - 0 0 0.0177864461018739 -36558.7284872997 -661.829206399894 1274.398774669 0 -36558.7284872997 - 20 0.002 0.0177863981273124 -36558.7389378386 -661.839683504262 1259.94177798388 0.00986992629371963 -36558.7284878582 - 40 0.004 0.0177864622701489 -36558.7684525586 -661.869582908114 1224.05908191331 0.0377451510479599 -36558.7284891308 - 60 0.006 0.0177865625037858 -36558.8126238326 -661.915330472361 1184.24389640891 0.0794630890177406 -36558.72849071 - 80 0.008 0.0177865898045059 -36558.8659241943 -661.972562439245 1152.05483020781 0.129803443061299 -36558.7284922226 - 100 0.01 0.017786565190115 -36558.9229549058 -662.037138735432 1129.51495182843 0.183667434061771 -36558.7284933646 -Loop time of 4.35911 on 4 procs for 100 steps with 8192 atoms - -Performance: 0.198 ns/day, 121.086 hours/ns, 22.940 timesteps/s -99.7% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 1.0924 | 1.1043 | 1.1117 | 0.7 | 25.33 -Neigh | 0.93575 | 0.94926 | 0.98325 | 2.0 | 21.78 -Comm | 0.044663 | 0.088288 | 0.11128 | 8.7 | 2.03 -Output | 0.64199 | 0.6587 | 0.67226 | 1.4 | 15.11 -Modify | 1.5412 | 1.5535 | 1.5706 | 0.9 | 35.64 -Other | | 0.005046 | | | 0.12 - -Nlocal: 2048 ave 2061 max 2035 min -Histogram: 1 0 0 1 0 0 1 0 0 1 -Nghost: 5765 ave 5778 max 5752 min -Histogram: 1 0 0 1 0 0 1 0 0 1 -Neighs: 143360 ave 144262 max 142469 min -Histogram: 1 0 0 1 0 0 1 0 0 1 -FullNghs: 286720 ave 288540 max 284900 min -Histogram: 1 0 0 1 0 0 1 0 0 1 - -Total # of neighbors = 1146880 -Ave neighs/atom = 140 -Neighbor list builds = 100 -Dangerous builds not checked - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:04 diff --git a/examples/SPIN/read_restart/log.14Apr20.spin.restart.g++.1 b/examples/SPIN/read_restart/log.14Apr20.spin.restart.g++.1 deleted file mode 100644 index 652f7da474..0000000000 --- a/examples/SPIN/read_restart/log.14Apr20.spin.restart.g++.1 +++ /dev/null @@ -1,116 +0,0 @@ -LAMMPS (19 Mar 2020) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:94) - using 1 OpenMP thread(s) per MPI task -# start a spin-lattice simulation from a data file -units metal -atom_style spin - -dimension 3 -boundary p p p - -# necessary for the serial algorithm (sametag) -atom_modify map array - -read_restart restart_hcp_cobalt.equil -WARNING: Restart file used different # of processors: 4 vs. 1 (../read_restart.cpp:736) - restoring atom style spin from restart - orthogonal box = (0 0 0) to (12.5355 21.7121 20.4704) - 1 by 1 by 1 MPI processor grid - restoring pair style spin/exchange from restart - 500 atoms - read_restart CPU = 0.00179696 secs - -# setting mass, mag. moments, and interactions - -mass 1 58.93 - -pair_style hybrid/overlay eam/alloy spin/exchange 4.0 -pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co -pair_coeff * * spin/exchange exchange 4.0 0.3593 1.135028015e-05 1.064568567 - -neighbor 1.0 bin -neigh_modify every 1 check no delay 0 - -fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 -fix 2 all langevin/spin 0.0 0.0 21 - -fix 3 all nve/spin lattice moving -timestep 0.0001 - -# define outputs - -compute out_mag all spin -compute out_pe all pe -compute out_ke all ke -compute out_temp all temp - -variable magz equal c_out_mag[3] -variable magnorm equal c_out_mag[4] -variable emag equal c_out_mag[5] -variable tmag equal c_out_mag[6] - -thermo 20 -thermo_style custom step time v_magnorm pe v_emag v_tmag temp etotal -thermo_modify format float %20.15g - -compute outsp all property/atom spx spy spz sp fmx fmy fmz -dump 100 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7] - -run 100 -Neighbor list info ... - update every 1 steps, delay 0 steps, check no - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 7.49954 - ghost atom cutoff = 7.49954 - binsize = 3.74977, bins = 4 6 6 - 2 neighbor lists, perpetual/occasional/extra = 2 0 0 - (1) pair eam/alloy, perpetual, half/full from (2) - attributes: half, newton on - pair build: halffull/newton - stencil: none - bin: none - (2) pair spin/exchange, perpetual - attributes: full, newton on - pair build: full/bin/atomonly - stencil: full/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 7.422 | 7.422 | 7.422 Mbytes -Step Time v_magnorm PotEng v_emag v_tmag Temp TotEng - 1000 0 0.108317262557656 -2200.38241212222 -5.38245988668244 2538.4247868621 0 -2200.38241212222 - 1020 0.002 0.108317318495042 -2200.39172132133 -5.39179331134703 2513.42968070374 0.144319963844279 -2200.38241256643 - 1040 0.004 0.108317415558744 -2200.41811580407 -5.418541526637 2478.87571728648 0.553516420254567 -2200.38241354532 - 1060 0.006 0.108317473592946 -2200.45801216332 -5.45990062771403 2449.77257658726 1.17203792179707 -2200.38241476526 - 1080 0.008 0.108317450745396 -2200.5068824087 -5.51245983698347 2427.25022669715 1.92968606059505 -2200.3824160902 - 1100 0.01 0.108317381572202 -2200.55976028827 -5.57250071024394 2400.86131889957 2.74946927499959 -2200.38241728649 -Loop time of 0.954493 on 1 procs for 100 steps with 500 atoms - -Performance: 0.905 ns/day, 26.514 hours/ns, 104.768 timesteps/s -100.0% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.27043 | 0.27043 | 0.27043 | 0.0 | 28.33 -Neigh | 0.26148 | 0.26148 | 0.26148 | 0.0 | 27.40 -Comm | 0.0071123 | 0.0071123 | 0.0071123 | 0.0 | 0.75 -Output | 0.14169 | 0.14169 | 0.14169 | 0.0 | 14.84 -Modify | 0.2726 | 0.2726 | 0.2726 | 0.0 | 28.56 -Other | | 0.001178 | | | 0.12 - -Nlocal: 500 ave 500 max 500 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 2534 ave 2534 max 2534 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 36500 ave 36500 max 36500 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 73000 ave 73000 max 73000 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 73000 -Ave neighs/atom = 146 -Neighbor list builds = 100 -Dangerous builds not checked - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:01 diff --git a/examples/SPIN/read_restart/log.14Apr20.spin.restart.g++.4 b/examples/SPIN/read_restart/log.14Apr20.spin.restart.g++.4 deleted file mode 100644 index c22c672f6b..0000000000 --- a/examples/SPIN/read_restart/log.14Apr20.spin.restart.g++.4 +++ /dev/null @@ -1,115 +0,0 @@ -LAMMPS (19 Mar 2020) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:94) - using 1 OpenMP thread(s) per MPI task -# start a spin-lattice simulation from a data file -units metal -atom_style spin - -dimension 3 -boundary p p p - -# necessary for the serial algorithm (sametag) -atom_modify map array - -read_restart restart_hcp_cobalt.equil - restoring atom style spin from restart - orthogonal box = (0 0 0) to (12.5355 21.7121 20.4704) - 1 by 2 by 2 MPI processor grid - restoring pair style spin/exchange from restart - 500 atoms - read_restart CPU = 0.00173593 secs - -# setting mass, mag. moments, and interactions - -mass 1 58.93 - -pair_style hybrid/overlay eam/alloy spin/exchange 4.0 -pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co -pair_coeff * * spin/exchange exchange 4.0 0.3593 1.135028015e-05 1.064568567 - -neighbor 1.0 bin -neigh_modify every 1 check no delay 0 - -fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 -fix 2 all langevin/spin 0.0 0.0 21 - -fix 3 all nve/spin lattice moving -timestep 0.0001 - -# define outputs - -compute out_mag all spin -compute out_pe all pe -compute out_ke all ke -compute out_temp all temp - -variable magz equal c_out_mag[3] -variable magnorm equal c_out_mag[4] -variable emag equal c_out_mag[5] -variable tmag equal c_out_mag[6] - -thermo 20 -thermo_style custom step time v_magnorm pe v_emag v_tmag temp etotal -thermo_modify format float %20.15g - -compute outsp all property/atom spx spy spz sp fmx fmy fmz -dump 100 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7] - -run 100 -Neighbor list info ... - update every 1 steps, delay 0 steps, check no - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 7.49954 - ghost atom cutoff = 7.49954 - binsize = 3.74977, bins = 4 6 6 - 2 neighbor lists, perpetual/occasional/extra = 2 0 0 - (1) pair eam/alloy, perpetual, half/full from (2) - attributes: half, newton on - pair build: halffull/newton - stencil: none - bin: none - (2) pair spin/exchange, perpetual - attributes: full, newton on - pair build: full/bin/atomonly - stencil: full/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 7.324 | 7.324 | 7.324 Mbytes -Step Time v_magnorm PotEng v_emag v_tmag Temp TotEng - 1000 0 0.108317262557656 -2200.38241212182 -5.38245988668244 2538.4247868621 0 -2200.38241212182 - 1020 0.002 0.108317316216432 -2200.39172132147 -5.39179331147409 2513.42945241007 0.14431996581917 -2200.38241256644 - 1040 0.004 0.108317347939802 -2200.41811580574 -5.41854152831072 2478.87544274124 0.553516446104432 -2200.38241354532 - 1060 0.006 0.108317342440309 -2200.45801216927 -5.45990063373049 2449.77218633122 1.17203801398165 -2200.38241476526 - 1080 0.008 0.108317320345284 -2200.50688241767 -5.51245984623572 2427.2497145488 1.92968619968329 -2200.3824160902 - 1100 0.01 0.10831728372281 -2200.55976028296 -5.57250070536486 2400.86059511731 2.74946919265255 -2200.38241728649 -Loop time of 0.405615 on 4 procs for 100 steps with 500 atoms - -Performance: 2.130 ns/day, 11.267 hours/ns, 246.539 timesteps/s -99.7% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.075661 | 0.076798 | 0.077343 | 0.2 | 18.93 -Neigh | 0.063154 | 0.064974 | 0.066991 | 0.5 | 16.02 -Comm | 0.012538 | 0.013787 | 0.015151 | 0.8 | 3.40 -Output | 0.039155 | 0.040842 | 0.042502 | 0.6 | 10.07 -Modify | 0.20709 | 0.20883 | 0.21036 | 0.3 | 51.49 -Other | | 0.0003826 | | | 0.09 - -Nlocal: 125 ave 127 max 122 min -Histogram: 1 0 0 0 1 0 0 0 0 2 -Nghost: 1387 ave 1390 max 1385 min -Histogram: 2 0 0 0 0 0 1 0 0 1 -Neighs: 9125 ave 9272 max 8945 min -Histogram: 1 0 0 1 0 0 0 0 1 1 -FullNghs: 18250 ave 18542 max 17812 min -Histogram: 1 0 0 0 1 0 0 0 0 2 - -Total # of neighbors = 73000 -Ave neighs/atom = 146 -Neighbor list builds = 100 -Dangerous builds not checked - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:00 diff --git a/examples/SPIN/read_restart/log.14Apr20.spin.write_restart.g++.1 b/examples/SPIN/read_restart/log.14Apr20.spin.write_restart.g++.1 deleted file mode 100644 index 8ad14c55c0..0000000000 --- a/examples/SPIN/read_restart/log.14Apr20.spin.write_restart.g++.1 +++ /dev/null @@ -1,120 +0,0 @@ -LAMMPS (19 Mar 2020) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:94) - using 1 OpenMP thread(s) per MPI task -# fcc cobalt in a 3d periodic box - -units metal -atom_style spin - -dimension 3 -boundary p p p - -# necessary for the serial algorithm (sametag) -atom_modify map array - -lattice hcp 2.5071 -Lattice spacing in x,y,z = 2.5071 4.34242 4.09408 -region box block 0.0 5.0 0.0 5.0 0.0 5.0 -create_box 1 box -Created orthogonal box = (0 0 0) to (12.5355 21.7121 20.4704) - 1 by 1 by 1 MPI processor grid -create_atoms 1 box -Created 500 atoms - create_atoms CPU = 0.000952005 secs - -# setting mass, mag. moments, and interactions for cobalt - -mass 1 58.93 - -set group all spin/random 31 1.72 - 500 settings made for spin/random - -pair_style spin/exchange 4.0 -pair_coeff * * exchange 4.0 0.3593 1.135028015e-05 1.064568567 - -neighbor 0.1 bin -neigh_modify every 10 check yes delay 20 - -fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 -fix 2 all langevin/spin 100.0 0.01 21 - -fix 3 all nve/spin lattice frozen -timestep 0.0001 - -# compute and output options - -compute out_mag all spin -compute out_pe all pe -compute out_ke all ke -compute out_temp all temp - -variable magz equal c_out_mag[3] -variable magnorm equal c_out_mag[4] -variable emag equal c_out_mag[5] -variable tmag equal c_out_mag[6] - -thermo_style custom step time v_magnorm pe v_emag temp etotal -thermo 100 - -compute outsp all property/atom spx spy spz sp fmx fmy fmz -dump 100 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7] - -run 1000 -Neighbor list info ... - update every 10 steps, delay 20 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 4.1 - ghost atom cutoff = 4.1 - binsize = 2.05, bins = 7 11 10 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair spin/exchange, perpetual - attributes: full, newton on - pair build: full/bin/atomonly - stencil: full/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 6.947 | 6.947 | 6.947 Mbytes -Step Time v_magnorm PotEng v_emag Temp TotEng - 0 0 0.076558814 0.89911794 0.89911794 0 0.89911794 - 100 0.01 0.077628154 0.36693917 0.36693917 0 0.36693917 - 200 0.02 0.076678996 -0.20242315 -0.20242315 0 -0.20242315 - 300 0.03 0.079174837 -0.67595514 -0.67595514 0 -0.67595514 - 400 0.04 0.085031632 -1.5172851 -1.5172851 0 -1.5172851 - 500 0.05 0.08702747 -2.0426628 -2.0426628 0 -2.0426628 - 600 0.06 0.087066482 -2.6297745 -2.6297745 0 -2.6297745 - 700 0.07 0.089788894 -3.314538 -3.314538 0 -3.314538 - 800 0.08 0.091699611 -4.0287043 -4.0287043 0 -4.0287043 - 900 0.09 0.090038899 -4.600601 -4.600601 0 -4.600601 - 1000 0.1 0.093257309 -5.2352261 -5.2352261 0 -5.2352261 -Loop time of 3.30071 on 1 procs for 1000 steps with 500 atoms - -Performance: 2.618 ns/day, 9.169 hours/ns, 302.965 timesteps/s -99.3% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.3844 | 0.3844 | 0.3844 | 0.0 | 11.65 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.019863 | 0.019863 | 0.019863 | 0.0 | 0.60 -Output | 1.3844 | 1.3844 | 1.3844 | 0.0 | 41.94 -Modify | 1.5084 | 1.5084 | 1.5084 | 0.0 | 45.70 -Other | | 0.00367 | | | 0.11 - -Nlocal: 500 ave 500 max 500 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 1221 ave 1221 max 1221 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 10000 ave 10000 max 10000 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 10000 -Ave neighs/atom = 20 -Neighbor list builds = 0 -Dangerous builds = 0 -write_restart restart_hcp_cobalt.equil - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:03 diff --git a/examples/SPIN/read_restart/log.14Apr20.spin.write_restart.g++.4 b/examples/SPIN/read_restart/log.14Apr20.spin.write_restart.g++.4 deleted file mode 100644 index c0c1ec130c..0000000000 --- a/examples/SPIN/read_restart/log.14Apr20.spin.write_restart.g++.4 +++ /dev/null @@ -1,120 +0,0 @@ -LAMMPS (19 Mar 2020) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:94) - using 1 OpenMP thread(s) per MPI task -# fcc cobalt in a 3d periodic box - -units metal -atom_style spin - -dimension 3 -boundary p p p - -# necessary for the serial algorithm (sametag) -atom_modify map array - -lattice hcp 2.5071 -Lattice spacing in x,y,z = 2.5071 4.34242 4.09408 -region box block 0.0 5.0 0.0 5.0 0.0 5.0 -create_box 1 box -Created orthogonal box = (0 0 0) to (12.5355 21.7121 20.4704) - 1 by 2 by 2 MPI processor grid -create_atoms 1 box -Created 500 atoms - create_atoms CPU = 0.000663042 secs - -# setting mass, mag. moments, and interactions for cobalt - -mass 1 58.93 - -set group all spin/random 31 1.72 - 500 settings made for spin/random - -pair_style spin/exchange 4.0 -pair_coeff * * exchange 4.0 0.3593 1.135028015e-05 1.064568567 - -neighbor 0.1 bin -neigh_modify every 10 check yes delay 20 - -fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 -fix 2 all langevin/spin 100.0 0.01 21 - -fix 3 all nve/spin lattice frozen -timestep 0.0001 - -# compute and output options - -compute out_mag all spin -compute out_pe all pe -compute out_ke all ke -compute out_temp all temp - -variable magz equal c_out_mag[3] -variable magnorm equal c_out_mag[4] -variable emag equal c_out_mag[5] -variable tmag equal c_out_mag[6] - -thermo_style custom step time v_magnorm pe v_emag temp etotal -thermo 100 - -compute outsp all property/atom spx spy spz sp fmx fmy fmz -dump 100 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7] - -run 1000 -Neighbor list info ... - update every 10 steps, delay 20 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 4.1 - ghost atom cutoff = 4.1 - binsize = 2.05, bins = 7 11 10 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair spin/exchange, perpetual - attributes: full, newton on - pair build: full/bin/atomonly - stencil: full/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 6.868 | 6.868 | 6.868 Mbytes -Step Time v_magnorm PotEng v_emag Temp TotEng - 0 0 0.076558814 0.89911794 0.89911794 0 0.89911794 - 100 0.01 0.078299981 0.44129792 0.44129792 0 0.44129792 - 200 0.02 0.081260508 -0.21742361 -0.21742361 0 -0.21742361 - 300 0.03 0.081195603 -0.87041046 -0.87041046 0 -0.87041046 - 400 0.04 0.087298495 -1.7069519 -1.7069519 0 -1.7069519 - 500 0.05 0.087663924 -2.1883045 -2.1883045 0 -2.1883045 - 600 0.06 0.091713683 -2.9267461 -2.9267461 0 -2.9267461 - 700 0.07 0.093779119 -3.353314 -3.353314 0 -3.353314 - 800 0.08 0.097960611 -3.9344284 -3.9344284 0 -3.9344284 - 900 0.09 0.10193463 -4.7944004 -4.7944004 0 -4.7944004 - 1000 0.1 0.10831726 -5.3824599 -5.3824599 0 -5.3824599 -Loop time of 1.7839 on 4 procs for 1000 steps with 500 atoms - -Performance: 4.843 ns/day, 4.955 hours/ns, 560.569 timesteps/s -99.5% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.10068 | 0.10749 | 0.11461 | 1.5 | 6.03 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.052378 | 0.062171 | 0.07177 | 2.8 | 3.49 -Output | 0.4054 | 0.42334 | 0.44025 | 2.0 | 23.73 -Modify | 1.174 | 1.1893 | 1.2043 | 1.1 | 66.67 -Other | | 0.001558 | | | 0.09 - -Nlocal: 125 ave 125 max 125 min -Histogram: 4 0 0 0 0 0 0 0 0 0 -Nghost: 597.5 ave 600 max 595 min -Histogram: 2 0 0 0 0 0 0 0 0 2 -Neighs: 0 ave 0 max 0 min -Histogram: 4 0 0 0 0 0 0 0 0 0 -FullNghs: 2500 ave 2500 max 2500 min -Histogram: 4 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 10000 -Ave neighs/atom = 20 -Neighbor list builds = 0 -Dangerous builds = 0 -write_restart restart_hcp_cobalt.equil - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:01 diff --git a/examples/SPIN/read_restart/restart_hcp_cobalt.equil b/examples/SPIN/read_restart/restart_hcp_cobalt.equil index 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z-^`FxU;4f0iUxsTG2W2n3o%gEtFX@J9CH@*0iuMiAw&BK<=0Fi<_C z&@|o+-COWvzBpW^acvU(KEEt*q&EclD1H)*-BXBp{+SFEZ)K5#c9fWh3^2r@(rc1)@n{F& zTGBcyV?T~MTPEdil0NWQ8=HF3+ppDwx0h(avJ(1RGuo^1Ehc?O2Y?=Tae&gs5_zS( zncDHH9IX0aIVxY_iOA!pVnv`{yA^5Gv0(SPks;J5{`}LdW(%UG*h9RL4Q^)&TP-0f!d{XwKWeQf$? zP!s67w<#*sqz^#F`*=yXn?<}yF-m<@Gyr~$+SwPn4FKd~docVxobASyd!sk?PBRH8 zcwBnFB((-z-TTqc^fd>^vADPHVUgd3cfIzh+Xk-j&X=?QJqeQMF5J6)l@FHnY%;0u z%;<`RdB~V!61?^JFc_rI2|bnV|C{Of^wPw&BQ;w(Q@inx$!32G8-GBN^-tz#eS)36 z4EZR3oz&9L<7kJ=s&fV7t)SGtOnSuVH(T0Gu}i?<$fQ|Log+zq$&cm_fAG7VjGS=@;IX+czn zXyWFjQuil3qev%yp-lL~8njHKTQoNS`VTQw!Y0~$?$%*&OC-_oI|=daWW0KA;g~vwKi+7*6`***s1Yd2R(!oM-ouW$w~jM{PJr zzry96_9&E}U`XLRDHYuTgUFy!HX}=_3<+=-KF)|6fL#H2Hc!xm(!~1Ej+OWrCTV$g SZ!JX`Ulo(iN<(qZ^8W`je4XL| From 01698ddc2ee952328c4e6318c62cd95038abe820 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 10 Mar 2025 17:06:37 -0400 Subject: [PATCH 062/113] improve error messages for easier debugging --- src/SPIN/fix_nve_spin.cpp | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/src/SPIN/fix_nve_spin.cpp b/src/SPIN/fix_nve_spin.cpp index 1a08e2cf00..89a77b31ce 100644 --- a/src/SPIN/fix_nve_spin.cpp +++ b/src/SPIN/fix_nve_spin.cpp @@ -584,7 +584,8 @@ void FixNVESpin::sectoring() } if (rv == 0.0) - error->all(FLERR,"Illegal sectoring operation"); + error->all(FLERR, Error::NOLASTLINE, + "No suitable cutoff found for sectoring operation: rv = {}", rv); double rax = rsx/rv; double ray = rsy/rv; @@ -600,7 +601,8 @@ void FixNVESpin::sectoring() nsectors = sec[0]*sec[1]*sec[2]; if (sector_flag && (nsectors != 8)) - error->all(FLERR,"Illegal sectoring operation"); + error->all(FLERR, Error::NOLASTLINE, + "Illegal sectoring operation resulting in {} sectors instead of 8", nsectors); rsec[0] = rsx; rsec[1] = rsy; From 1e819efcf846cd852a97912fbbfd0fd1e960a66c Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 10 Mar 2025 17:11:53 -0400 Subject: [PATCH 063/113] update examples for consistency --- .../log.10Mar25.spin.read_data.g++.1 | 18 +++---- .../log.10Mar25.spin.read_data.g++.4 | 18 +++---- .../log.10Mar25.spin.restart.g++.1 | 35 ++++++------- .../log.10Mar25.spin.restart.g++.4 | 49 +++++++++--------- .../log.10Mar25.spin.write_restart.g++.1 | 18 +++---- .../log.10Mar25.spin.write_restart.g++.4 | 18 +++---- .../read_restart/restart_hcp_cobalt.equil | Bin 60984 -> 60960 bytes 7 files changed, 78 insertions(+), 78 deletions(-) diff --git a/examples/SPIN/read_restart/log.10Mar25.spin.read_data.g++.1 b/examples/SPIN/read_restart/log.10Mar25.spin.read_data.g++.1 index 6cc2175cbb..8edfd17527 100644 --- a/examples/SPIN/read_restart/log.10Mar25.spin.read_data.g++.1 +++ b/examples/SPIN/read_restart/log.10Mar25.spin.read_data.g++.1 @@ -1,4 +1,4 @@ -LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-210-g8af31ca28c-modified) +LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-212-g01698ddc2e-modified) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99) using 1 OpenMP thread(s) per MPI task units metal @@ -105,20 +105,20 @@ Per MPI rank memory allocation (min/avg/max) = 9.082 | 9.082 | 9.082 Mbytes 60 0.006 0.995669394598344 69647.7523345612 -845.585158124559 36.100016238044 177502.681559427 116614.166097826 80 0.008 0.995669395756676 107415.560454437 -846.200871523815 37.9775024824566 35031.4099604677 116684.714477685 100 0.01 0.995669403283478 63849.6798250643 -836.341677782106 39.680777051272 199492.565587335 116634.518317396 -Loop time of 2.9685 on 1 procs for 100 steps with 2048 atoms +Loop time of 2.97847 on 1 procs for 100 steps with 2048 atoms -Performance: 0.291 ns/day, 82.458 hours/ns, 33.687 timesteps/s, 68.991 katom-step/s +Performance: 0.290 ns/day, 82.735 hours/ns, 33.574 timesteps/s, 68.760 katom-step/s 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 1.0382 | 1.0382 | 1.0382 | 0.0 | 34.97 -Neigh | 0.78323 | 0.78323 | 0.78323 | 0.0 | 26.38 -Comm | 0.013266 | 0.013266 | 0.013266 | 0.0 | 0.45 -Output | 0.00021367 | 0.00021367 | 0.00021367 | 0.0 | 0.01 -Modify | 1.1318 | 1.1318 | 1.1318 | 0.0 | 38.13 -Other | | 0.00176 | | | 0.06 +Pair | 1.0361 | 1.0361 | 1.0361 | 0.0 | 34.79 +Neigh | 0.78559 | 0.78559 | 0.78559 | 0.0 | 26.38 +Comm | 0.013262 | 0.013262 | 0.013262 | 0.0 | 0.45 +Output | 0.00026908 | 0.00026908 | 0.00026908 | 0.0 | 0.01 +Modify | 1.1415 | 1.1415 | 1.1415 | 0.0 | 38.33 +Other | | 0.001761 | | | 0.06 Nlocal: 2048 ave 2048 max 2048 min Histogram: 1 0 0 0 0 0 0 0 0 0 diff --git a/examples/SPIN/read_restart/log.10Mar25.spin.read_data.g++.4 b/examples/SPIN/read_restart/log.10Mar25.spin.read_data.g++.4 index cd15387170..9945bc79fd 100644 --- a/examples/SPIN/read_restart/log.10Mar25.spin.read_data.g++.4 +++ b/examples/SPIN/read_restart/log.10Mar25.spin.read_data.g++.4 @@ -1,4 +1,4 @@ -LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-210-g8af31ca28c-modified) +LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-212-g01698ddc2e-modified) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99) using 1 OpenMP thread(s) per MPI task units metal @@ -105,20 +105,20 @@ Per MPI rank memory allocation (min/avg/max) = 5.812 | 5.812 | 5.812 Mbytes 60 0.006 0.99566940895435 69647.7523345112 -845.585157291247 36.1001312564486 177502.681560664 116614.166098104 80 0.008 0.995669417344697 107415.560454912 -846.200874451992 37.9776090859263 35031.4099596403 116684.714477941 100 0.01 0.995669427709463 63849.6798245944 -836.341678212079 39.6809090980074 199492.565591024 116634.518317902 -Loop time of 0.981181 on 4 procs for 100 steps with 2048 atoms +Loop time of 0.991506 on 4 procs for 100 steps with 2048 atoms -Performance: 0.881 ns/day, 27.255 hours/ns, 101.918 timesteps/s, 208.728 katom-step/s +Performance: 0.871 ns/day, 27.542 hours/ns, 100.857 timesteps/s, 206.554 katom-step/s 99.0% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.3068 | 0.31135 | 0.31472 | 0.5 | 31.73 -Neigh | 0.21997 | 0.22967 | 0.23853 | 1.6 | 23.41 -Comm | 0.013651 | 0.026146 | 0.03694 | 6.4 | 2.66 -Output | 0.00010966 | 0.0001265 | 0.00017442 | 0.0 | 0.01 -Modify | 0.41246 | 0.41281 | 0.41313 | 0.0 | 42.07 -Other | | 0.001083 | | | 0.11 +Pair | 0.31016 | 0.31287 | 0.31496 | 0.3 | 31.56 +Neigh | 0.21999 | 0.22957 | 0.23793 | 1.7 | 23.15 +Comm | 0.015231 | 0.025975 | 0.036137 | 6.0 | 2.62 +Output | 0.00012037 | 0.00014855 | 0.0001849 | 0.0 | 0.01 +Modify | 0.4213 | 0.42166 | 0.42201 | 0.0 | 42.53 +Other | | 0.001272 | | | 0.13 Nlocal: 512 ave 521 max 503 min Histogram: 2 0 0 0 0 0 0 0 0 2 diff --git a/examples/SPIN/read_restart/log.10Mar25.spin.restart.g++.1 b/examples/SPIN/read_restart/log.10Mar25.spin.restart.g++.1 index 2d80452e77..9ca8ef3521 100644 --- a/examples/SPIN/read_restart/log.10Mar25.spin.restart.g++.1 +++ b/examples/SPIN/read_restart/log.10Mar25.spin.restart.g++.1 @@ -1,4 +1,4 @@ -LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-209-g9c494d0a25-modified) +LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-212-g01698ddc2e-modified) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99) using 1 OpenMP thread(s) per MPI task # start a spin-lattice simulation from a data file @@ -14,13 +14,12 @@ atom_modify map array read_restart restart_hcp_cobalt.equil Reading restart file ... restart file = 4 Feb 2025, LAMMPS = 4 Feb 2025 -WARNING: Restart file used different # of processors: 4 vs. 1 (src/read_restart.cpp:628) restoring atom style spin from restart orthogonal box = (0 0 0) to (12.5355 21.712123 20.470386) 1 by 1 by 1 MPI processor grid restoring pair style spin/exchange from restart 500 atoms - read_restart CPU = 0.001 seconds + read_restart CPU = 0.000 seconds # setting mass, mag. moments, and interactions @@ -99,26 +98,26 @@ Neighbor list info ... WARNING: Dump 100 includes no atom IDs and is not sorted by ID. This may complicate post-processing tasks or visualization (src/dump.cpp:220) Per MPI rank memory allocation (min/avg/max) = 5.255 | 5.255 | 5.255 Mbytes Step Time v_magnorm PotEng v_emag v_tmag Temp TotEng - 1000 0.1 0.108329626151838 -2200.38234464056 -5.38239240501934 2538.4004919406 0 -2200.38234464056 - 1020 0.102 0.108329682386499 -2200.39166154869 -5.39173355873446 2513.35505416838 0.14443948124536 -2200.38234508481 - 1040 0.104 0.108329779277802 -2200.41807807023 -5.41850411117855 2478.80774498816 0.553977603827987 -2200.38234606476 - 1060 0.106 0.10832983679925 -2200.45800593865 -5.45989595459997 2449.72742607971 1.1729875955989 -2200.38234728585 - 1080 0.108 0.108329813608032 -2200.50691109393 -5.5124931569671 2427.22111176668 1.93117695188971 -2200.38234861173 - 1100 0.11 0.108329744840252 -2200.5598219415 -5.57257298837707 2400.88858161056 2.75147127466091 -2200.38234980911 -Loop time of 0.469378 on 1 procs for 100 steps with 500 atoms + 1000 0.1 0.0932563992120983 -2200.23506043127 -5.23510819573568 2608.1272233749 0 -2200.23506043127 + 1020 0.102 0.0932564226983496 -2200.24431693921 -5.24438874766875 2636.89284253705 0.143502110493468 -2200.23506093651 + 1040 0.104 0.0932564330551733 -2200.27026761331 -5.27068764778909 2646.09012775508 0.545814389665464 -2200.23506214178 + 1060 0.106 0.0932564065525508 -2200.30841491752 -5.31025431862422 2627.26990645217 1.13721564075693 -2200.23506358487 + 1080 0.108 0.0932563850278094 -2200.35339675793 -5.35874497582981 2585.24230543411 1.83458183455181 -2200.23506473927 + 1100 0.11 0.0932563977118321 -2200.40087596139 -5.41289411193204 2540.00857034711 2.5706738278606 -2200.23506541119 +Loop time of 0.473574 on 1 procs for 100 steps with 500 atoms -Performance: 1.841 ns/day, 13.038 hours/ns, 213.048 timesteps/s, 106.524 katom-step/s -99.2% CPU use with 1 MPI tasks x 1 OpenMP threads +Performance: 1.824 ns/day, 13.155 hours/ns, 211.160 timesteps/s, 105.580 katom-step/s +98.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.12016 | 0.12016 | 0.12016 | 0.0 | 25.60 -Neigh | 0.1469 | 0.1469 | 0.1469 | 0.0 | 31.30 -Comm | 0.0045348 | 0.0045348 | 0.0045348 | 0.0 | 0.97 -Output | 0.071711 | 0.071711 | 0.071711 | 0.0 | 15.28 -Modify | 0.12549 | 0.12549 | 0.12549 | 0.0 | 26.74 -Other | | 0.0005849 | | | 0.12 +Pair | 0.12025 | 0.12025 | 0.12025 | 0.0 | 25.39 +Neigh | 0.14912 | 0.14912 | 0.14912 | 0.0 | 31.49 +Comm | 0.0047587 | 0.0047587 | 0.0047587 | 0.0 | 1.00 +Output | 0.07234 | 0.07234 | 0.07234 | 0.0 | 15.28 +Modify | 0.12645 | 0.12645 | 0.12645 | 0.0 | 26.70 +Other | | 0.0006494 | | | 0.14 Nlocal: 500 ave 500 max 500 min Histogram: 1 0 0 0 0 0 0 0 0 0 diff --git a/examples/SPIN/read_restart/log.10Mar25.spin.restart.g++.4 b/examples/SPIN/read_restart/log.10Mar25.spin.restart.g++.4 index a6509783e9..2fe8f44691 100644 --- a/examples/SPIN/read_restart/log.10Mar25.spin.restart.g++.4 +++ b/examples/SPIN/read_restart/log.10Mar25.spin.restart.g++.4 @@ -1,4 +1,4 @@ -LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-209-g9c494d0a25-modified) +LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-212-g01698ddc2e-modified) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99) using 1 OpenMP thread(s) per MPI task # start a spin-lattice simulation from a data file @@ -14,6 +14,7 @@ atom_modify map array read_restart restart_hcp_cobalt.equil Reading restart file ... restart file = 4 Feb 2025, LAMMPS = 4 Feb 2025 +WARNING: Restart file used different # of processors: 1 vs. 4 (src/read_restart.cpp:628) restoring atom style spin from restart orthogonal box = (0 0 0) to (12.5355 21.712123 20.470386) 1 by 2 by 2 MPI processor grid @@ -98,35 +99,35 @@ Neighbor list info ... WARNING: Dump 100 includes no atom IDs and is not sorted by ID. This may complicate post-processing tasks or visualization (src/dump.cpp:220) Per MPI rank memory allocation (min/avg/max) = 5.188 | 5.188 | 5.188 Mbytes Step Time v_magnorm PotEng v_emag v_tmag Temp TotEng - 1000 0.1 0.108329626151837 -2200.38234464016 -5.38239240501934 2538.4004919406 0 -2200.38234464016 - 1020 0.102 0.108329679130501 -2200.39166154883 -5.39173355888088 2513.35482198786 0.144439483520248 -2200.3823450848 - 1040 0.104 0.108329711621363 -2200.41807807205 -5.41850411300556 2478.80746282814 0.553977632037396 -2200.38234606475 - 1060 0.106 0.108329705919754 -2200.4580059451 -5.45989596110734 2449.72703106051 1.17298769526935 -2200.38234728587 - 1080 0.108 0.108329685101234 -2200.50691110405 -5.51249316740617 2427.22060141747 1.93117710885529 -2200.38234861172 - 1100 0.11 0.108329648174842 -2200.55982193806 -5.57257298547573 2400.88784946371 2.75147122140813 -2200.38234980911 -Loop time of 0.170658 on 4 procs for 100 steps with 500 atoms + 1000 0.1 0.0932563992120983 -2200.23506043087 -5.23510819573568 2608.1272233749 0 -2200.23506043087 + 1020 0.102 0.0932564663999882 -2200.24431693996 -5.24438874845296 2636.89226887198 0.14350212264756 -2200.23506093648 + 1040 0.104 0.0932565837400281 -2200.27026761822 -5.27068765273516 2646.08966888271 0.545814465748645 -2200.23506214179 + 1060 0.106 0.0932567073488227 -2200.30841492456 -5.31025432590717 2627.27001685206 1.13721574991944 -2200.23506358486 + 1080 0.108 0.0932567401022577 -2200.35339675946 -5.35874497805351 2585.24242001276 1.83458185842719 -2200.23506473925 + 1100 0.11 0.0932566884738387 -2200.4008759633 -5.41289411525345 2540.00813568378 2.57067385759474 -2200.23506541119 +Loop time of 0.180477 on 4 procs for 100 steps with 500 atoms -Performance: 5.063 ns/day, 4.740 hours/ns, 585.968 timesteps/s, 292.984 katom-step/s -97.6% CPU use with 4 MPI tasks x 1 OpenMP threads +Performance: 4.787 ns/day, 5.013 hours/ns, 554.088 timesteps/s, 277.044 katom-step/s +97.3% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.031046 | 0.031556 | 0.031914 | 0.2 | 18.49 -Neigh | 0.036174 | 0.036592 | 0.037219 | 0.2 | 21.44 -Comm | 0.0051867 | 0.0053356 | 0.0055157 | 0.2 | 3.13 -Output | 0.020206 | 0.022625 | 0.025235 | 1.2 | 13.26 -Modify | 0.071608 | 0.074173 | 0.076565 | 0.7 | 43.46 -Other | | 0.0003758 | | | 0.22 +Pair | 0.033968 | 0.034363 | 0.035109 | 0.2 | 19.04 +Neigh | 0.035043 | 0.03728 | 0.040013 | 0.9 | 20.66 +Comm | 0.0049574 | 0.0073867 | 0.0089549 | 1.7 | 4.09 +Output | 0.021087 | 0.023594 | 0.026417 | 1.3 | 13.07 +Modify | 0.074785 | 0.07749 | 0.079892 | 0.7 | 42.94 +Other | | 0.0003627 | | | 0.20 -Nlocal: 125 ave 127 max 122 min -Histogram: 1 0 0 0 1 0 0 0 0 2 -Nghost: 1387 ave 1390 max 1385 min -Histogram: 2 0 0 0 0 0 1 0 0 1 -Neighs: 9125 ave 9271 max 8945 min -Histogram: 1 0 0 1 0 0 0 0 1 1 -FullNghs: 18250 ave 18542 max 17812 min -Histogram: 1 0 0 0 1 0 0 0 0 2 +Nlocal: 125 ave 136 max 117 min +Histogram: 1 0 1 0 1 0 0 0 0 1 +Nghost: 1387 ave 1395 max 1376 min +Histogram: 1 0 0 0 0 1 0 1 0 1 +Neighs: 9125 ave 9972 max 8559 min +Histogram: 1 0 1 1 0 0 0 0 0 1 +FullNghs: 18250 ave 19856 max 17082 min +Histogram: 1 0 1 0 1 0 0 0 0 1 Total # of neighbors = 73000 Ave neighs/atom = 146 diff --git a/examples/SPIN/read_restart/log.10Mar25.spin.write_restart.g++.1 b/examples/SPIN/read_restart/log.10Mar25.spin.write_restart.g++.1 index f5eca88e4a..b1dc9fbba6 100644 --- a/examples/SPIN/read_restart/log.10Mar25.spin.write_restart.g++.1 +++ b/examples/SPIN/read_restart/log.10Mar25.spin.write_restart.g++.1 @@ -1,4 +1,4 @@ -LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-209-g9c494d0a25-modified) +LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-212-g01698ddc2e-modified) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99) using 1 OpenMP thread(s) per MPI task # fcc cobalt in a 3d periodic box @@ -108,20 +108,20 @@ Per MPI rank memory allocation (min/avg/max) = 4.78 | 4.78 | 4.78 Mbytes 800 0.08 0.091698615 -4.028707 -4.028707 0 -4.028707 900 0.09 0.090031988 -4.6007241 -4.6007241 0 -4.6007241 1000 0.1 0.093256399 -5.2351082 -5.2351082 0 -5.2351082 -Loop time of 0.710237 on 1 procs for 1000 steps with 500 atoms +Loop time of 0.710555 on 1 procs for 1000 steps with 500 atoms -Performance: 12.165 ns/day, 1.973 hours/ns, 1407.980 timesteps/s, 703.990 katom-step/s -99.5% CPU use with 1 MPI tasks x 1 OpenMP threads +Performance: 12.160 ns/day, 1.974 hours/ns, 1407.350 timesteps/s, 703.675 katom-step/s +99.6% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.12753 | 0.12753 | 0.12753 | 0.0 | 17.96 +Pair | 0.12852 | 0.12852 | 0.12852 | 0.0 | 18.09 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.012846 | 0.012846 | 0.012846 | 0.0 | 1.81 -Output | 0.00014416 | 0.00014416 | 0.00014416 | 0.0 | 0.02 -Modify | 0.56854 | 0.56854 | 0.56854 | 0.0 | 80.05 -Other | | 0.001178 | | | 0.17 +Comm | 0.012387 | 0.012387 | 0.012387 | 0.0 | 1.74 +Output | 0.00014522 | 0.00014522 | 0.00014522 | 0.0 | 0.02 +Modify | 0.56835 | 0.56835 | 0.56835 | 0.0 | 79.99 +Other | | 0.001145 | | | 0.16 Nlocal: 500 ave 500 max 500 min Histogram: 1 0 0 0 0 0 0 0 0 0 diff --git a/examples/SPIN/read_restart/log.10Mar25.spin.write_restart.g++.4 b/examples/SPIN/read_restart/log.10Mar25.spin.write_restart.g++.4 index 38dbc7abd8..1d5c10bc67 100644 --- a/examples/SPIN/read_restart/log.10Mar25.spin.write_restart.g++.4 +++ b/examples/SPIN/read_restart/log.10Mar25.spin.write_restart.g++.4 @@ -1,4 +1,4 @@ -LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-209-g9c494d0a25-modified) +LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-212-g01698ddc2e-modified) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99) using 1 OpenMP thread(s) per MPI task # fcc cobalt in a 3d periodic box @@ -108,20 +108,20 @@ Per MPI rank memory allocation (min/avg/max) = 4.732 | 4.732 | 4.733 Mbytes 800 0.08 0.097960251 -3.9343481 -3.9343481 0 -3.9343481 900 0.09 0.10193598 -4.7944099 -4.7944099 0 -4.7944099 1000 0.1 0.10832963 -5.3823924 -5.3823924 0 -5.3823924 -Loop time of 0.391762 on 4 procs for 1000 steps with 500 atoms +Loop time of 0.40066 on 4 procs for 1000 steps with 500 atoms -Performance: 22.054 ns/day, 1.088 hours/ns, 2552.571 timesteps/s, 1.276 Matom-step/s -98.1% CPU use with 4 MPI tasks x 1 OpenMP threads +Performance: 21.564 ns/day, 1.113 hours/ns, 2495.885 timesteps/s, 1.248 Matom-step/s +97.9% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.031554 | 0.032024 | 0.032587 | 0.2 | 8.17 +Pair | 0.032435 | 0.033013 | 0.033957 | 0.3 | 8.24 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.014944 | 0.015944 | 0.016873 | 0.6 | 4.07 -Output | 0.00010694 | 0.00012063 | 0.00015425 | 0.0 | 0.03 -Modify | 0.34232 | 0.34279 | 0.34327 | 0.1 | 87.50 -Other | | 0.0008836 | | | 0.23 +Comm | 0.016106 | 0.016898 | 0.017915 | 0.5 | 4.22 +Output | 0.00012331 | 0.00013523 | 0.00016852 | 0.0 | 0.03 +Modify | 0.34913 | 0.34974 | 0.35017 | 0.1 | 87.29 +Other | | 0.0008755 | | | 0.22 Nlocal: 125 ave 125 max 125 min Histogram: 4 0 0 0 0 0 0 0 0 0 diff --git a/examples/SPIN/read_restart/restart_hcp_cobalt.equil b/examples/SPIN/read_restart/restart_hcp_cobalt.equil index b74ecbc95cc009de7184672c148443deb9083f18..8caa9da7ddbb10c2ef7f5a2fd0e38dd539865cf1 100644 GIT binary patch literal 60960 zcmbWA2|QK7`~Q(jLK2ZuDoSZl+O*A;XrZE{q>U_<$kwJ5m69S_P?DsOWS2@BOR{9& zcdmVxXwky|-tRT;w=@6y`@YP1y*Ni#=k0lB<}=UCJZFxEzL}ZDF6o^{);9W9Hria= zTwGkE7+=g|JmYJbw3?BD^iqYT%m4EcFXNvS7+=gY&(N9q>wH7kV;E;MBOCn_T%#FR 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zYNgM-+4%f-I9^fob`Ww`Uyj&%v*$K^uyV?j2j<<-PGgD)#~^+`E*iI^dOOnFL&!B< z`C)ndvljR*R@yOw@m#r#0ImZr9{BnK8edVleT3ZAdh?t9D7M1E^XdYR Date: Tue, 11 Mar 2025 16:10:04 -0500 Subject: [PATCH 064/113] fixed issues with several input scripts, added reference log files --- examples/COUPLE/multiple/in.chain | 2 +- examples/PACKAGES/atc/elastic/Au_u3.eam | 1 + examples/PACKAGES/ti/in.ti_spring | 2 +- .../validation_nve/in.spin.iron-nve | 2 +- .../log.11Mar25.spin.iron-nve.g++.1 | 188 ++++++++++++++ .../validation_nvt/in.spin.nvt_lattice | 2 +- .../validation_nvt/in.spin.nvt_spin | 4 +- .../log.11Mar25.spin.nvt_lattice.g++.1 | 240 +++++++++++++++++ .../log.11Mar25.spin.nvt_spin.g++.1 | 241 ++++++++++++++++++ examples/rerun/in.rdf.first | 2 +- 10 files changed, 677 insertions(+), 7 deletions(-) create mode 120000 examples/PACKAGES/atc/elastic/Au_u3.eam create mode 100644 examples/SPIN/test_problems/validation_nve/log.11Mar25.spin.iron-nve.g++.1 create mode 100644 examples/SPIN/test_problems/validation_nvt/log.11Mar25.spin.nvt_lattice.g++.1 create mode 100644 examples/SPIN/test_problems/validation_nvt/log.11Mar25.spin.nvt_spin.g++.1 diff --git a/examples/COUPLE/multiple/in.chain b/examples/COUPLE/multiple/in.chain index ed72441aa1..6aa3b455ad 100644 --- a/examples/COUPLE/multiple/in.chain +++ b/examples/COUPLE/multiple/in.chain @@ -1,5 +1,5 @@ # FENE beadspring benchmark - +variable t index 1.0 units lj atom_style bond special_bonds fene diff --git a/examples/PACKAGES/atc/elastic/Au_u3.eam b/examples/PACKAGES/atc/elastic/Au_u3.eam new file mode 120000 index 0000000000..2ace8a4162 --- /dev/null +++ b/examples/PACKAGES/atc/elastic/Au_u3.eam @@ -0,0 +1 @@ +../../../../potentials/Au_u3.eam \ No newline at end of file diff --git a/examples/PACKAGES/ti/in.ti_spring b/examples/PACKAGES/ti/in.ti_spring index 383d4b688c..05f4902aad 100644 --- a/examples/PACKAGES/ti/in.ti_spring +++ b/examples/PACKAGES/ti/in.ti_spring @@ -13,7 +13,7 @@ create_atoms 1 box pair_style eam/alloy - pair_coeff * * ../../../../potentials/Cu_mishin1.eam.alloy Cu + pair_coeff * * Cu_mishin1.eam.alloy Cu #------------------------------------------------------------------------------# diff --git a/examples/SPIN/test_problems/validation_nve/in.spin.iron-nve b/examples/SPIN/test_problems/validation_nve/in.spin.iron-nve index 38c669e166..1d98901702 100644 --- a/examples/SPIN/test_problems/validation_nve/in.spin.iron-nve +++ b/examples/SPIN/test_problems/validation_nve/in.spin.iron-nve @@ -50,5 +50,5 @@ thermo 200 compute outsp all property/atom spx spy spz sp fmx fmy fmz dump 1 all custom 10 dump_iron.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] -run 100000 +run 10000 # run 1 diff --git a/examples/SPIN/test_problems/validation_nve/log.11Mar25.spin.iron-nve.g++.1 b/examples/SPIN/test_problems/validation_nve/log.11Mar25.spin.iron-nve.g++.1 new file mode 100644 index 0000000000..249c7b1bfe --- /dev/null +++ b/examples/SPIN/test_problems/validation_nve/log.11Mar25.spin.iron-nve.g++.1 @@ -0,0 +1,188 @@ +LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-169-g4246fab500) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99) + using 1 OpenMP thread(s) per MPI task +# bcc iron in a 3d periodic box + +clear +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99) + using 1 OpenMP thread(s) per MPI task +units metal +atom_style spin +# atom_style spin/kk + +dimension 3 +boundary p p p + +# necessary for the serial algorithm (sametag) +atom_modify map array + +lattice bcc 2.8665 +Lattice spacing in x,y,z = 2.8665 2.8665 2.8665 +region box block 0.0 3.0 0.0 3.0 0.0 3.0 +create_box 1 box +Created orthogonal box = (0 0 0) to (8.5995 8.5995 8.5995) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 54 atoms + using lattice units in orthogonal box = (0 0 0) to (8.5995 8.5995 8.5995) + create_atoms CPU = 0.001 seconds + +# setting mass, mag. moments, and interactions for bcc iron + +mass 1 55.845 +set group all spin/random 31 2.2 +Setting atom values ... +WARNING: Set attribute spin/random is deprecated. Please use spin/atom/random instead. (src/set.cpp:293) + 54 settings made for spin/random +velocity all create 100 4928459 rot yes dist gaussian + +pair_style hybrid/overlay eam/alloy spin/exchange 3.5 +pair_coeff * * eam/alloy Fe_Mishin2006.eam.alloy Fe +pair_coeff * * spin/exchange exchange 3.4 0.02726 0.2171 1.841 + +neighbor 0.1 bin +neigh_modify every 10 check yes delay 20 + +fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 +fix 2 all langevin/spin 0.0 0.00 21 +fix 3 all nve/spin lattice moving +timestep 0.0001 + +# compute and output options + +compute out_mag all spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo_style custom step time v_tmag temp v_emag ke pe etotal +thermo 200 + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 1 all custom 10 dump_iron.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] + +run 10000 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- fix nve/spin command: doi:10.1016/j.jcp.2018.06.042 + +@article{tranchida2018massively, +title={Massively Parallel Symplectic Algorithm for Coupled Magnetic Spin Dynamics and Molecular Dynamics}, +author={Tranchida, J and Plimpton, S J and Thibaudeau, P and Thompson, A P}, +journal={Journal of Computational Physics}, +volume={372}, +pages={406--425}, +year={2018}, +publisher={Elsevier} +doi={10.1016/j.jcp.2018.06.042} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Neighbor list info ... + update: every = 10 steps, delay = 20 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5.773367 + ghost atom cutoff = 5.773367 + binsize = 2.8866835, bins = 3 3 3 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair eam/alloy, perpetual, half/full from (2) + attributes: half, newton on, cut 5.7733670002446 + pair build: halffull/newton + stencil: none + bin: none + (2) pair spin/exchange, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +WARNING: Dump 1 includes no atom IDs and is not sorted by ID. This may complicate post-processing tasks or visualization (src/dump.cpp:220) +Per MPI rank memory allocation (min/avg/max) = 5.626 | 5.626 | 5.626 Mbytes + Step Time v_tmag Temp v_emag KinEng PotEng TotEng + 0 0 1836.2373 100.00358 -0.26674297 0.6851033 -231.38675 -230.70164 + 200 0.02 1751.0384 48.019015 -0.27512361 0.32896808 -231.03061 -230.70164 + 400 0.04 1776.2639 19.035769 -0.28188188 0.13041001 -230.83205 -230.70164 + 600 0.06 1787.5802 60.069761 -0.2772323 0.41152518 -231.11317 -230.70164 + 800 0.08 1706.5552 50.79606 -0.27292548 0.34799302 -231.04963 -230.70164 + 1000 0.1 2120.1611 44.605193 -0.26987056 0.3055807 -231.00722 -230.70164 + 1200 0.12 1754.9393 64.57232 -0.26943293 0.44237126 -231.14401 -230.70164 + 1400 0.14 1912.6009 44.177766 -0.26857448 0.3026525 -231.00429 -230.70164 + 1600 0.16 1875.5315 40.249733 -0.27481087 0.27574238 -230.97738 -230.70164 + 1800 0.18 1837.1786 62.817536 -0.28092582 0.4303496 -231.13199 -230.70164 + 2000 0.2 1860.1719 54.167659 -0.28282659 0.37109113 -231.07273 -230.70164 + 2200 0.22 1691.658 46.643932 -0.29528237 0.31954767 -231.02119 -230.70164 + 2400 0.24 1525.2579 57.361866 -0.30189945 0.39297397 -231.09462 -230.70164 + 2600 0.26 1505.1726 56.239347 -0.30898994 0.38528383 -231.08693 -230.70164 + 2800 0.28 1415.9555 47.818074 -0.31351411 0.32759147 -231.02923 -230.70164 + 3000 0.3 1248.4308 49.608492 -0.31727375 0.33985725 -231.0415 -230.70164 + 3200 0.32 1200.7605 51.495405 -0.31565357 0.35278409 -231.05443 -230.70164 + 3400 0.34 1746.137 56.967184 -0.30906485 0.39027008 -231.09191 -230.70164 + 3600 0.36 1805.3667 55.030692 -0.30799197 0.37700359 -231.07865 -230.70164 + 3800 0.38 1609.9498 59.452017 -0.30520539 0.40729315 -231.10894 -230.70164 + 4000 0.4 1686.1863 57.338707 -0.30240026 0.39281531 -231.09446 -230.70164 + 4200 0.42 1961.3516 41.421108 -0.30479326 0.28376722 -230.98541 -230.70164 + 4400 0.44 1971.1808 54.038289 -0.30876936 0.37020484 -231.07185 -230.70164 + 4600 0.46 1819.428 56.766201 -0.3129157 0.38889319 -231.09054 -230.70164 + 4800 0.48 1494.1263 47.402453 -0.32868332 0.32474414 -231.02639 -230.70164 + 5000 0.5 1601.6127 63.404101 -0.33283819 0.43436803 -231.13601 -230.70164 + 5200 0.52 1567.7429 62.783792 -0.34753005 0.43011843 -231.13176 -230.70164 + 5400 0.54 1686.234 40.450417 -0.3603489 0.27711722 -230.97876 -230.70164 + 5600 0.56 1651.1927 64.255456 -0.36569031 0.44020049 -231.14184 -230.70164 + 5800 0.58 1380.639 75.386226 -0.36870019 0.51645503 -231.2181 -230.70164 + 6000 0.6 1539.07 40.611642 -0.36303517 0.27822173 -230.97986 -230.70164 + 6200 0.62 1442.2286 50.254503 -0.36560331 0.34428293 -231.04592 -230.70164 + 6400 0.64 1263.6928 69.095161 -0.36822748 0.47335628 -231.175 -230.70164 + 6600 0.66 1468.1529 54.534243 -0.37319988 0.37360252 -231.07524 -230.70164 + 6800 0.68 1289.4927 60.381892 -0.38478834 0.41366352 -231.11531 -230.70164 + 7000 0.7 1121.6702 58.691171 -0.39652609 0.40208075 -231.10372 -230.70164 + 7200 0.72 1018.1068 53.528417 -0.40711639 0.36671182 -231.06835 -230.70164 + 7400 0.74 1115.0342 78.62129 -0.41729373 0.53861776 -231.24026 -230.70164 + 7600 0.76 1329.4621 65.650574 -0.41928751 0.44975815 -231.1514 -230.70164 + 7800 0.78 1154.164 45.603278 -0.41263444 0.31241837 -231.01406 -230.70164 + 8000 0.8 1090.2959 62.148282 -0.40987933 0.42576469 -231.12741 -230.70164 + 8200 0.82 1303.4698 63.864431 -0.41301445 0.43752166 -231.13916 -230.70164 + 8400 0.84 1144.2181 52.222297 -0.41645089 0.35776387 -231.05941 -230.70164 + 8600 0.86 1005.3359 61.59129 -0.41282114 0.42194885 -231.12359 -230.70164 + 8800 0.88 1453.8465 70.876149 -0.41920851 0.48555745 -231.1872 -230.70164 + 9000 0.9 1325.9116 63.675151 -0.42450864 0.43622494 -231.13787 -230.70164 + 9200 0.92 1213.5738 58.297881 -0.42722791 0.3993864 -231.10103 -230.70164 + 9400 0.94 1227.437 57.375795 -0.44309693 0.39306939 -231.09471 -230.70164 + 9600 0.96 1192.79 65.822598 -0.44760999 0.45093664 -231.15258 -230.70164 + 9800 0.98 1231.5166 69.119896 -0.45335245 0.47352573 -231.17517 -230.70164 + 10000 1 1284.2809 66.166068 -0.45872955 0.45328969 -231.15493 -230.70164 +Loop time of 5.97474 on 1 procs for 10000 steps with 54 atoms + +Performance: 14.461 ns/day, 1.660 hours/ns, 1673.714 timesteps/s, 90.381 katom-step/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.501 | 2.501 | 2.501 | 0.0 | 41.86 +Neigh | 0.016481 | 0.016481 | 0.016481 | 0.0 | 0.28 +Comm | 0.37576 | 0.37576 | 0.37576 | 0.0 | 6.29 +Output | 0.12311 | 0.12311 | 0.12311 | 0.0 | 2.06 +Modify | 2.9317 | 2.9317 | 2.9317 | 0.0 | 49.07 +Other | | 0.02661 | | | 0.45 + +Nlocal: 54 ave 54 max 54 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 777 ave 777 max 777 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 1700 ave 1700 max 1700 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 3400 ave 3400 max 3400 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 3400 +Ave neighs/atom = 62.962963 +Neighbor list builds = 58 +Dangerous builds = 0 +# run 1 +Total wall time: 0:00:06 diff --git a/examples/SPIN/test_problems/validation_nvt/in.spin.nvt_lattice b/examples/SPIN/test_problems/validation_nvt/in.spin.nvt_lattice index a1f739fe54..e65aff510f 100644 --- a/examples/SPIN/test_problems/validation_nvt/in.spin.nvt_lattice +++ b/examples/SPIN/test_problems/validation_nvt/in.spin.nvt_lattice @@ -49,4 +49,4 @@ variable tmag equal c_out_mag[6] thermo_style custom step time v_tmag temp v_emag ke pe etotal thermo 200 -run 200000 +run 20000 diff --git a/examples/SPIN/test_problems/validation_nvt/in.spin.nvt_spin b/examples/SPIN/test_problems/validation_nvt/in.spin.nvt_spin index 102f76a2a6..f88c2c51a2 100644 --- a/examples/SPIN/test_problems/validation_nvt/in.spin.nvt_spin +++ b/examples/SPIN/test_problems/validation_nvt/in.spin.nvt_spin @@ -32,7 +32,7 @@ neighbor 0.1 bin neigh_modify every 10 check yes delay 20 fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 -fix 2 all langevin 0.0 0.0 0.0 48279 +fix 2 all langevin 0.0 0.0 0.001 48279 fix 3 all langevin/spin 200.0 0.01 321 fix 4 all nve/spin lattice moving timestep 0.001 @@ -50,4 +50,4 @@ variable tmag equal c_out_mag[6] thermo_style custom step time v_tmag temp v_emag ke pe etotal thermo 200 -run 200000 +run 20000 diff --git a/examples/SPIN/test_problems/validation_nvt/log.11Mar25.spin.nvt_lattice.g++.1 b/examples/SPIN/test_problems/validation_nvt/log.11Mar25.spin.nvt_lattice.g++.1 new file mode 100644 index 0000000000..11ba5e8c1e --- /dev/null +++ b/examples/SPIN/test_problems/validation_nvt/log.11Mar25.spin.nvt_lattice.g++.1 @@ -0,0 +1,240 @@ +LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-169-g4246fab500) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99) + using 1 OpenMP thread(s) per MPI task +# bcc iron in a 3d periodic box + +clear +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99) + using 1 OpenMP thread(s) per MPI task +units metal +atom_style spin +# atom_style spin/kk + +dimension 3 +boundary p p p + +# necessary for the serial algorithm (sametag) +atom_modify map array + +lattice bcc 2.8665 +Lattice spacing in x,y,z = 2.8665 2.8665 2.8665 +region box block 0.0 3.0 0.0 3.0 0.0 3.0 +create_box 1 box +Created orthogonal box = (0 0 0) to (8.5995 8.5995 8.5995) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 54 atoms + using lattice units in orthogonal box = (0 0 0) to (8.5995 8.5995 8.5995) + create_atoms CPU = 0.001 seconds + +# setting mass, mag. moments, and interactions for bcc iron + +mass 1 55.845 +set group all spin 2.2 0.0 0.0 1.0 +Setting atom values ... +WARNING: Set attribute spin is deprecated. Please use spin/atom instead. (src/set.cpp:268) + 54 settings made for spin +velocity all create 400 4928459 rot yes dist gaussian + +pair_style hybrid/overlay eam/alloy spin/exchange 4.0 spin/neel 4.0 +pair_coeff * * eam/alloy Fe_Mishin2006.eam.alloy Fe +pair_coeff * * spin/exchange exchange 3.4 0.1 0.2171 1.841 +pair_coeff * * spin/neel neel 4.0 0.02 0.0 1.841 0.0 0.0 1.0 + +neighbor 0.1 bin +neigh_modify every 10 check yes delay 20 + +fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 +fix 2 all langevin 200.0 200.0 0.1 48279 +fix 3 all langevin/spin 0.0 0.0 321 +fix 4 all nve/spin lattice moving +timestep 0.001 + +# compute and output options + +compute out_mag all spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo_style custom step time v_tmag temp v_emag ke pe etotal +thermo 200 + +run 20000 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- fix nve/spin command: doi:10.1016/j.jcp.2018.06.042 + +@article{tranchida2018massively, +title={Massively Parallel Symplectic Algorithm for Coupled Magnetic Spin Dynamics and Molecular Dynamics}, +author={Tranchida, J and Plimpton, S J and Thibaudeau, P and Thompson, A P}, +journal={Journal of Computational Physics}, +volume={372}, +pages={406--425}, +year={2018}, +publisher={Elsevier} +doi={10.1016/j.jcp.2018.06.042} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Neighbor list info ... + update: every = 10 steps, delay = 20 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5.773367 + ghost atom cutoff = 5.773367 + binsize = 2.8866835, bins = 3 3 3 + 3 neighbor lists, perpetual/occasional/extra = 3 0 0 + (1) pair eam/alloy, perpetual, half/full from (2) + attributes: half, newton on, cut 5.7733670002446 + pair build: halffull/newton + stencil: none + bin: none + (2) pair spin/exchange, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (3) pair spin/neel, perpetual, copy from (2) + attributes: full, newton on + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 6.008 | 6.008 | 6.008 Mbytes + Step Time v_tmag Temp v_emag KinEng PotEng TotEng + 0 0 1.4336203e-31 400.01433 -22.021022 2.7404132 -253.14103 -250.40061 + 200 0.2 0.26275543 188.91786 -21.983513 1.2942362 -251.94911 -250.65488 + 400 0.4 0.56095049 204.95947 -21.977046 1.4041338 -251.914 -250.50987 + 600 0.6 0.81480981 203.28763 -21.98548 1.3926804 -251.88478 -250.4921 + 800 0.8 0.97590428 184.8694 -21.974142 1.266501 -251.73716 -250.47066 + 1000 1 1.1324742 184.65547 -21.986309 1.2650354 -252.03248 -250.76744 + 1200 1.2 1.5284342 207.55788 -21.974821 1.421935 -251.7769 -250.35497 + 1400 1.4 1.8310776 220.75396 -21.979994 1.5123385 -251.93989 -250.42755 + 1600 1.6 2.2057174 236.04272 -21.973951 1.6170785 -251.98625 -250.36917 + 1800 1.8 2.7760928 195.92697 -21.96808 1.3422541 -251.7495 -250.40725 + 2000 2 3.2171354 161.33811 -21.975129 1.1052932 -251.86337 -250.75808 + 2200 2.2 3.8284998 193.21861 -21.968067 1.3236997 -251.86609 -250.54239 + 2400 2.4 4.4109629 203.79368 -21.971813 1.3961472 -251.92264 -250.52649 + 2600 2.6 4.5056291 200.81431 -21.960649 1.3757362 -251.80976 -250.43403 + 2800 2.8 4.6221125 185.57027 -21.972664 1.2713025 -252.0384 -250.76709 + 3000 3 4.9059897 216.00877 -21.966875 1.4798302 -252.13406 -250.65423 + 3200 3.2 5.3958965 152.77626 -21.956779 1.0466377 -251.66 -250.61337 + 3400 3.4 5.9881406 170.70538 -21.964189 1.1694663 -251.9061 -250.73663 + 3600 3.6 6.134982 210.99981 -21.945137 1.4455149 -251.75025 -250.30474 + 3800 3.8 6.5940545 239.12527 -21.953159 1.6381964 -251.90813 -250.26993 + 4000 4 6.9355034 181.99614 -21.938591 1.2468169 -251.59724 -250.35043 + 4200 4.2 7.3712919 242.52183 -21.932318 1.6614656 -251.71104 -250.04957 + 4400 4.4 7.5924709 164.34328 -21.942361 1.1258809 -251.64032 -250.51444 + 4600 4.6 8.1833481 205.94973 -21.941491 1.4109179 -251.57627 -250.16536 + 4800 4.8 8.40416 169.96914 -21.945774 1.1644225 -251.87887 -250.71444 + 5000 5 8.4422416 189.79518 -21.94955 1.3002465 -251.80055 -250.50031 + 5200 5.2 8.3667008 195.86473 -21.934302 1.3418277 -251.64678 -250.30495 + 5400 5.4 8.7075519 204.82319 -21.947339 1.4032002 -251.85712 -250.45392 + 5600 5.6 8.6582399 191.25854 -21.933614 1.3102717 -251.51648 -250.2062 + 5800 5.8 8.896287 180.44446 -21.923523 1.2361867 -251.68003 -250.44384 + 6000 6 9.1379808 248.49596 -21.938845 1.7023931 -251.84502 -250.14263 + 6200 6.2 8.9724294 181.67979 -21.939567 1.2446497 -251.81639 -250.57174 + 6400 6.4 8.7735241 198.31668 -21.952115 1.3586255 -251.97841 -250.61979 + 6600 6.6 9.0394523 218.6735 -21.934717 1.4980857 -251.85133 -250.35325 + 6800 6.8 9.5779186 203.83536 -21.937873 1.3964328 -251.98448 -250.58804 + 7000 7 9.7893273 185.56096 -21.949319 1.2712387 -252.09057 -250.81934 + 7200 7.2 9.5292481 205.53224 -21.936466 1.4080577 -251.98037 -250.57231 + 7400 7.4 9.7369072 200.76528 -21.944609 1.3754003 -251.88128 -250.50588 + 7600 7.6 9.9385522 217.68239 -21.920768 1.4912959 -251.6169 -250.1256 + 7800 7.8 9.8656638 219.17274 -21.92302 1.5015059 -251.50189 -250.00039 + 8000 8 9.2380618 264.13229 -21.936112 1.8095143 -251.71532 -249.9058 + 8200 8.2 9.3384949 239.58029 -21.941834 1.6413137 -251.73551 -250.0942 + 8400 8.4 9.1684312 207.27974 -21.938426 1.4200295 -251.59062 -250.17059 + 8600 8.6 8.8407032 200.79452 -21.933328 1.3756006 -251.48006 -250.10446 + 8800 8.8 8.84683 218.44316 -21.949738 1.4965077 -251.92925 -250.43275 + 9000 9 9.0686442 216.06373 -21.942255 1.4802067 -251.79797 -250.31776 + 9200 9.2 9.2783597 187.56662 -21.93374 1.2849791 -251.87884 -250.59386 + 9400 9.4 9.2794158 203.78139 -21.955284 1.396063 -252.09328 -250.69722 + 9600 9.6 9.3563189 196.15871 -21.948544 1.3438417 -251.85685 -250.51301 + 9800 9.8 9.6458819 215.38334 -21.94895 1.4755455 -251.92219 -250.44665 + 10000 10 9.5073837 178.61601 -21.955281 1.2236604 -251.97306 -250.7494 + 10200 10.2 9.3510908 185.21136 -21.94749 1.2688437 -251.83233 -250.56349 + 10400 10.4 9.8171891 194.92192 -21.945394 1.3353687 -251.86067 -250.5253 + 10600 10.6 9.5996138 213.90302 -21.945461 1.4654042 -251.72508 -250.25968 + 10800 10.8 9.8602813 208.57912 -21.936736 1.4289312 -251.55778 -250.12885 + 11000 11 10.652287 202.88507 -21.933085 1.3899225 -251.69631 -250.30639 + 11200 11.2 10.413298 171.86972 -21.919711 1.1774429 -251.16232 -249.98488 + 11400 11.4 10.589727 179.33897 -21.927537 1.2286132 -251.65266 -250.42405 + 11600 11.6 11.099271 176.43012 -21.925025 1.2086853 -251.65796 -250.44927 + 11800 11.8 11.49558 216.78529 -21.935923 1.48515 -251.51958 -250.03443 + 12000 12 11.190687 206.45545 -21.941866 1.4143824 -251.55494 -250.14055 + 12200 12.2 11.372777 216.26373 -21.934028 1.4815769 -251.75482 -250.27324 + 12400 12.4 11.303952 218.67625 -21.928577 1.4981046 -251.73908 -250.24098 + 12600 12.6 11.065605 188.25083 -21.925979 1.2896665 -251.49808 -250.20841 + 12800 12.8 11.289265 209.423 -21.933529 1.4347125 -251.85142 -250.41671 + 13000 13 11.412931 148.86392 -21.93732 1.0198351 -251.88347 -250.86364 + 13200 13.2 11.677538 187.03356 -21.923919 1.2813272 -251.52124 -250.23991 + 13400 13.4 12.451801 237.44268 -21.93385 1.6266694 -251.70112 -250.07445 + 13600 13.6 12.981208 196.47947 -21.926751 1.3460391 -251.80509 -250.45905 + 13800 13.8 13.301789 191.61721 -21.921891 1.3127288 -251.85541 -250.54268 + 14000 14 13.726635 212.61693 -21.922086 1.4565934 -252.06804 -250.61145 + 14200 14.2 13.715662 197.51397 -21.915949 1.3531263 -251.71314 -250.36002 + 14400 14.4 13.340257 210.15601 -21.927197 1.4397342 -251.73271 -250.29297 + 14600 14.6 14.118672 175.1782 -21.923635 1.2001087 -251.54286 -250.34275 + 14800 14.8 14.52801 211.5541 -21.919371 1.4493122 -251.74119 -250.29188 + 15000 15 14.522566 207.59406 -21.919623 1.4221828 -251.74192 -250.31974 + 15200 15.2 15.1446 191.32404 -21.902291 1.3107204 -251.52754 -250.21682 + 15400 15.4 15.815481 160.35385 -21.918453 1.0985502 -251.75506 -250.65651 + 15600 15.6 16.942896 211.32891 -21.89554 1.4477695 -251.42064 -249.97287 + 15800 15.8 17.339057 213.03178 -21.903747 1.4594355 -251.5815 -250.12207 + 16000 16 17.610695 211.72009 -21.899083 1.4504494 -251.51043 -250.05998 + 16200 16.2 18.352293 236.99887 -21.9043 1.623629 -251.79466 -250.17103 + 16400 16.4 17.898896 208.62272 -21.904247 1.42923 -251.66653 -250.2373 + 16600 16.6 18.005606 169.07581 -21.910252 1.1583025 -251.84184 -250.68353 + 16800 16.8 18.884686 198.75251 -21.900417 1.3616113 -251.8573 -250.49569 + 17000 17 19.454235 182.70172 -21.904544 1.2516507 -251.66187 -250.41021 + 17200 17.2 19.497759 157.47203 -21.904461 1.0788075 -251.88582 -250.80701 + 17400 17.4 19.470705 215.43531 -21.887158 1.4759016 -251.82426 -250.34836 + 17600 17.6 19.553888 212.82066 -21.89372 1.4579892 -251.79955 -250.34157 + 17800 17.8 19.646117 236.85339 -21.8983 1.6226323 -251.75304 -250.13041 + 18000 18 20.205554 253.85283 -21.909061 1.7390919 -251.84228 -250.10319 + 18200 18.2 20.065135 233.11058 -21.882631 1.5969911 -251.54972 -249.95273 + 18400 18.4 20.76763 209.7018 -21.895306 1.4366225 -251.79971 -250.36309 + 18600 18.6 21.369833 214.39422 -21.882332 1.4687693 -251.53344 -250.06467 + 18800 18.8 21.939164 216.25928 -21.89097 1.4815464 -251.82112 -250.33958 + 19000 19 22.817363 215.27695 -21.882698 1.4748166 -251.82572 -250.3509 + 19200 19.2 23.705114 182.22745 -21.879076 1.2484016 -251.43044 -250.18204 + 19400 19.4 23.441248 222.83743 -21.879144 1.5266119 -251.76376 -250.23715 + 19600 19.6 23.435558 218.16026 -21.86114 1.4945696 -251.59729 -250.10272 + 19800 19.8 24.074607 222.78958 -21.87264 1.5262841 -251.7863 -250.26001 + 20000 20 23.618814 222.44332 -21.870985 1.5239119 -251.37299 -249.84908 +Loop time of 22.6158 on 1 procs for 20000 steps with 54 atoms + +Performance: 76.407 ns/day, 0.314 hours/ns, 884.338 timesteps/s, 47.754 katom-step/s +99.9% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 8.9116 | 8.9116 | 8.9116 | 0.0 | 39.40 +Neigh | 0.26535 | 0.26535 | 0.26535 | 0.0 | 1.17 +Comm | 0.65637 | 0.65637 | 0.65637 | 0.0 | 2.90 +Output | 0.0036141 | 0.0036141 | 0.0036141 | 0.0 | 0.02 +Modify | 12.725 | 12.725 | 12.725 | 0.0 | 56.26 +Other | | 0.05425 | | | 0.24 + +Nlocal: 54 ave 54 max 54 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 632 ave 632 max 632 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 1677 ave 1677 max 1677 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 3354 ave 3354 max 3354 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 3354 +Ave neighs/atom = 62.111111 +Neighbor list builds = 1000 +Dangerous builds = 1000 +Total wall time: 0:00:22 diff --git a/examples/SPIN/test_problems/validation_nvt/log.11Mar25.spin.nvt_spin.g++.1 b/examples/SPIN/test_problems/validation_nvt/log.11Mar25.spin.nvt_spin.g++.1 new file mode 100644 index 0000000000..e8a14b259c --- /dev/null +++ b/examples/SPIN/test_problems/validation_nvt/log.11Mar25.spin.nvt_spin.g++.1 @@ -0,0 +1,241 @@ +LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-169-g4246fab500) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99) + using 1 OpenMP thread(s) per MPI task +# bcc iron in a 3d periodic box + +clear +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99) + using 1 OpenMP thread(s) per MPI task +units metal +atom_style spin +# atom_style spin/kk + +dimension 3 +boundary p p p + +# necessary for the serial algorithm (sametag) +atom_modify map array + +lattice bcc 2.8665 +Lattice spacing in x,y,z = 2.8665 2.8665 2.8665 +region box block 0.0 3.0 0.0 3.0 0.0 3.0 +create_box 1 box +Created orthogonal box = (0 0 0) to (8.5995 8.5995 8.5995) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 54 atoms + using lattice units in orthogonal box = (0 0 0) to (8.5995 8.5995 8.5995) + create_atoms CPU = 0.001 seconds + +# setting mass, mag. moments, and interactions for bcc iron + +mass 1 55.845 +set group all spin 2.2 0.0 0.0 1.0 +Setting atom values ... +WARNING: Set attribute spin is deprecated. Please use spin/atom instead. (src/set.cpp:268) + 54 settings made for spin +velocity all create 0 4928459 rot yes dist gaussian + +# pair_style hybrid/overlay eam/alloy spin/exchange 3.5 +pair_style hybrid/overlay eam/alloy spin/exchange 4.0 spin/neel 4.0 +pair_coeff * * eam/alloy Fe_Mishin2006.eam.alloy Fe +pair_coeff * * spin/exchange exchange 3.4 0.1 0.2171 1.841 +pair_coeff * * spin/neel neel 4.0 0.02 0.0 1.841 0.0 0.0 1.0 + +neighbor 0.1 bin +neigh_modify every 10 check yes delay 20 + +fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 +fix 2 all langevin 0.0 0.0 0.001 48279 +fix 3 all langevin/spin 200.0 0.01 321 +fix 4 all nve/spin lattice moving +timestep 0.001 + +# compute and output options + +compute out_mag all spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo_style custom step time v_tmag temp v_emag ke pe etotal +thermo 200 + +run 20000 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- fix nve/spin command: doi:10.1016/j.jcp.2018.06.042 + +@article{tranchida2018massively, +title={Massively Parallel Symplectic Algorithm for Coupled Magnetic Spin Dynamics and Molecular Dynamics}, +author={Tranchida, J and Plimpton, S J and Thibaudeau, P and Thompson, A P}, +journal={Journal of Computational Physics}, +volume={372}, +pages={406--425}, +year={2018}, +publisher={Elsevier} +doi={10.1016/j.jcp.2018.06.042} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Neighbor list info ... + update: every = 10 steps, delay = 20 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5.773367 + ghost atom cutoff = 5.773367 + binsize = 2.8866835, bins = 3 3 3 + 3 neighbor lists, perpetual/occasional/extra = 3 0 0 + (1) pair eam/alloy, perpetual, half/full from (2) + attributes: half, newton on, cut 5.7733670002446 + pair build: halffull/newton + stencil: none + bin: none + (2) pair spin/exchange, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (3) pair spin/neel, perpetual, copy from (2) + attributes: full, newton on + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 6.008 | 6.008 | 6.008 Mbytes + Step Time v_tmag Temp v_emag KinEng PotEng TotEng + 0 0 1.4336203e-31 0 -22.021022 0 -253.14103 -253.14103 + 200 0.2 185.03537 7.1508965e-05 -21.172867 4.8989274e-07 -252.29287 -252.29287 + 400 0.4 209.70221 8.8414079e-05 -21.060203 6.0570608e-07 -252.1802 -252.1802 + 600 0.6 185.48899 0.00010245242 -21.112413 7.0187977e-07 -252.23241 -252.23241 + 800 0.8 223.05275 8.1457051e-05 -21.018423 5.5804496e-07 -252.13842 -252.13842 + 1000 1 213.0164 8.9515898e-05 -21.048926 6.1325441e-07 -252.16892 -252.16892 + 1200 1.2 246.36673 0.0001154676 -20.930718 7.9104402e-07 -252.05072 -252.05072 + 1400 1.4 196.53774 6.2911172e-05 -21.154732 4.3099109e-07 -252.27473 -252.27473 + 1600 1.6 182.01716 0.00010355261 -21.16282 7.0941692e-07 -252.28282 -252.28282 + 1800 1.8 210.96677 8.7541641e-05 -21.088701 5.997292e-07 -252.2087 -252.2087 + 2000 2 253.99717 0.00010826381 -20.86351 7.416924e-07 -251.98351 -251.98351 + 2200 2.2 216.1501 9.6113637e-05 -21.030784 6.5845412e-07 -252.15078 -252.15078 + 2400 2.4 223.43699 8.5950374e-05 -21.009537 5.8882776e-07 -252.12954 -252.12954 + 2600 2.6 218.14727 0.00010110952 -20.970036 6.9267987e-07 -252.09004 -252.09004 + 2800 2.8 232.40923 0.00011013217 -20.973661 7.5449212e-07 -252.09366 -252.09366 + 3000 3 237.03942 0.0001227047 -20.923005 8.4062388e-07 -252.043 -252.043 + 3200 3.2 193.18057 6.4453691e-05 -21.192632 4.4155855e-07 -252.31263 -252.31263 + 3400 3.4 215.89559 0.00010926778 -20.99777 7.4857038e-07 -252.11777 -252.11777 + 3600 3.6 166.54235 7.286928e-05 -21.241556 4.9921196e-07 -252.36156 -252.36156 + 3800 3.8 159.38579 5.7560855e-05 -21.290065 3.9433719e-07 -252.41007 -252.41007 + 4000 4 170.59358 7.7217892e-05 -21.234059 5.2900339e-07 -252.35406 -252.35406 + 4200 4.2 215.77287 8.7497504e-05 -21.031438 5.9942683e-07 -252.15144 -252.15144 + 4400 4.4 197.99439 8.3188835e-05 -21.136708 5.6990905e-07 -252.25671 -252.25671 + 4600 4.6 225.89271 0.00015400081 -20.963516 1.0550269e-06 -252.08352 -252.08352 + 4800 4.8 202.99311 0.00014034452 -21.013112 9.614705e-07 -252.13311 -252.13311 + 5000 5 213.82643 0.00011505981 -21.058401 7.8825036e-07 -252.1784 -252.1784 + 5200 5.2 185.50349 8.6160092e-05 -21.172207 5.902645e-07 -252.29221 -252.29221 + 5400 5.4 201.98179 0.00010791717 -21.096481 7.3931764e-07 -252.21648 -252.21648 + 5600 5.6 171.20549 6.8869235e-05 -21.197869 4.718085e-07 -252.31787 -252.31787 + 5800 5.8 227.95465 0.00012603913 -21.009323 8.6346729e-07 -252.12932 -252.12932 + 6000 6 200.21111 0.00010449734 -21.110701 7.1588912e-07 -252.2307 -252.2307 + 6200 6.2 160.58077 7.2836942e-05 -21.267151 4.9899042e-07 -252.38715 -252.38715 + 6400 6.4 200.05407 9.0509705e-05 -21.073988 6.2006277e-07 -252.19399 -252.19399 + 6600 6.6 190.65275 0.0001033421 -21.158207 7.0797478e-07 -252.27821 -252.27821 + 6800 6.8 228.26898 0.00014786596 -20.911618 1.0129983e-06 -252.03162 -252.03162 + 7000 7 181.38559 7.164051e-05 -21.178965 4.9079392e-07 -252.29897 -252.29897 + 7200 7.2 206.68689 0.00014900154 -20.996098 1.0207779e-06 -252.1161 -252.1161 + 7400 7.4 192.31745 7.9639216e-05 -21.152927 5.4559136e-07 -252.27293 -252.27293 + 7600 7.6 190.74433 8.1341909e-05 -21.140079 5.5725615e-07 -252.26008 -252.26008 + 7800 7.8 174.0955 6.4367878e-05 -21.239195 4.4097067e-07 -252.3592 -252.35919 + 8000 8 160.00011 0.00012761576 -21.159302 8.7426845e-07 -252.2793 -252.2793 + 8200 8.2 210.43151 0.00014479042 -21.034928 9.9192846e-07 -252.15493 -252.15493 + 8400 8.4 234.76455 0.00017824488 -20.929712 1.2211178e-06 -252.04971 -252.04971 + 8600 8.6 186.41675 8.9522862e-05 -21.152624 6.1330212e-07 -252.27262 -252.27262 + 8800 8.8 182.51437 8.1196096e-05 -21.169538 5.5625721e-07 -252.28954 -252.28954 + 9000 9 205.7602 8.1712224e-05 -21.069704 5.597931e-07 -252.1897 -252.1897 + 9200 9.2 169.12461 4.5311332e-05 -21.260803 3.1041832e-07 -252.3808 -252.3808 + 9400 9.4 226.30809 0.00011391282 -20.976322 7.8039252e-07 -252.09632 -252.09632 + 9600 9.6 167.17205 9.1023114e-05 -21.226931 6.2358003e-07 -252.34693 -252.34693 + 9800 9.8 204.63476 0.00010727562 -21.045363 7.3492253e-07 -252.16536 -252.16536 + 10000 10 236.18563 8.998006e-05 -20.973452 6.1643429e-07 -252.09345 -252.09345 + 10200 10.2 194.32863 7.2352023e-05 -21.144235 4.9566835e-07 -252.26424 -252.26424 + 10400 10.4 212.89479 0.00011913313 -21.041706 8.1615576e-07 -252.16171 -252.1617 + 10600 10.6 215.20168 9.7714692e-05 -21.032571 6.6942261e-07 -252.15257 -252.15257 + 10800 10.8 297.63322 0.00013498385 -20.721355 9.2474566e-07 -251.84135 -251.84135 + 11000 11 221.40055 0.00010205784 -21.051231 6.9917662e-07 -252.17123 -252.17123 + 11200 11.2 242.39307 0.00013617253 -20.890742 9.3288909e-07 -252.01074 -252.01074 + 11400 11.4 165.26613 7.2237463e-05 -21.24741 4.9488352e-07 -252.36741 -252.36741 + 11600 11.6 216.24435 8.1150764e-05 -21.036156 5.5594665e-07 -252.15616 -252.15616 + 11800 11.8 183.53912 0.00010117662 -21.186918 6.9313953e-07 -252.30692 -252.30692 + 12000 12 220.44994 9.647801e-05 -21.023611 6.6095036e-07 -252.14361 -252.14361 + 12200 12.2 225.17986 9.472867e-05 -21.009823 6.48966e-07 -252.12982 -252.12982 + 12400 12.4 216.68616 8.9352492e-05 -21.025818 6.1213495e-07 -252.14582 -252.14582 + 12600 12.6 179.65027 6.5355297e-05 -21.199208 4.4773526e-07 -252.31921 -252.31921 + 12800 12.8 210.22912 7.5167585e-05 -21.071447 5.1495716e-07 -252.19145 -252.19145 + 13000 13 157.423 9.2895323e-05 -21.250615 6.3640614e-07 -252.37062 -252.37061 + 13200 13.2 204.52025 0.00012645764 -21.049044 8.6633447e-07 -252.16904 -252.16904 + 13400 13.4 198.28053 0.00012118522 -21.066084 8.3021421e-07 -252.18609 -252.18608 + 13600 13.6 237.99318 8.644348e-05 -20.978488 5.9220593e-07 -252.09849 -252.09849 + 13800 13.8 222.81023 0.00015789536 -20.951387 1.0817076e-06 -252.07139 -252.07139 + 14000 14 218.31245 0.00011842157 -21.008674 8.1128101e-07 -252.12867 -252.12867 + 14200 14.2 197.5018 0.00011399102 -21.081911 7.8092826e-07 -252.20191 -252.20191 + 14400 14.4 228.11014 0.00015934606 -20.963235 1.091646e-06 -252.08323 -252.08323 + 14600 14.6 216.45102 9.6033576e-05 -21.034352 6.5790564e-07 -252.15435 -252.15435 + 14800 14.8 205.97376 0.00014278574 -21.018847 9.7819479e-07 -252.13885 -252.13885 + 15000 15 230.09259 0.00012803086 -20.986446 8.7711221e-07 -252.10645 -252.10644 + 15200 15.2 248.21379 0.0001784321 -20.84502 1.2224004e-06 -251.96502 -251.96502 + 15400 15.4 223.07119 0.00013057001 -20.984451 8.9450744e-07 -252.10445 -252.10445 + 15600 15.6 194.42126 8.4530618e-05 -21.127055 5.7910131e-07 -252.24705 -252.24705 + 15800 15.8 207.23453 0.00013807606 -21.035173 9.4592974e-07 -252.15517 -252.15517 + 16000 16 175.93234 8.2440767e-05 -21.208299 5.6478419e-07 -252.3283 -252.3283 + 16200 16.2 225.63746 7.4767651e-05 -21.012845 5.1221731e-07 -252.13285 -252.13284 + 16400 16.4 149.12667 6.624179e-05 -21.331981 4.5380844e-07 -252.45198 -252.45198 + 16600 16.6 211.41275 0.00012606898 -21.042094 8.6367183e-07 -252.16209 -252.16209 + 16800 16.8 199.88466 8.2345231e-05 -21.116203 5.641297e-07 -252.2362 -252.2362 + 17000 17 212.37144 0.00010445794 -21.041826 7.1561919e-07 -252.16183 -252.16183 + 17200 17.2 160.83603 5.4109632e-05 -21.294207 3.706936e-07 -252.41421 -252.41421 + 17400 17.4 254.84209 0.00013687967 -20.886397 9.3773358e-07 -252.0064 -252.0064 + 17600 17.6 237.6091 0.00012462019 -20.958967 8.5374644e-07 -252.07897 -252.07897 + 17800 17.8 194.26242 7.0286952e-05 -21.145006 4.8152099e-07 -252.26501 -252.26501 + 18000 18 175.14964 6.1470052e-05 -21.239458 4.2111827e-07 -252.35946 -252.35946 + 18200 18.2 181.99258 7.2295849e-05 -21.195184 4.9528351e-07 -252.31519 -252.31519 + 18400 18.4 197.11115 9.9207898e-05 -21.116471 6.7965225e-07 -252.23647 -252.23647 + 18600 18.6 211.2814 8.4543325e-05 -21.074729 5.7918837e-07 -252.19473 -252.19473 + 18800 18.8 198.62813 9.4052117e-05 -21.097909 6.4433109e-07 -252.21791 -252.21791 + 19000 19 226.11003 0.00013827389 -20.951669 9.4728506e-07 -252.07167 -252.07167 + 19200 19.2 233.61049 0.00013363448 -20.917911 9.1550145e-07 -252.03791 -252.03791 + 19400 19.4 182.94749 9.0400181e-05 -21.139686 6.1931245e-07 -252.25969 -252.25968 + 19600 19.6 155.99677 5.9871119e-05 -21.282519 4.1016433e-07 -252.40252 -252.40252 + 19800 19.8 179.57217 8.5624245e-05 -21.193447 5.8659353e-07 -252.31345 -252.31345 + 20000 20 243.60222 0.00015451915 -20.911769 1.0585779e-06 -252.03177 -252.03177 +Loop time of 21.9748 on 1 procs for 20000 steps with 54 atoms + +Performance: 78.636 ns/day, 0.305 hours/ns, 910.134 timesteps/s, 49.147 katom-step/s +100.0% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 8.1863 | 8.1863 | 8.1863 | 0.0 | 37.25 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.77445 | 0.77445 | 0.77445 | 0.0 | 3.52 +Output | 0.0037256 | 0.0037256 | 0.0037256 | 0.0 | 0.02 +Modify | 12.954 | 12.954 | 12.954 | 0.0 | 58.95 +Other | | 0.05601 | | | 0.25 + +Nlocal: 54 ave 54 max 54 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 801 ave 801 max 801 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 1728 ave 1728 max 1728 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 3456 ave 3456 max 3456 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 3456 +Ave neighs/atom = 64 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:22 diff --git a/examples/rerun/in.rdf.first b/examples/rerun/in.rdf.first index f9d1ecf55e..a72eae975a 100644 --- a/examples/rerun/in.rdf.first +++ b/examples/rerun/in.rdf.first @@ -27,7 +27,7 @@ neigh_modify delay 0 every 20 check no fix 1 all nve -dump 1 all custom 100 lj.dump id type x y z +dump 1 all custom 100 lj.dump id type x y z vx vy vz compute myRDF all rdf 50 cutoff 2.5 fix 2 all ave/time 100 10 1000 c_myRDF[*] file rdf.first mode vector From 5068406c03ec8534d307a4654194197ff40c9a01 Mon Sep 17 00:00:00 2001 From: Trung Nguyen Date: Tue, 11 Mar 2025 16:41:41 -0500 Subject: [PATCH 065/113] fixed incorrect path to the potential file --- examples/PACKAGES/pafi/in.pafi | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/examples/PACKAGES/pafi/in.pafi b/examples/PACKAGES/pafi/in.pafi index 9e9efb156b..ebfe419a6d 100644 --- a/examples/PACKAGES/pafi/in.pafi +++ b/examples/PACKAGES/pafi/in.pafi @@ -9,7 +9,7 @@ read_data pafipath.4.data fix pa NULL PafiPath ## EAM potential pair_style eam/fs -pair_coeff * * ../../../../potentials/Fe_mm.eam.fs Fe +pair_coeff * * Fe_mm.eam.fs Fe mass * 55.85 thermo 100 From 2c2eaf09e6441c57d78e19cb7f1854d37decf461 Mon Sep 17 00:00:00 2001 From: megmcca Date: Wed, 12 Mar 2025 07:22:47 -0600 Subject: [PATCH 066/113] add urls for error 06 --- src/domain.cpp | 2 +- src/nbin.cpp | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/src/domain.cpp b/src/domain.cpp index 572575ad22..db20605ce2 100644 --- a/src/domain.cpp +++ b/src/domain.cpp @@ -787,7 +787,7 @@ void Domain::pbc() int flag = 0; for (i = 0; i < n3; i++) if (!std::isfinite(*coord++)) flag = 1; - if (flag) error->one(FLERR,"Non-numeric atom coords - simulation unstable"); + if (flag) error->one(FLERR,"Non-numeric atom coords - simulation unstable" + utils::errorurl(06)); // setup for PBC checks diff --git a/src/nbin.cpp b/src/nbin.cpp index f9bdc2ac50..404ea381c2 100644 --- a/src/nbin.cpp +++ b/src/nbin.cpp @@ -141,7 +141,7 @@ int NBin::coord2bin(double *x) int ix,iy,iz; if (!std::isfinite(x[0]) || !std::isfinite(x[1]) || !std::isfinite(x[2])) - error->one(FLERR,"Non-numeric positions - simulation unstable"); + error->one(FLERR,"Non-numeric positions - simulation unstable" + utils::errorurl(06)); if (x[0] >= bboxhi[0]) ix = static_cast ((x[0]-bboxhi[0])*bininvx) + nbinx; @@ -181,7 +181,7 @@ int NBin::coord2bin_multi(double *x, int ic) int ibin; if (!std::isfinite(x[0]) || !std::isfinite(x[1]) || !std::isfinite(x[2])) - error->one(FLERR,"Non-numeric positions - simulation unstable"); + error->one(FLERR,"Non-numeric positions - simulation unstable" + utils::errorurl(06)); if (x[0] >= bboxhi[0]) ix = static_cast ((x[0]-bboxhi[0])*bininvx_multi[ic]) + nbinx_multi[ic]; From ab639932264aae5e688cd750ee12997ddee4ff89 Mon Sep 17 00:00:00 2001 From: megmcca Date: Wed, 12 Mar 2025 07:23:56 -0600 Subject: [PATCH 067/113] add urls for error 07 --- src/fix_box_relax.cpp | 4 ++-- src/fix_nh.cpp | 4 ++-- src/npair.cpp | 4 ++-- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/src/fix_box_relax.cpp b/src/fix_box_relax.cpp index 1362095a28..ef58f1a508 100644 --- a/src/fix_box_relax.cpp +++ b/src/fix_box_relax.cpp @@ -700,7 +700,7 @@ void FixBoxRelax::couple() } if (!std::isfinite(p_current[0]) || !std::isfinite(p_current[1]) || !std::isfinite(p_current[2])) - error->all(FLERR,"Non-numeric pressure - simulation unstable"); + error->all(FLERR,"Non-numeric pressure - simulation unstable" + utils::errorurl(07)); // switch order from xy-xz-yz to Voigt ordering @@ -710,7 +710,7 @@ void FixBoxRelax::couple() p_current[5] = tensor[3]; if (!std::isfinite(p_current[3]) || !std::isfinite(p_current[4]) || !std::isfinite(p_current[5])) - error->all(FLERR,"Non-numeric pressure - simulation unstable"); + error->all(FLERR,"Non-numeric pressure - simulation unstable" + utils::errorurl(07)); } } diff --git a/src/fix_nh.cpp b/src/fix_nh.cpp index b56033d6d6..c7e35eaec5 100644 --- a/src/fix_nh.cpp +++ b/src/fix_nh.cpp @@ -1045,7 +1045,7 @@ void FixNH::couple() } if (!std::isfinite(p_current[0]) || !std::isfinite(p_current[1]) || !std::isfinite(p_current[2])) - error->all(FLERR,"Non-numeric pressure - simulation unstable"); + error->all(FLERR,"Non-numeric pressure - simulation unstable" + utils::errorurl(07)); // switch order from xy-xz-yz to Voigt ordering @@ -1055,7 +1055,7 @@ void FixNH::couple() p_current[5] = tensor[3]; if (!std::isfinite(p_current[3]) || !std::isfinite(p_current[4]) || !std::isfinite(p_current[5])) - error->all(FLERR,"Non-numeric pressure - simulation unstable"); + error->all(FLERR,"Non-numeric pressure - simulation unstable" + utils::errorurl(07)); } } diff --git a/src/npair.cpp b/src/npair.cpp index d98d5716dd..4c2c03a4a0 100644 --- a/src/npair.cpp +++ b/src/npair.cpp @@ -238,7 +238,7 @@ int NPair::exclusion(int i, int j, int itype, int jtype, int NPair::coord2bin(double *x, int &ix, int &iy, int &iz) { if (!std::isfinite(x[0]) || !std::isfinite(x[1]) || !std::isfinite(x[2])) - error->one(FLERR,"Non-numeric positions - simulation unstable"); + error->one(FLERR,"Non-numeric positions - simulation unstable" + utils::errorurl(07)); if (x[0] >= bboxhi[0]) ix = static_cast ((x[0]-bboxhi[0])*bininvx) + nbinx; @@ -281,7 +281,7 @@ int NPair::coord2bin(double *x, int ic) int ibin; if (!std::isfinite(x[0]) || !std::isfinite(x[1]) || !std::isfinite(x[2])) - error->one(FLERR,"Non-numeric positions - simulation unstable"); + error->one(FLERR,"Non-numeric positions - simulation unstable" + utils::errorurl(07)); if (x[0] >= bboxhi[0]) ix = static_cast ((x[0]-bboxhi[0])*bininvx_multi[ic]) + nbinx_multi[ic]; From 70faf860404476d99edfbcbd96cebbca7d4aa471 Mon Sep 17 00:00:00 2001 From: megmcca Date: Wed, 12 Mar 2025 07:25:09 -0600 Subject: [PATCH 068/113] add urls for error 08 --- src/balance.cpp | 2 +- src/change_box.cpp | 2 +- src/displace_atoms.cpp | 2 +- src/thermo.cpp | 4 ++-- 4 files changed, 5 insertions(+), 5 deletions(-) diff --git a/src/balance.cpp b/src/balance.cpp index fa4e68a8b8..a6db94ddd1 100644 --- a/src/balance.cpp +++ b/src/balance.cpp @@ -379,7 +379,7 @@ void Balance::command(int narg, char **arg) bigint nblocal = atom->nlocal; MPI_Allreduce(&nblocal,&natoms,1,MPI_LMP_BIGINT,MPI_SUM,world); if (natoms != atom->natoms) - error->all(FLERR,"Lost atoms via balance: original {} current {}", + error->all(FLERR,"Lost atoms via balance: original {} current {}"+utils::errorurl(08), atom->natoms,natoms); // imbfinal = final imbalance diff --git a/src/change_box.cpp b/src/change_box.cpp index eb7ce7f136..023208d766 100644 --- a/src/change_box.cpp +++ b/src/change_box.cpp @@ -381,7 +381,7 @@ void ChangeBox::command(int narg, char **arg) MPI_Allreduce(&nblocal,&natoms,1,MPI_LMP_BIGINT,MPI_SUM,world); if (natoms != atom->natoms && comm->me == 0) error->warning(FLERR,"Lost atoms via change_box: original {} " - "current {}", atom->natoms,natoms); + "current {}"+utils::errorurl(08),atom->natoms,natoms); } /* ---------------------------------------------------------------------- diff --git a/src/displace_atoms.cpp b/src/displace_atoms.cpp index 5ecf5a2c9e..9f32175815 100644 --- a/src/displace_atoms.cpp +++ b/src/displace_atoms.cpp @@ -364,7 +364,7 @@ void DisplaceAtoms::command(int narg, char **arg) MPI_Allreduce(&nblocal,&natoms,1,MPI_LMP_BIGINT,MPI_SUM,world); if (natoms != atom->natoms && comm->me == 0) error->warning(FLERR,"Lost atoms via displace_atoms: original {} " - "current {}",atom->natoms,natoms); + "current {}"+utils::errorurl(08),atom->natoms,natoms); } /* ---------------------------------------------------------------------- diff --git a/src/thermo.cpp b/src/thermo.cpp index ca60b48687..9ba4a03b94 100644 --- a/src/thermo.cpp +++ b/src/thermo.cpp @@ -509,12 +509,12 @@ bigint Thermo::lost_check() // error message if (lostflag == Thermo::ERROR) - error->all(FLERR, "Lost atoms: original {} current {}", atom->natoms, ntotal[0]); + error->all(FLERR, "Lost atoms: original {} current {}" + utils::errorurl(08), atom->natoms, ntotal[0]); // warning message if (comm->me == 0) - error->warning(FLERR, "Lost atoms: original {} current {}", atom->natoms, ntotal[0]); + error->warning(FLERR, "Lost atoms: original {} current {}" + utils::errorurl(08), atom->natoms, ntotal[0]); // reset total atom count From 6d42040b9d49e96e933ca11b49c9b4ab837af6bc Mon Sep 17 00:00:00 2001 From: megmcca Date: Wed, 12 Mar 2025 07:26:59 -0600 Subject: [PATCH 069/113] add url for error 13 --- src/input.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/input.cpp b/src/input.cpp index 814f900fbd..710ff45b3f 100644 --- a/src/input.cpp +++ b/src/input.cpp @@ -663,7 +663,7 @@ void Input::substitute(char *&str, char *&str2, int &max, int &max2, int flag) } if (value == nullptr) - error->one(FLERR,"Substitution for illegal variable {}",var); + error->one(FLERR,"Substitution for illegal variable {}"+utils::errorurl(13),var); // check if storage in str2 needs to be expanded // re-initialize ptr and ptr2 to the point beyond the variable. From fa262967e6abb3f0450a19fe33586e03894195d5 Mon Sep 17 00:00:00 2001 From: megmcca Date: Wed, 12 Mar 2025 07:28:22 -0600 Subject: [PATCH 070/113] add url for error 10 --- src/utils.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/utils.cpp b/src/utils.cpp index 940faa3eed..1572f18bff 100644 --- a/src/utils.cpp +++ b/src/utils.cpp @@ -442,7 +442,7 @@ std::string utils::check_packages_for_style(const std::string &style, const std: if (LAMMPS::is_installed_pkg(pkg)) errmsg += ", but seems to be missing because of a dependency"; else - errmsg += " which is not enabled in this LAMMPS binary."; + errmsg += " which is not enabled in this LAMMPS binary." + utils::errorurl(10); } return errmsg; } From d1671c24c46077d959edafcde8444b260581483f Mon Sep 17 00:00:00 2001 From: megmcca Date: Wed, 12 Mar 2025 07:28:58 -0600 Subject: [PATCH 071/113] add url for warning 28 --- src/verlet.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/verlet.cpp b/src/verlet.cpp index f0a307bdd2..ae9217b896 100644 --- a/src/verlet.cpp +++ b/src/verlet.cpp @@ -57,7 +57,7 @@ void Verlet::init() if (fix->time_integrate) do_time_integrate = true; if (!do_time_integrate && (comm->me == 0)) - error->warning(FLERR,"No fixes with time integration, atoms won't move"); + error->warning(FLERR,"No fixes with time integration, atoms won't move" + utils::errorurl(28)); // virial_style: // VIRIAL_PAIR if computed explicitly in pair via sum over pair interactions From 90c713d0656634dee1baa5ea6ecca80b565305a0 Mon Sep 17 00:00:00 2001 From: megmcca Date: Wed, 12 Mar 2025 07:33:07 -0600 Subject: [PATCH 072/113] update details on errors 6, 7, 8, 10, 13, and warning 28 --- doc/src/Errors_details.rst | 89 +++++++++++++++++++++++++++++++++----- 1 file changed, 77 insertions(+), 12 deletions(-) diff --git a/doc/src/Errors_details.rst b/doc/src/Errors_details.rst index 820721a581..6b37447174 100644 --- a/doc/src/Errors_details.rst +++ b/doc/src/Errors_details.rst @@ -102,8 +102,15 @@ those cases using (temporarily) :doc:`fix nve/limit ` or :doc:`fix dt/reset ` can help to avoid too large updates or adapt the timestep according to the displacements. +Ignoring lost atoms +^^^^^^^^^^^^^^^^^^^ -Pressure, forces, positions becoming NaN of Inf +It is tempting to use the :doc:`thermo_modify lost ignore ` +to avoid that LAMMPS stops with an error on lost atoms. This setting should, however, +*only* be used when atoms *should* leave the system. In general, ignoring +a problem does not solve it. + +Pressure, forces, positions becoming NaN or Inf ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Some potentials can overflow or have a division by zero with close contacts @@ -129,7 +136,7 @@ angle, dihedral or improper with just one atom in the actual sub-domain. Typically, this cutoff is set to the largest cutoff from the :doc:`pair style(s) ` plus the :doc:`neighbor list skin distance ` and will be more than sufficient for all bonded -interactions. But if the pair style cutoff is small this may bot be +interactions. But if the pair style cutoff is small this may not be enough. LAMMPS will print a warning in this case using some heuristic based on the equilibrium bond length, but that may not be sufficient for cases where the force constants are small and thus bonds may be @@ -145,16 +152,8 @@ for "lost" or "missing" atoms. Thus it can help to use very conservative :doc:`neighbor list settings ` and then examine the neighbor list statistics if the neighbor list rebuild can be safely delayed. Rebuilding the neighbor list less frequently -(i.e. through increasing the *delay* or *every* setting has diminishing -returns and increasing risks). - -Ignoring lost atoms -^^^^^^^^^^^^^^^^^^^ - -It is tempting to use the :doc:`thermo_modify lost ignore ` -to avoid that LAMMPS stops with an error. This setting should, however, -*only* be used when atoms *should* leave the system. In general, ignoring -a problem does not solve it. +(i.e. through increasing the *delay* or *every*) setting has diminishing +returns and increasing risks. Units ^^^^^ @@ -320,11 +319,40 @@ potentially at different times than other atoms they are bonded to, this error can be converted to a warning or turned off using the *lost/bond* keyword in the :doc:`thermo_modify ` command. +.. _err0006: + +Non-numeric atom coords - simulation unstable +--------------------------------------------- +This error usually occurs due to issues with system geometry or the potential in +use. See :ref:`Pressure, forces, positions becoming NaN or Inf` above in the +general troubleshooting section. + +.. _err0007: + +Non-numeric pressure - simulation unstable +------------------------------------------ +This error usually occurs due to issues with system geometry or the potential in +use. See :ref:`Pressure, forces, positions becoming NaN or Inf` above in the +general troubleshooting section. + + .. _err0008: Lost atoms ... -------------- +A simulation erroring out due to lost atoms can have multiple causes. In the +majority of cases, lost atoms are unexpected and a result of extremely high +velocities causing instabilities in the system, and those velocities can result +from a variety of issues. For ideas on how to track down issues with unexpected +lost atoms, see :ref:`Fast moving atoms` and :ref:`Neighbor list settings` in +the general troubleshooting section above. In specific situations however, +losing atoms is expected material behavior (e.g. with sputtering and surface +evaporation simulations) and an unwanted crash can be resolved by changing the +:doc:`thermo_modify lost ` keyword from the default 'error' to +'warn' or 'ignore' (though heed the advice in :ref:`Ignoring lost atoms` +above!). + .. _err0009: Too many neighbor bins @@ -370,6 +398,24 @@ You should contact the LAMMPS developers and report the bug as a `GitHub Bug Report Issue `_ along with sufficient information to easily reproduce it. + +.. _err0013: + +Substitution for illegal variable +--------------------------------- + +A variable in an input script was not able to be parsed by LAMMPS on read-in. +LAMMPS has a few different accepted formats for variables, as detailed in the +:doc:`variable ` doc page. One cause for this error beyond simple +typos is missing brackets, for example when changing a variable definition from +a single letter (which does not require brackets) to one with multiple letters, +for example ``variable a equal 1.0`` (which can be evaluated later as ``$a`` or +``${a}``) to ``variable a0 equal 1.0`` (which can only be evaluated as +``${a0}``). Another potential source off this error may be invalid command line +variables used when launching LAMMPS from an interactive shell or shell scripts. +Users with harder-to-track variable errors might also find reading :doc:`Section +5.2. Parsing rules for input scripts` helpful. + .. _err0015: Cannot use neighbor bins - box size \<\< cutoff @@ -522,6 +568,25 @@ atom type. Thus it would not be required to have a Masses section and the included data would be ignored. LAMMPS prints this warning to inform about this case. + +.. _err0028: + +No fixes with time integration, atoms won't move +------------------------------------------------ + +This warning will be issued if LAMMPS encounters a :doc:`run ` command that +does not have a preceding :doc:`fix ` command that updates atom/object +positions and velocities per step. In other words, there are no fixes detected +that perform velocity-Verlet time integration, such as :doc:`fix nve `. +Note that this alert does not mean that there are no active fixes. LAMMPS has a +very wide variety of fixes, many of which do not move objects but also operate +through steps, such as printing outputs (e.g. :doc:`fix print `), +performing calculations (e.g. :doc:`fix ave/time `), or changing +other system parameters (e.g. :doc:`fix dt/reset `). It is up to +the user to determine whether the lack of a time-integrating fix is intentional +or not. + + .. _err0029: System is not charge neutral, net charge = ... From ebf6ba36bf67442f67d30bb269b2406a76d71c33 Mon Sep 17 00:00:00 2001 From: megmcca Date: Wed, 12 Mar 2025 07:39:45 -0600 Subject: [PATCH 073/113] remove leading 0 in single-digit url codes --- src/balance.cpp | 2 +- src/change_box.cpp | 2 +- src/displace_atoms.cpp | 2 +- src/domain.cpp | 2 +- src/fix_box_relax.cpp | 4 ++-- src/fix_nh.cpp | 4 ++-- src/nbin.cpp | 4 ++-- src/npair.cpp | 4 ++-- src/thermo.cpp | 4 ++-- 9 files changed, 14 insertions(+), 14 deletions(-) diff --git a/src/balance.cpp b/src/balance.cpp index a6db94ddd1..f838eed748 100644 --- a/src/balance.cpp +++ b/src/balance.cpp @@ -379,7 +379,7 @@ void Balance::command(int narg, char **arg) bigint nblocal = atom->nlocal; MPI_Allreduce(&nblocal,&natoms,1,MPI_LMP_BIGINT,MPI_SUM,world); if (natoms != atom->natoms) - error->all(FLERR,"Lost atoms via balance: original {} current {}"+utils::errorurl(08), + error->all(FLERR,"Lost atoms via balance: original {} current {}"+utils::errorurl(8), atom->natoms,natoms); // imbfinal = final imbalance diff --git a/src/change_box.cpp b/src/change_box.cpp index 023208d766..dd6c427a18 100644 --- a/src/change_box.cpp +++ b/src/change_box.cpp @@ -381,7 +381,7 @@ void ChangeBox::command(int narg, char **arg) MPI_Allreduce(&nblocal,&natoms,1,MPI_LMP_BIGINT,MPI_SUM,world); if (natoms != atom->natoms && comm->me == 0) error->warning(FLERR,"Lost atoms via change_box: original {} " - "current {}"+utils::errorurl(08),atom->natoms,natoms); + "current {}"+utils::errorurl(8),atom->natoms,natoms); } /* ---------------------------------------------------------------------- diff --git a/src/displace_atoms.cpp b/src/displace_atoms.cpp index 9f32175815..6f237c03c9 100644 --- a/src/displace_atoms.cpp +++ b/src/displace_atoms.cpp @@ -364,7 +364,7 @@ void DisplaceAtoms::command(int narg, char **arg) MPI_Allreduce(&nblocal,&natoms,1,MPI_LMP_BIGINT,MPI_SUM,world); if (natoms != atom->natoms && comm->me == 0) error->warning(FLERR,"Lost atoms via displace_atoms: original {} " - "current {}"+utils::errorurl(08),atom->natoms,natoms); + "current {}"+utils::errorurl(8),atom->natoms,natoms); } /* ---------------------------------------------------------------------- diff --git a/src/domain.cpp b/src/domain.cpp index db20605ce2..0b1bbf2c77 100644 --- a/src/domain.cpp +++ b/src/domain.cpp @@ -787,7 +787,7 @@ void Domain::pbc() int flag = 0; for (i = 0; i < n3; i++) if (!std::isfinite(*coord++)) flag = 1; - if (flag) error->one(FLERR,"Non-numeric atom coords - simulation unstable" + utils::errorurl(06)); + if (flag) error->one(FLERR,"Non-numeric atom coords - simulation unstable" + utils::errorurl(6)); // setup for PBC checks diff --git a/src/fix_box_relax.cpp b/src/fix_box_relax.cpp index ef58f1a508..c8540e1d9c 100644 --- a/src/fix_box_relax.cpp +++ b/src/fix_box_relax.cpp @@ -700,7 +700,7 @@ void FixBoxRelax::couple() } if (!std::isfinite(p_current[0]) || !std::isfinite(p_current[1]) || !std::isfinite(p_current[2])) - error->all(FLERR,"Non-numeric pressure - simulation unstable" + utils::errorurl(07)); + error->all(FLERR,"Non-numeric pressure - simulation unstable" + utils::errorurl(7)); // switch order from xy-xz-yz to Voigt ordering @@ -710,7 +710,7 @@ void FixBoxRelax::couple() p_current[5] = tensor[3]; if (!std::isfinite(p_current[3]) || !std::isfinite(p_current[4]) || !std::isfinite(p_current[5])) - error->all(FLERR,"Non-numeric pressure - simulation unstable" + utils::errorurl(07)); + error->all(FLERR,"Non-numeric pressure - simulation unstable" + utils::errorurl(7)); } } diff --git a/src/fix_nh.cpp b/src/fix_nh.cpp index c7e35eaec5..d13ddcb819 100644 --- a/src/fix_nh.cpp +++ b/src/fix_nh.cpp @@ -1045,7 +1045,7 @@ void FixNH::couple() } if (!std::isfinite(p_current[0]) || !std::isfinite(p_current[1]) || !std::isfinite(p_current[2])) - error->all(FLERR,"Non-numeric pressure - simulation unstable" + utils::errorurl(07)); + error->all(FLERR,"Non-numeric pressure - simulation unstable" + utils::errorurl(7)); // switch order from xy-xz-yz to Voigt ordering @@ -1055,7 +1055,7 @@ void FixNH::couple() p_current[5] = tensor[3]; if (!std::isfinite(p_current[3]) || !std::isfinite(p_current[4]) || !std::isfinite(p_current[5])) - error->all(FLERR,"Non-numeric pressure - simulation unstable" + utils::errorurl(07)); + error->all(FLERR,"Non-numeric pressure - simulation unstable" + utils::errorurl(7)); } } diff --git a/src/nbin.cpp b/src/nbin.cpp index 404ea381c2..4482c62ca7 100644 --- a/src/nbin.cpp +++ b/src/nbin.cpp @@ -141,7 +141,7 @@ int NBin::coord2bin(double *x) int ix,iy,iz; if (!std::isfinite(x[0]) || !std::isfinite(x[1]) || !std::isfinite(x[2])) - error->one(FLERR,"Non-numeric positions - simulation unstable" + utils::errorurl(06)); + error->one(FLERR,"Non-numeric positions - simulation unstable" + utils::errorurl(6)); if (x[0] >= bboxhi[0]) ix = static_cast ((x[0]-bboxhi[0])*bininvx) + nbinx; @@ -181,7 +181,7 @@ int NBin::coord2bin_multi(double *x, int ic) int ibin; if (!std::isfinite(x[0]) || !std::isfinite(x[1]) || !std::isfinite(x[2])) - error->one(FLERR,"Non-numeric positions - simulation unstable" + utils::errorurl(06)); + error->one(FLERR,"Non-numeric positions - simulation unstable" + utils::errorurl(6)); if (x[0] >= bboxhi[0]) ix = static_cast ((x[0]-bboxhi[0])*bininvx_multi[ic]) + nbinx_multi[ic]; diff --git a/src/npair.cpp b/src/npair.cpp index 4c2c03a4a0..586522e249 100644 --- a/src/npair.cpp +++ b/src/npair.cpp @@ -238,7 +238,7 @@ int NPair::exclusion(int i, int j, int itype, int jtype, int NPair::coord2bin(double *x, int &ix, int &iy, int &iz) { if (!std::isfinite(x[0]) || !std::isfinite(x[1]) || !std::isfinite(x[2])) - error->one(FLERR,"Non-numeric positions - simulation unstable" + utils::errorurl(07)); + error->one(FLERR,"Non-numeric positions - simulation unstable" + utils::errorurl(7)); if (x[0] >= bboxhi[0]) ix = static_cast ((x[0]-bboxhi[0])*bininvx) + nbinx; @@ -281,7 +281,7 @@ int NPair::coord2bin(double *x, int ic) int ibin; if (!std::isfinite(x[0]) || !std::isfinite(x[1]) || !std::isfinite(x[2])) - error->one(FLERR,"Non-numeric positions - simulation unstable" + utils::errorurl(07)); + error->one(FLERR,"Non-numeric positions - simulation unstable" + utils::errorurl(7)); if (x[0] >= bboxhi[0]) ix = static_cast ((x[0]-bboxhi[0])*bininvx_multi[ic]) + nbinx_multi[ic]; diff --git a/src/thermo.cpp b/src/thermo.cpp index 9ba4a03b94..8491dc2719 100644 --- a/src/thermo.cpp +++ b/src/thermo.cpp @@ -509,12 +509,12 @@ bigint Thermo::lost_check() // error message if (lostflag == Thermo::ERROR) - error->all(FLERR, "Lost atoms: original {} current {}" + utils::errorurl(08), atom->natoms, ntotal[0]); + error->all(FLERR, "Lost atoms: original {} current {}" + utils::errorurl(8), atom->natoms, ntotal[0]); // warning message if (comm->me == 0) - error->warning(FLERR, "Lost atoms: original {} current {}" + utils::errorurl(08), atom->natoms, ntotal[0]); + error->warning(FLERR, "Lost atoms: original {} current {}" + utils::errorurl(8), atom->natoms, ntotal[0]); // reset total atom count From 930d3ddc176a1596fa2cc14850e8b8ddd6672615 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 10 Mar 2025 06:25:11 -0400 Subject: [PATCH 074/113] resolve spelling and formatting issues --- doc/src/bond_bpm_spring.rst | 2 +- doc/src/bond_bpm_spring_plastic.rst | 19 ++++++++++--------- doc/utils/sphinx-config/false_positives.txt | 1 + 3 files changed, 12 insertions(+), 10 deletions(-) diff --git a/doc/src/bond_bpm_spring.rst b/doc/src/bond_bpm_spring.rst index 69d8e2d491..0d087a41cd 100644 --- a/doc/src/bond_bpm_spring.rst +++ b/doc/src/bond_bpm_spring.rst @@ -142,7 +142,7 @@ is accordingly replaced with a square root. This approximation assumes bonds are evenly distributed on a spherical surface and neglects constant prefactors which are irrelevant since only the ratio of volumes matters. This term may be used to adjust the Poisson's ratio. See the simulation in the -examples/bpm/poissons_ratio directory for a demonstration of this effect. +``examples/bpm/poissons_ratio`` directory for a demonstration of this effect. If a bond is broken (or created), :math:`V_{0,i}` is updated by subtracting (or adding) that bond's contribution. diff --git a/doc/src/bond_bpm_spring_plastic.rst b/doc/src/bond_bpm_spring_plastic.rst index fb0c50e9d3..c8f32bede1 100644 --- a/doc/src/bond_bpm_spring_plastic.rst +++ b/doc/src/bond_bpm_spring_plastic.rst @@ -133,16 +133,17 @@ Restart and other info """"""""""""""""""""""""""""""""""""""""""""""""""""""""""" This bond style writes the reference state and plastic history of each -bond to :doc:`binary restart files `. Loading a restart -file will properly restore bonds. However, the reference state is NOT -written to data files. Therefore reading a data file will not -restore bonds and will cause their reference states to be redefined. +bond to :doc:`binary restart files `. Loading a restart file +will properly restore bonds. However, the reference state is NOT written +to data files. Therefore reading a data file will not restore bonds and +will cause their reference states to be redefined. -The potential energy and the single() function of this bond style returns zero. -The single() function also calculates two extra bond quantities, the initial -distance :math:`r_0` and the current equilbrium length :math:`r_eq`. These extra -quantities can be accessed by the :doc:`compute bond/local ` -command as *b1* and *b2*, respectively. +The potential energy and the single() function of this bond style +returns zero. The single() function also calculates two extra bond +quantities, the initial distance :math:`r_0` and the current equilibrium +length :math:`r_eq`. These extra quantities can be accessed by the +:doc:`compute bond/local ` command as *b1* and *b2*, +respectively. Restrictions """""""""""" diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index 43067f76f9..98be9c2daf 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -2950,6 +2950,7 @@ pKa pKb pKs planeforce +plastically Plathe Plimpton plog From e3bf1a194da778d842c451f1683948d619c384fd Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 9 Mar 2025 22:46:03 -0400 Subject: [PATCH 075/113] fix typos --- doc/src/bond_bpm_spring.rst | 2 +- doc/src/bond_bpm_spring_plastic.rst | 4 ++-- doc/src/bond_rheo_shell.rst | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/doc/src/bond_bpm_spring.rst b/doc/src/bond_bpm_spring.rst index 0d087a41cd..27962c81a1 100644 --- a/doc/src/bond_bpm_spring.rst +++ b/doc/src/bond_bpm_spring.rst @@ -153,7 +153,7 @@ the data file or restart files read by the :doc:`read_data ` or :doc:`read_restart ` commands: * :math:`k` (force/distance units) -* :math:`\epsilon_c` (unit less) +* :math:`\epsilon_c` (unitless) * :math:`\gamma` (force/velocity units) Additionally, if *volume/factor* is set to *yes*, a fourth coefficient diff --git a/doc/src/bond_bpm_spring_plastic.rst b/doc/src/bond_bpm_spring_plastic.rst index c8f32bede1..3bc2c4ee46 100644 --- a/doc/src/bond_bpm_spring_plastic.rst +++ b/doc/src/bond_bpm_spring_plastic.rst @@ -108,9 +108,9 @@ the data file or restart files read by the :doc:`read_data ` or :doc:`read_restart ` commands: * :math:`k` (force/distance units) -* :math:`\epsilon_c` (unit less) +* :math:`\epsilon_c` (unitless) * :math:`\gamma` (force/velocity units) -* :math:`\epsilon_p (unit less) +* :math:`\epsilon_p` (unitless) See the :doc:`bpm/spring doc page ` for information on the *smooth*, *normalize*, *break*, *overlay/pair*, and *store/local* diff --git a/doc/src/bond_rheo_shell.rst b/doc/src/bond_rheo_shell.rst index 090f5ab7aa..ef8d7d4249 100644 --- a/doc/src/bond_rheo_shell.rst +++ b/doc/src/bond_rheo_shell.rst @@ -94,7 +94,7 @@ the data file or restart files read by the :doc:`read_data ` or :doc:`read_restart ` commands: * :math:`k` (force/distance units) -* :math:`\epsilon_c` (unit less) +* :math:`\epsilon_c` (unitless) * :math:`\gamma` (force/velocity units) Unlike other BPM-style bonds, this bond style does not update special From 1cc69bd0df606ca64434354864515d2a2a94e576 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 12 Mar 2025 11:58:30 -0400 Subject: [PATCH 076/113] support referencing the general advice paragraphs --- doc/src/Errors_details.rst | 53 +++++++++++++++++++++++++++----------- 1 file changed, 38 insertions(+), 15 deletions(-) diff --git a/doc/src/Errors_details.rst b/doc/src/Errors_details.rst index 6b37447174..1e2ae1c2f6 100644 --- a/doc/src/Errors_details.rst +++ b/doc/src/Errors_details.rst @@ -18,6 +18,8 @@ General troubleshooting advice Below are suggestions that can help to understand the causes of problems with simulations leading to errors or unexpected results. +.. _hint01: + Create a small test system ^^^^^^^^^^^^^^^^^^^^^^^^^^ @@ -27,6 +29,8 @@ a small test system input that has the same issue, but will take much time until it triggers the error condition. Also, it will be easier to see what happens. +.. _hint02: + Visualize your trajectory ^^^^^^^^^^^^^^^^^^^^^^^^^ @@ -37,6 +41,8 @@ avoid gigantic files, you can use :doc:`dump_modify delay ` to delay output until the critical section is reached, and you can use a smaller test system (see above). +.. _hint03: + Parallel versus serial ^^^^^^^^^^^^^^^^^^^^^^ @@ -46,6 +52,8 @@ only the symptoms are not triggering an error quickly. Correspondingly, errors may be triggered faster with more processors and thus smaller sub-domains. +.. _hint04: + Segmentation Fault ^^^^^^^^^^^^^^^^^^ @@ -75,6 +83,8 @@ the information about the :doc:`exact LAMMPS version ` and platform you are running on, you can contact the LAMMPS developers or post in the LAMMPS forum to get assistance. +.. _hint05: + Fast moving atoms ^^^^^^^^^^^^^^^^^ @@ -102,6 +112,8 @@ those cases using (temporarily) :doc:`fix nve/limit ` or :doc:`fix dt/reset ` can help to avoid too large updates or adapt the timestep according to the displacements. +.. _hint06: + Ignoring lost atoms ^^^^^^^^^^^^^^^^^^^ @@ -110,6 +122,8 @@ to avoid that LAMMPS stops with an error on lost atoms. This setting should, ho *only* be used when atoms *should* leave the system. In general, ignoring a problem does not solve it. +.. _hint07: + Pressure, forces, positions becoming NaN or Inf ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ @@ -126,6 +140,8 @@ package it may be beneficial to run with double precision initially before switching to mixed or single precision for faster execution when the system has relaxed. +.. _hint08: + Communication cutoff ^^^^^^^^^^^^^^^^^^^^ @@ -144,6 +160,8 @@ stretched very far. The communication cutoff can be adjusted with :doc:`comm_modify cutoff \ `, but setting this too large will waste CPU time and memory. +.. _hint09: + Neighbor list settings ^^^^^^^^^^^^^^^^^^^^^^ @@ -155,6 +173,8 @@ safely delayed. Rebuilding the neighbor list less frequently (i.e. through increasing the *delay* or *every*) setting has diminishing returns and increasing risks. +.. _hint10: + Units ^^^^^ @@ -174,6 +194,8 @@ taken from publications or other MD software, may need to be converted and sometimes in unexpected ways. Thus some careful checking is recommended. +.. _hint11: + No error message printed ^^^^^^^^^^^^^^^^^^^^^^^^ @@ -324,16 +346,16 @@ keyword in the :doc:`thermo_modify ` command. Non-numeric atom coords - simulation unstable --------------------------------------------- This error usually occurs due to issues with system geometry or the potential in -use. See :ref:`Pressure, forces, positions becoming NaN or Inf` above in the -general troubleshooting section. +use. See :ref:`Pressure, forces, positions becoming NaN or Inf ` above in the +general troubleshooting section. .. _err0007: Non-numeric pressure - simulation unstable ------------------------------------------ This error usually occurs due to issues with system geometry or the potential in -use. See :ref:`Pressure, forces, positions becoming NaN or Inf` above in the -general troubleshooting section. +use. See :ref:`Pressure, forces, positions becoming NaN or Inf ` above in the +general troubleshooting section. .. _err0008: @@ -341,17 +363,18 @@ general troubleshooting section. Lost atoms ... -------------- -A simulation erroring out due to lost atoms can have multiple causes. In the -majority of cases, lost atoms are unexpected and a result of extremely high -velocities causing instabilities in the system, and those velocities can result -from a variety of issues. For ideas on how to track down issues with unexpected -lost atoms, see :ref:`Fast moving atoms` and :ref:`Neighbor list settings` in -the general troubleshooting section above. In specific situations however, -losing atoms is expected material behavior (e.g. with sputtering and surface -evaporation simulations) and an unwanted crash can be resolved by changing the -:doc:`thermo_modify lost ` keyword from the default 'error' to -'warn' or 'ignore' (though heed the advice in :ref:`Ignoring lost atoms` -above!). +A simulation erroring out due to lost atoms can have multiple causes. In +the majority of cases, lost atoms are unexpected and a result of +extremely high velocities causing instabilities in the system, and those +velocities can result from a variety of issues. For ideas on how to +track down issues with unexpected lost atoms, see :ref:`Fast moving +atoms ` and :ref:`Neighbor list settings ` in the +general troubleshooting section above. In specific situations however, +losing atoms is expected material behavior (e.g. with sputtering and +surface evaporation simulations) and an unwanted crash can be resolved +by changing the :doc:`thermo_modify lost ` keyword from +the default 'error' to 'warn' or 'ignore' (though heed the advice in +:ref:`Ignoring lost atoms ` above!). .. _err0009: From d0aabe57bcc51624117f29d644c590fab11e1c99 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 12 Mar 2025 11:59:34 -0400 Subject: [PATCH 077/113] better grammar --- doc/src/Errors_details.rst | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/doc/src/Errors_details.rst b/doc/src/Errors_details.rst index 1e2ae1c2f6..8a8e00184a 100644 --- a/doc/src/Errors_details.rst +++ b/doc/src/Errors_details.rst @@ -363,11 +363,11 @@ general troubleshooting section. Lost atoms ... -------------- -A simulation erroring out due to lost atoms can have multiple causes. In -the majority of cases, lost atoms are unexpected and a result of -extremely high velocities causing instabilities in the system, and those -velocities can result from a variety of issues. For ideas on how to -track down issues with unexpected lost atoms, see :ref:`Fast moving +A simulation stopping with an error due to lost atoms can have multiple +causes. In the majority of cases, lost atoms are unexpected and a result +of extremely high velocities causing instabilities in the system, and +those velocities can result from a variety of issues. For ideas on how +to track down issues with unexpected lost atoms, see :ref:`Fast moving atoms ` and :ref:`Neighbor list settings ` in the general troubleshooting section above. In specific situations however, losing atoms is expected material behavior (e.g. with sputtering and From 9aba2c91c91d933dfbc240eb718803378022a7ef Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 12 Mar 2025 14:25:58 -0400 Subject: [PATCH 078/113] add citation reminder to fix qtpie/reaxff --- src/REAXFF/fix_qtpie_reaxff.cpp | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) diff --git a/src/REAXFF/fix_qtpie_reaxff.cpp b/src/REAXFF/fix_qtpie_reaxff.cpp index 22866fc363..427cf837b1 100644 --- a/src/REAXFF/fix_qtpie_reaxff.cpp +++ b/src/REAXFF/fix_qtpie_reaxff.cpp @@ -23,6 +23,7 @@ #include "fix_qtpie_reaxff.h" #include "atom.h" +#include "citeme.h" #include "comm.h" #include "domain.h" #include "error.h" @@ -52,6 +53,19 @@ static constexpr double CONV_TO_EV = 14.4; static constexpr double QSUMSMALL = 0.00001; static constexpr double ANGSTROM_TO_BOHRRADIUS = 1.8897261259; +static const char cite_fix_qtpie_reax[] = + "fix qtpie/reaxff command: \n\n" + "@Article{Kritikos20,\n" + " author = {E. Kritikos and A. Giusti},\n" + " title = {Reactive Molecular Dynamics Investigation of Toluene Oxidation under Electrostatic Fields: Effect of the Modeling of Local Charge Distribution},\n" + " journal = {The Journal of Physical Chemistry A},\n" + " volume = {124},\n" + " number = {51},\n" + " pages = {10705--10716},\n" + " year = {2020},\n" + " publisher = {ACS Publications}\n" + "}\n\n"; + /* ---------------------------------------------------------------------- */ FixQtpieReaxFF::FixQtpieReaxFF(LAMMPS *lmp, int narg, char **arg) : @@ -165,6 +179,8 @@ FixQtpieReaxFF::~FixQtpieReaxFF() void FixQtpieReaxFF::post_constructor() { + if (lmp->citeme) lmp->citeme->add(cite_fix_qtpie_reax); + grow_arrays(atom->nmax); for (int i = 0; i < atom->nmax; i++) for (int j = 0; j < nprev; ++j) From 38903fb7d2401d755b9752f84bc87320174a6aa1 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 12 Mar 2025 14:30:33 -0400 Subject: [PATCH 079/113] replace (evil) tabs with spaces --- examples/melt/in.melt | 44 +++++++++++++++++------------------ examples/peptide/in.peptide | 46 ++++++++++++++++++------------------- 2 files changed, 45 insertions(+), 45 deletions(-) diff --git a/examples/melt/in.melt b/examples/melt/in.melt index f169dc2ffc..6b67bfb774 100644 --- a/examples/melt/in.melt +++ b/examples/melt/in.melt @@ -1,33 +1,33 @@ # 3d Lennard-Jones melt -units lj -atom_style atomic +units lj +atom_style atomic -lattice fcc 0.8442 -region box block 0 10 0 10 0 10 -create_box 1 box -create_atoms 1 box -mass 1 1.0 +lattice fcc 0.8442 +region box block 0 10 0 10 0 10 +create_box 1 box +create_atoms 1 box +mass 1 1.0 -velocity all create 3.0 87287 loop geom +velocity all create 3.0 87287 loop geom -pair_style lj/cut 2.5 -pair_coeff 1 1 1.0 1.0 2.5 +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 -neighbor 0.3 bin -neigh_modify every 20 delay 0 check no +neighbor 0.3 bin +neigh_modify every 20 delay 0 check no -fix 1 all nve +fix 1 all nve -#dump id all atom 50 dump.melt +#dump id all atom 50 dump.melt -#dump 2 all image 25 image.*.jpg type type & -# axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 3 +#dump 2 all image 25 image.*.jpg type type & +# axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 3 -#dump 3 all movie 25 movie.mpg type type & -# axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 3 +#dump 3 all movie 25 movie.mpg type type & +# axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 3 -thermo 50 -run 250 +thermo 50 +run 250 diff --git a/examples/peptide/in.peptide b/examples/peptide/in.peptide index 1a4bc6df31..fc74ec4161 100644 --- a/examples/peptide/in.peptide +++ b/examples/peptide/in.peptide @@ -1,42 +1,42 @@ # Solvated 5-mer peptide -units real -atom_style full +units real +atom_style full -pair_style lj/charmm/coul/long 8.0 10.0 10.0 +pair_style lj/charmm/coul/long 8.0 10.0 10.0 bond_style harmonic angle_style charmm dihedral_style charmm improper_style harmonic -kspace_style pppm 0.0001 +kspace_style pppm 0.0001 -read_data data.peptide +read_data data.peptide -neighbor 2.0 bin -neigh_modify delay 5 +neighbor 2.0 bin +neigh_modify delay 5 -timestep 2.0 +timestep 2.0 -thermo_style multi -thermo 50 +thermo_style multi +thermo 50 -fix 1 all nvt temp 275.0 275.0 100.0 tchain 1 -fix 2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31 +fix 1 all nvt temp 275.0 275.0 100.0 tchain 1 +fix 2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31 -group peptide type <= 12 +group peptide type <= 12 -#dump 1 peptide atom 10 dump.peptide +#dump 1 peptide atom 10 dump.peptide -#dump 2 peptide image 25 image.*.jpg type type & -# axes yes 0.8 0.02 view 60 -30 bond atom 0.5 -#dump_modify 2 pad 3 +#dump 2 peptide image 25 image.*.jpg type type & +# axes yes 0.8 0.02 view 60 -30 bond atom 0.5 +#dump_modify 2 pad 3 -#dump 3 peptide movie 25 movie.mpg type type & -# axes yes 0.8 0.02 view 60 -30 bond atom 0.5 -#dump_modify 3 pad 3 +#dump 3 peptide movie 25 movie.mpg type type & +# axes yes 0.8 0.02 view 60 -30 bond atom 0.5 +#dump_modify 3 pad 3 -#compute bnd all property/local btype batom1 batom2 -#dump 2 peptide local 300 dump.bond index c_bnd[1] c_bnd[2] c_bnd[3] +#compute bnd all property/local btype batom1 batom2 +#dump 2 peptide local 300 dump.bond index c_bnd[1] c_bnd[2] c_bnd[3] -run 300 +run 300 From 42219ac7842b72d23ba0dc155ef3d33c9c14d2f8 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 12 Mar 2025 15:53:33 -0400 Subject: [PATCH 080/113] modernize LaTeX for formatting text in math mode --- doc/src/Howto_peri.rst | 8 ++++---- doc/src/Howto_triclinic.rst | 24 +++++++++++----------- doc/src/compute_cna_atom.rst | 2 +- doc/src/compute_cnp_atom.rst | 2 +- doc/src/compute_efield_wolf_atom.rst | 4 ++-- doc/src/compute_hexorder_atom.rst | 2 +- doc/src/compute_stress_atom.rst | 4 ++-- doc/src/fitpod_command.rst | 4 ++-- doc/src/fix_nh.rst | 20 +++++++++--------- doc/src/fix_npt_cauchy.rst | 8 ++++---- doc/src/fix_orient.rst | 18 ++++++++-------- doc/src/min_modify.rst | 4 ++-- doc/src/min_spin.rst | 4 ++-- doc/src/neb_spin.rst | 2 +- doc/src/pair_aip_water_2dm.rst | 4 ++-- doc/src/pair_coul.rst | 4 ++-- doc/src/pair_coul_shield.rst | 4 ++-- doc/src/pair_dpd_ext.rst | 4 ++-- doc/src/pair_hbond_dreiding.rst | 22 ++++++++++---------- doc/src/pair_ilp_graphene_hbn.rst | 4 ++-- doc/src/pair_ilp_tmd.rst | 4 ++-- doc/src/pair_lj_cut_coul.rst | 4 ++-- doc/src/pair_mesodpd.rst | 4 ++-- doc/src/pair_mgpt.rst | 2 +- doc/src/pair_saip_metal.rst | 4 ++-- doc/src/pair_spin_dipole.rst | 2 +- doc/src/pair_spin_dmi.rst | 2 +- doc/src/pair_spin_exchange.rst | 2 +- doc/utils/sphinx-config/conf.py.in | 2 +- tools/lammps-gui/org.lammps.lammps-gui.yml | 4 ++-- 30 files changed, 89 insertions(+), 89 deletions(-) diff --git a/doc/src/Howto_peri.rst b/doc/src/Howto_peri.rst index 29eb685c81..fa299e7f84 100644 --- a/doc/src/Howto_peri.rst +++ b/doc/src/Howto_peri.rst @@ -197,7 +197,7 @@ The LPS model has a force scalar state .. math:: \underline{t} = \frac{3K\theta}{m}\underline{\omega}\,\underline{x} + - \alpha \underline{\omega}\,\underline{e}^{\rm d}, \qquad\qquad\textrm{(3)} + \alpha \underline{\omega}\,\underline{e}^\mathrm{d}, \qquad\qquad\textrm{(3)} with :math:`K` the bulk modulus and :math:`\alpha` related to the shear modulus :math:`G` as @@ -242,14 +242,14 @@ scalar state are defined, respectively, as .. math:: - \underline{e}^{\rm i}=\frac{\theta \underline{x}}{3}, \qquad - \underline{e}^{\rm d} = \underline{e}- \underline{e}^{\rm i}, + \underline{e}^\mathrm{i}=\frac{\theta \underline{x}}{3}, \qquad + \underline{e}^\mathrm{d} = \underline{e}- \underline{e}^\mathrm{i}, where the arguments of the state functions and the vectors on which they operate are omitted for simplicity. We note that the LPS model is linear in the dilatation :math:`\theta`, and in the deviatoric part of the -extension :math:`\underline{e}^{\rm d}`. +extension :math:`\underline{e}^\mathrm{d}`. .. note:: diff --git a/doc/src/Howto_triclinic.rst b/doc/src/Howto_triclinic.rst index 3529579d65..24ac66e103 100644 --- a/doc/src/Howto_triclinic.rst +++ b/doc/src/Howto_triclinic.rst @@ -249,23 +249,23 @@ as follows: .. math:: - a = & {\rm lx} \\ - b^2 = & {\rm ly}^2 + {\rm xy}^2 \\ - c^2 = & {\rm lz}^2 + {\rm xz}^2 + {\rm yz}^2 \\ - \cos{\alpha} = & \frac{{\rm xy}*{\rm xz} + {\rm ly}*{\rm yz}}{b*c} \\ - \cos{\beta} = & \frac{\rm xz}{c} \\ - \cos{\gamma} = & \frac{\rm xy}{b} \\ + a = & \mathrm{lx} \\ + b^2 = & \mathrm{ly}^2 + \mathrm{xy}^2 \\ + c^2 = & \mathrm{lz}^2 + \mathrm{xz}^2 + \mathrm{yz}^2 \\ + \cos{\alpha} = & \frac{\mathrm{xy}*\mathrm{xz} + \mathrm{ly}*\mathrm{yz}}{b*c} \\ + \cos{\beta} = & \frac{\mathrm{xz}}{c} \\ + \cos{\gamma} = & \frac{\mathrm{xy}}{b} \\ The inverse relationship can be written as follows: .. math:: - {\rm lx} = & a \\ - {\rm xy} = & b \cos{\gamma} \\ - {\rm xz} = & c \cos{\beta}\\ - {\rm ly}^2 = & b^2 - {\rm xy}^2 \\ - {\rm yz} = & \frac{b*c \cos{\alpha} - {\rm xy}*{\rm xz}}{\rm ly} \\ - {\rm lz}^2 = & c^2 - {\rm xz}^2 - {\rm yz}^2 \\ + \mathrm{lx} = & a \\ + \mathrm{xy} = & b \cos{\gamma} \\ + \mathrm{xz} = & c \cos{\beta}\\ + \mathrm{ly}^2 = & b^2 - \mathrm{xy}^2 \\ + \mathrm{yz} = & \frac{b*c \cos{\alpha} - \mathrm{xy}*\mathrm{xz}}{\mathrm{ly}} \\ + \mathrm{lz}^2 = & c^2 - \mathrm{xz}^2 - \mathrm{yz}^2 \\ The values of *a*, *b*, *c*, :math:`\alpha` , :math:`\beta`, and :math:`\gamma` can be printed out or accessed by computes using the diff --git a/doc/src/compute_cna_atom.rst b/doc/src/compute_cna_atom.rst index 925159951c..33329d88d6 100644 --- a/doc/src/compute_cna_atom.rst +++ b/doc/src/compute_cna_atom.rst @@ -67,7 +67,7 @@ following relation should also be satisfied: .. math:: - r_c + r_s > 2*{\rm cutoff} + r_c + r_s > 2*\mathrm{cutoff} where :math:`r_c` is the cutoff distance of the potential, :math:`r_s` is the skin diff --git a/doc/src/compute_cnp_atom.rst b/doc/src/compute_cnp_atom.rst index 41fdb8324e..94dec390f4 100644 --- a/doc/src/compute_cnp_atom.rst +++ b/doc/src/compute_cnp_atom.rst @@ -74,7 +74,7 @@ following relation should also be satisfied: .. math:: - r_c + r_s > 2*{\rm cutoff} + r_c + r_s > 2*\mathrm{cutoff} where :math:`r_c` is the cutoff distance of the potential, :math:`r_s` is the skin diff --git a/doc/src/compute_efield_wolf_atom.rst b/doc/src/compute_efield_wolf_atom.rst index 93bfa55151..572ca59ab4 100644 --- a/doc/src/compute_efield_wolf_atom.rst +++ b/doc/src/compute_efield_wolf_atom.rst @@ -50,9 +50,9 @@ the potential energy using the Wolf summation method, described in .. math:: E_i = \frac{1}{2} \sum_{j \neq i} - \frac{q_i q_j {\rm erfc}(\alpha r_{ij})}{r_{ij}} + + \frac{q_i q_j \mathrm{erfc}(\alpha r_{ij})}{r_{ij}} + \frac{1}{2} \sum_{j \neq i} - \frac{q_i q_j {\rm erf}(\alpha r_{ij})}{r_{ij}} \qquad r < r_c + \frac{q_i q_j \mathrm{erf}(\alpha r_{ij})}{r_{ij}} \qquad r < r_c where :math:`\alpha` is the damping parameter, and *erf()* and *erfc()* are error-function and complementary error-function terms. This diff --git a/doc/src/compute_hexorder_atom.rst b/doc/src/compute_hexorder_atom.rst index 1fb8113a89..ea937f2e00 100644 --- a/doc/src/compute_hexorder_atom.rst +++ b/doc/src/compute_hexorder_atom.rst @@ -40,7 +40,7 @@ is a complex number (stored as two real numbers) defined as follows: .. math:: - q_n = \frac{1}{nnn}\sum_{j = 1}^{nnn} e^{n i \theta({\bf r}_{ij})} + q_n = \frac{1}{nnn}\sum_{j = 1}^{nnn} e^{n i \theta({\textbf{r}}_{ij})} where the sum is over the *nnn* nearest neighbors of the central atom. The angle :math:`\theta` diff --git a/doc/src/compute_stress_atom.rst b/doc/src/compute_stress_atom.rst index e047423640..6c4e0b690c 100644 --- a/doc/src/compute_stress_atom.rst +++ b/doc/src/compute_stress_atom.rst @@ -65,7 +65,7 @@ In case of compute *stress/atom*, the virial contribution is: W_{ab} & = \frac{1}{2} \sum_{n = 1}^{N_p} (r_{1_a} F_{1_b} + r_{2_a} F_{2_b}) + \frac{1}{2} \sum_{n = 1}^{N_b} (r_{1_a} F_{1_b} + r_{2_a} F_{2_b}) \\ & + \frac{1}{3} \sum_{n = 1}^{N_a} (r_{1_a} F_{1_b} + r_{2_a} F_{2_b} + r_{3_a} F_{3_b}) + \frac{1}{4} \sum_{n = 1}^{N_d} (r_{1_a} F_{1_b} + r_{2_a} F_{2_b} + r_{3_a} F_{3_b} + r_{4_a} F_{4_b}) \\ - & + \frac{1}{4} \sum_{n = 1}^{N_i} (r_{1_a} F_{1_b} + r_{2_a} F_{2_b} + r_{3_a} F_{3_b} + r_{4_a} F_{4_b}) + {\rm Kspace}(r_{i_a},F_{i_b}) + \sum_{n = 1}^{N_f} r_{i_a} F_{i_b} + & + \frac{1}{4} \sum_{n = 1}^{N_i} (r_{1_a} F_{1_b} + r_{2_a} F_{2_b} + r_{3_a} F_{3_b} + r_{4_a} F_{4_b}) + \mathrm{Kspace}(r_{i_a},F_{i_b}) + \sum_{n = 1}^{N_f} r_{i_a} F_{i_b} The first term is a pairwise energy contribution where :math:`n` loops over the :math:`N_p` neighbors of atom :math:`I`, :math:`\mathbf{r}_1` @@ -97,7 +97,7 @@ In case of compute *centroid/stress/atom*, the virial contribution is: .. math:: W_{ab} & = \sum_{n = 1}^{N_p} r_{I0_a} F_{I_b} + \sum_{n = 1}^{N_b} r_{I0_a} F_{I_b} + \sum_{n = 1}^{N_a} r_{I0_a} F_{I_b} + \sum_{n = 1}^{N_d} r_{I0_a} F_{I_b} + \sum_{n = 1}^{N_i} r_{I0_a} F_{I_b} \\ - & + {\rm Kspace}(r_{i_a},F_{i_b}) + \sum_{n = 1}^{N_f} r_{i_a} F_{i_b} + & + \mathrm{Kspace}(r_{i_a},F_{i_b}) + \sum_{n = 1}^{N_f} r_{i_a} F_{i_b} As with compute *stress/atom*, the first, second, third, fourth and fifth terms are pairwise, bond, angle, dihedral and improper diff --git a/doc/src/fitpod_command.rst b/doc/src/fitpod_command.rst index de52e0545b..e1f2c47c60 100644 --- a/doc/src/fitpod_command.rst +++ b/doc/src/fitpod_command.rst @@ -263,10 +263,10 @@ then the globally defined weights from the ``fitting_weight_energy`` and POD Potential """"""""""""" -We consider a multi-element system of *N* atoms with :math:`N_{\rm e}` +We consider a multi-element system of *N* atoms with :math:`N_\mathrm{e}` unique elements. We denote by :math:`\boldsymbol r_n` and :math:`Z_n` position vector and type of an atom *n* in the system, -respectively. Note that we have :math:`Z_n \in \{1, \ldots, N_{\rm e} +respectively. Note that we have :math:`Z_n \in \{1, \ldots, N_\mathrm{e} \}`, :math:`\boldsymbol R = (\boldsymbol r_1, \boldsymbol r_2, \ldots, \boldsymbol r_N) \in \mathbb{R}^{3N}`, and :math:`\boldsymbol Z = (Z_1, Z_2, \ldots, Z_N) \in \mathbb{N}^{N}`. The total energy of the diff --git a/doc/src/fix_nh.rst b/doc/src/fix_nh.rst index 0cfbc8f921..0a4076364c 100644 --- a/doc/src/fix_nh.rst +++ b/doc/src/fix_nh.rst @@ -208,19 +208,19 @@ The relaxation rate of the barostat is set by its inertia :math:`W`: .. math:: - W = (N + 1) k_B T_{\rm target} P_{\rm damp}^2 + W = (N + 1) k_B T_\mathrm{target} P_\mathrm{damp}^2 where :math:`N` is the number of atoms, :math:`k_B` is the Boltzmann constant, -and :math:`T_{\rm target}` is the target temperature of the barostat :ref:`(Martyna) `. -If a thermostat is defined, :math:`T_{\rm target}` is the target temperature -of the thermostat. If a thermostat is not defined, :math:`T_{\rm target}` +and :math:`T_\mathrm{target}` is the target temperature of the barostat :ref:`(Martyna) `. +If a thermostat is defined, :math:`T_\mathrm{target}` is the target temperature +of the thermostat. If a thermostat is not defined, :math:`T_\mathrm{target}` is set to the current temperature of the system when the barostat is initialized. If this temperature is too low the simulation will quit with an error. -Note: in previous versions of LAMMPS, :math:`T_{\rm target}` would default to +Note: in previous versions of LAMMPS, :math:`T_\mathrm{target}` would default to a value of 1.0 for *lj* units and 300.0 otherwise if the system had a temperature of exactly zero. -If a thermostat is not specified by this fix, :math:`T_{\rm target}` can be +If a thermostat is not specified by this fix, :math:`T_\mathrm{target}` can be manually specified using the *Ptemp* parameter. This may be useful if the barostat is initialized when the current temperature does not reflect the steady state temperature of the system. This keyword may also be useful in @@ -512,8 +512,8 @@ according to the following factorization of the Liouville propagator .. math:: \exp \left(\mathrm{i} L \Delta t \right) = & \hat{E} - \exp \left(\mathrm{i} L_{\rm T\textrm{-}baro} \frac{\Delta t}{2} \right) - \exp \left(\mathrm{i} L_{\rm T\textrm{-}part} \frac{\Delta t}{2} \right) + \exp \left(\mathrm{i} L_\mathrm{T\textrm{-}baro} \frac{\Delta t}{2} \right) + \exp \left(\mathrm{i} L_\mathrm{T\textrm{-}part} \frac{\Delta t}{2} \right) \exp \left(\mathrm{i} L_{\epsilon , 2} \frac{\Delta t}{2} \right) \exp \left(\mathrm{i} L_{2}^{(2)} \frac{\Delta t}{2} \right) \\ &\times \left[ @@ -526,8 +526,8 @@ according to the following factorization of the Liouville propagator &\times \exp \left(\mathrm{i} L_{2}^{(2)} \frac{\Delta t}{2} \right) \exp \left(\mathrm{i} L_{\epsilon , 2} \frac{\Delta t}{2} \right) - \exp \left(\mathrm{i} L_{\rm T\textrm{-}part} \frac{\Delta t}{2} \right) - \exp \left(\mathrm{i} L_{\rm T\textrm{-}baro} \frac{\Delta t}{2} \right) \\ + \exp \left(\mathrm{i} L_\mathrm{T\textrm{-}part} \frac{\Delta t}{2} \right) + \exp \left(\mathrm{i} L_\mathrm{T\textrm{-}baro} \frac{\Delta t}{2} \right) \\ &+ \mathcal{O} \left(\Delta t^3 \right) This factorization differs somewhat from that of Tuckerman et al, in diff --git a/doc/src/fix_npt_cauchy.rst b/doc/src/fix_npt_cauchy.rst index 6764f88eee..862a0b546e 100644 --- a/doc/src/fix_npt_cauchy.rst +++ b/doc/src/fix_npt_cauchy.rst @@ -426,8 +426,8 @@ according to the following factorization of the Liouville propagator .. math:: \exp \left(\mathrm{i} L \Delta t \right) = & \hat{E} - \exp \left(\mathrm{i} L_{\rm T\textrm{-}baro} \frac{\Delta t}{2} \right) - \exp \left(\mathrm{i} L_{\rm T\textrm{-}part} \frac{\Delta t}{2} \right) + \exp \left(\mathrm{i} L_\mathrm{T\textrm{-}baro} \frac{\Delta t}{2} \right) + \exp \left(\mathrm{i} L_\mathrm{T\textrm{-}part} \frac{\Delta t}{2} \right) \exp \left(\mathrm{i} L_{\epsilon , 2} \frac{\Delta t}{2} \right) \exp \left(\mathrm{i} L_{2}^{(2)} \frac{\Delta t}{2} \right) \\ &\times \left[ @@ -440,8 +440,8 @@ according to the following factorization of the Liouville propagator &\times \exp \left(\mathrm{i} L_{2}^{(2)} \frac{\Delta t}{2} \right) \exp \left(\mathrm{i} L_{\epsilon , 2} \frac{\Delta t}{2} \right) - \exp \left(\mathrm{i} L_{\rm T\textrm{-}part} \frac{\Delta t}{2} \right) - \exp \left(\mathrm{i} L_{\rm T\textrm{-}baro} \frac{\Delta t}{2} \right) \\ + \exp \left(\mathrm{i} L_\mathrm{T\textrm{-}part} \frac{\Delta t}{2} \right) + \exp \left(\mathrm{i} L_\mathrm{T\textrm{-}baro} \frac{\Delta t}{2} \right) \\ &+ \mathcal{O} \left(\Delta t^3 \right) This factorization differs somewhat from that of Tuckerman et al, in diff --git a/doc/src/fix_orient.rst b/doc/src/fix_orient.rst index 7e30b7bb01..881ae6c45c 100644 --- a/doc/src/fix_orient.rst +++ b/doc/src/fix_orient.rst @@ -62,19 +62,19 @@ The potential energy added to atom I is given by these formulas .. math:: - \xi_{i} = & \sum_{j=1}^{12} \left| \mathbf{r}_{j} - \mathbf{r}_{j}^{\rm I} \right| \qquad\qquad\left(1\right) \\ + \xi_{i} = & \sum_{j=1}^{12} \left| \mathbf{r}_{j} - \mathbf{r}_{j}^\mathrm{I} \right| \qquad\qquad\left(1\right) \\ \\ - \xi_{\rm IJ} = & \sum_{j=1}^{12} \left| \mathbf{r}_{j}^{\rm J} - \mathbf{r}_{j}^{\rm I} \right| \qquad\qquad\left(2\right)\\ + \xi_\mathrm{IJ} = & \sum_{j=1}^{12} \left| \mathbf{r}_{j}^\mathrm{J} - \mathbf{r}_{j}^\mathrm{I} \right| \qquad\qquad\left(2\right)\\ \\ - \xi_{\rm low} = & {\rm cutlo} \, \xi_{\rm IJ} \qquad\qquad\qquad\left(3\right)\\ - \xi_{\rm high} = & {\rm cuthi} \, \xi_{\rm IJ} \qquad\qquad\qquad\left(4\right) \\ + \xi_\mathrm{low} = & \mathrm{cutlo} \, \xi_\mathrm{IJ} \qquad\qquad\qquad\left(3\right)\\ + \xi_\mathrm{high} = & \mathrm{cuthi} \, \xi_\mathrm{IJ} \qquad\qquad\qquad\left(4\right) \\ \\ - \omega_{i} = & \frac{\pi}{2} \frac{\xi_{i} - \xi_{\rm low}}{\xi_{\rm high} - \xi_{\rm low}} \qquad\qquad\left(5\right)\\ + \omega_{i} = & \frac{\pi}{2} \frac{\xi_{i} - \xi_\mathrm{low}}{\xi_\mathrm{high} - \xi_\mathrm{low}} \qquad\qquad\left(5\right)\\ \\ - u_{i} = & 0 \quad\quad\qquad\qquad\qquad \textrm{ for } \qquad \xi_{i} < \xi_{\rm low}\\ - = & {\rm dE}\,\frac{1 - \cos(2 \omega_{i})}{2} - \qquad \mathrm{ for }\qquad \xi_{\rm low} < \xi_{i} < \xi_{\rm high} \quad \left(6\right) \\ - = & {\rm dE} \quad\qquad\qquad\qquad\textrm{ for } \qquad \xi_{\rm high} < \xi_{i} + u_{i} = & 0 \quad\quad\qquad\qquad\qquad \textrm{ for } \qquad \xi_{i} < \xi_\mathrm{low}\\ + = & \mathrm{dE}\,\frac{1 - \cos(2 \omega_{i})}{2} + \qquad \mathrm{for }\qquad \xi_\mathrm{low} < \xi_{i} < \xi_\mathrm{high} \quad \left(6\right) \\ + = & \mathrm{dE} \quad\qquad\qquad\qquad\textrm{ for } \qquad \xi_\mathrm{high} < \xi_{i} which are fully explained in :ref:`(Janssens) `. For fcc crystals this order parameter Xi for atom I in equation (1) is a sum over the diff --git a/doc/src/min_modify.rst b/doc/src/min_modify.rst index d36f19b0d5..9e4cb4fbc6 100644 --- a/doc/src/min_modify.rst +++ b/doc/src/min_modify.rst @@ -98,14 +98,14 @@ all atoms .. math:: - || \vec{F} ||_{max} = {\rm max}\left(||\vec{F}_1||, \cdots, ||\vec{F}_N||\right) + || \vec{F} ||_{max} = \mathrm{max}\left(||\vec{F}_1||, \cdots, ||\vec{F}_N||\right) The *inf* norm takes the maximum component across the forces of all atoms in the system: .. math:: - || \vec{F} ||_{inf} = {\rm max}\left(|F_1^1|, |F_1^2|, |F_1^3| \cdots, |F_N^1|, |F_N^2|, |F_N^3|\right) + || \vec{F} ||_{inf} = \mathrm{max}\left(|F_1^1|, |F_1^2|, |F_1^3| \cdots, |F_N^1|, |F_N^2|, |F_N^3|\right) For the min styles *spin*, *spin/cg* and *spin/lbfgs*, the force norm is replaced by the spin-torque norm. diff --git a/doc/src/min_spin.rst b/doc/src/min_spin.rst index 9b6841ae8c..c6ae2f26b1 100644 --- a/doc/src/min_spin.rst +++ b/doc/src/min_spin.rst @@ -50,9 +50,9 @@ system: .. math:: - {\Delta t}_{\rm max} = \frac{2\pi}{\kappa \left|\vec{\omega}_{\rm max} \right|} + {\Delta t}_\mathrm{max} = \frac{2\pi}{\kappa \left|\vec{\omega}_\mathrm{max} \right|} -with :math:`\left|\vec{\omega}_{\rm max}\right|` the norm of the largest precession +with :math:`\left|\vec{\omega}_\mathrm{max}\right|` the norm of the largest precession frequency in the system (across all processes, and across all replicas if a spin/neb calculation is performed). diff --git a/doc/src/neb_spin.rst b/doc/src/neb_spin.rst index 62ca9f32cb..ba8ea3a7cd 100644 --- a/doc/src/neb_spin.rst +++ b/doc/src/neb_spin.rst @@ -148,7 +148,7 @@ spin i, :math:`\omega_i^{\nu}` is a rotation angle defined as: .. math:: - \omega_i^{\nu} = (\nu - 1) \Delta \omega_i {\rm ~~and~~} \Delta \omega_i = \frac{\omega_i}{Q-1} + \omega_i^{\nu} = (\nu - 1) \Delta \omega_i \mathrm{~~and~~} \Delta \omega_i = \frac{\omega_i}{Q-1} with :math:`\nu` the image number, Q the total number of images, and :math:`\omega_i` the total rotation between the initial and final spins. diff --git a/doc/src/pair_aip_water_2dm.rst b/doc/src/pair_aip_water_2dm.rst index b84202e69e..65f2e4d912 100644 --- a/doc/src/pair_aip_water_2dm.rst +++ b/doc/src/pair_aip_water_2dm.rst @@ -53,14 +53,14 @@ materials as described in :ref:`(Feng1) ` and :ref:`(Feng2) `. .. math:: E = & \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\ - V_{ij} = & {\rm Tap}(r_{ij})\left \{ e^{-\alpha (r_{ij}/\beta -1)} + V_{ij} = & \mathrm{Tap}(r_{ij})\left \{ e^{-\alpha (r_{ij}/\beta -1)} \left [ \epsilon + f(\rho_{ij}) + f(\rho_{ji})\right ] - \frac{1}{1+e^{-d\left [ \left ( r_{ij}/\left (s_R \cdot r^{eff} \right ) \right )-1 \right ]}} \cdot \frac{C_6}{r^6_{ij}} \right \}\\ \rho_{ij}^2 = & r_{ij}^2 - ({\bf r}_{ij} \cdot {\bf n}_i)^2 \\ \rho_{ji}^2 = & r_{ij}^2 - ({\bf r}_{ij} \cdot {\bf n}_j)^2 \\ f(\rho) = & C e^{ -( \rho / \delta )^2 } \\ - {\rm Tap}(r_{ij}) = & 20\left ( \frac{r_{ij}}{R_{cut}} \right )^7 - + \mathrm{Tap}(r_{ij}) = & 20\left ( \frac{r_{ij}}{R_{cut}} \right )^7 - 70\left ( \frac{r_{ij}}{R_{cut}} \right )^6 + 84\left ( \frac{r_{ij}}{R_{cut}} \right )^5 - 35\left ( \frac{r_{ij}}{R_{cut}} \right )^4 + 1 diff --git a/doc/src/pair_coul.rst b/doc/src/pair_coul.rst index 77c0e0b18b..c8c1581c3c 100644 --- a/doc/src/pair_coul.rst +++ b/doc/src/pair_coul.rst @@ -241,9 +241,9 @@ summation method, described in :ref:`Wolf `, given by: .. math:: E_i = \frac{1}{2} \sum_{j \neq i} - \frac{q_i q_j {\rm erfc}(\alpha r_{ij})}{r_{ij}} + + \frac{q_i q_j \mathrm{erfc}(\alpha r_{ij})}{r_{ij}} + \frac{1}{2} \sum_{j \neq i} - \frac{q_i q_j {\rm erf}(\alpha r_{ij})}{r_{ij}} \qquad r < r_c + \frac{q_i q_j \mathrm{erf}(\alpha r_{ij})}{r_{ij}} \qquad r < r_c where :math:`\alpha` is the damping parameter, and *erf()* and *erfc()* are error-function and complementary error-function terms. This diff --git a/doc/src/pair_coul_shield.rst b/doc/src/pair_coul_shield.rst index a7f99500f5..5f580f9037 100644 --- a/doc/src/pair_coul_shield.rst +++ b/doc/src/pair_coul_shield.rst @@ -40,8 +40,8 @@ the pair style :doc:`ilp/graphene/hbn ` .. math:: E = & \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\ - V_{ij} = & {\rm Tap}(r_{ij})\frac{\kappa q_i q_j}{\sqrt[3]{r_{ij}^3+(1/\lambda_{ij})^3}}\\ - {\rm Tap}(r_{ij}) = & 20\left ( \frac{r_{ij}}{R_{cut}} \right )^7 - + V_{ij} = & \mathrm{Tap}(r_{ij})\frac{\kappa q_i q_j}{\sqrt[3]{r_{ij}^3+(1/\lambda_{ij})^3}}\\ + \mathrm{Tap}(r_{ij}) = & 20\left ( \frac{r_{ij}}{R_{cut}} \right )^7 - 70\left ( \frac{r_{ij}}{R_{cut}} \right )^6 + 84\left ( \frac{r_{ij}}{R_{cut}} \right )^5 - 35\left ( \frac{r_{ij}}{R_{cut}} \right )^4 + 1 diff --git a/doc/src/pair_dpd_ext.rst b/doc/src/pair_dpd_ext.rst index 1caed4689b..e84001235a 100644 --- a/doc/src/pair_dpd_ext.rst +++ b/doc/src/pair_dpd_ext.rst @@ -62,8 +62,8 @@ a sum of 3 terms \mathbf{f} = & f^C + f^D + f^R \qquad \qquad r < r_c \\ f^C = & A_{ij} w(r) \hat{\mathbf{r}}_{ij} \\ - f^D = & - \gamma_{\parallel} w_{\parallel}^2(r) (\hat{\mathbf{r}}_{ij} \cdot \mathbf{v}_{ij}) \hat{\mathbf{r}}_{ij} - \gamma_{\perp} w_{\perp}^2 (r) ( \mathbf{I} - \hat{\mathbf{r}}_{ij} \hat{\mathbf{r}}_{ij}^{\rm T} ) \mathbf{v}_{ij} \\ - f^R = & \sigma_{\parallel} w_{\parallel}(r) \frac{\alpha}{\sqrt{\Delta t}} \hat{\mathbf{r}}_{ij} + \sigma_{\perp} w_{\perp} (r) ( \mathbf{I} - \hat{\mathbf{r}}_{ij} \hat{\mathbf{r}}_{ij}^{\rm T} ) \frac{\mathbf{\xi}_{ij}}{\sqrt{\Delta t}}\\ + f^D = & - \gamma_{\parallel} w_{\parallel}^2(r) (\hat{\mathbf{r}}_{ij} \cdot \mathbf{v}_{ij}) \hat{\mathbf{r}}_{ij} - \gamma_{\perp} w_{\perp}^2 (r) ( \mathbf{I} - \hat{\mathbf{r}}_{ij} \hat{\mathbf{r}}_{ij}^\mathrm{T} ) \mathbf{v}_{ij} \\ + f^R = & \sigma_{\parallel} w_{\parallel}(r) \frac{\alpha}{\sqrt{\Delta t}} \hat{\mathbf{r}}_{ij} + \sigma_{\perp} w_{\perp} (r) ( \mathbf{I} - \hat{\mathbf{r}}_{ij} \hat{\mathbf{r}}_{ij}^\mathrm{T} ) \frac{\mathbf{\xi}_{ij}}{\sqrt{\Delta t}}\\ w(r) = & 1 - r/r_c \\ where :math:`\mathbf{f}^C` is a conservative force, :math:`\mathbf{f}^D` diff --git a/doc/src/pair_hbond_dreiding.rst b/doc/src/pair_hbond_dreiding.rst index a122fc5ea2..2c5059ffa9 100644 --- a/doc/src/pair_hbond_dreiding.rst +++ b/doc/src/pair_hbond_dreiding.rst @@ -68,21 +68,21 @@ force field, given by: .. math:: - E = & \left[LJ(r) | Morse(r) \right] \qquad \qquad \qquad r < r_{\rm in} \\ - = & S(r) * \left[LJ(r) | Morse(r) \right] \qquad \qquad r_{\rm in} < r < r_{\rm out} \\ - = & 0 \qquad \qquad \qquad \qquad \qquad \qquad \qquad r > r_{\rm out} \\ + E = & \left[LJ(r) | Morse(r) \right] \qquad \qquad \qquad r < r_\mathrm{in} \\ + = & S(r) * \left[LJ(r) | Morse(r) \right] \qquad \qquad r_\mathrm{in} < r < r_\mathrm{out} \\ + = & 0 \qquad \qquad \qquad \qquad \qquad \qquad \qquad r > r_\mathrm{out} \\ LJ(r) = & AR^{-12}-BR^{-10}cos^n\theta= \epsilon\left\lbrace 5\left[ \frac{\sigma}{r}\right]^{12}- 6\left[ \frac{\sigma}{r}\right]^{10} \right\rbrace cos^n\theta\\ Morse(r) = & D_0\left\lbrace \chi^2 - 2\chi\right\rbrace cos^n\theta= D_{0}\left\lbrace e^{- 2 \alpha (r - r_0)} - 2 e^{- \alpha (r - r_0)} \right\rbrace cos^n\theta \\ - S(r) = & \frac{ \left[r_{\rm out}^2 - r^2\right]^2 - \left[r_{\rm out}^2 + 2r^2 - 3{r_{\rm in}^2}\right]} - { \left[r_{\rm out}^2 - {r_{\rm in}}^2\right]^3 } + S(r) = & \frac{ \left[r_\mathrm{out}^2 - r^2\right]^2 + \left[r_\mathrm{out}^2 + 2r^2 - 3{r_\mathrm{in}^2}\right]} + { \left[r_\mathrm{out}^2 - {r_\mathrm{in}}^2\right]^3 } -where :math:`r_{\rm in}` is the inner spline distance cutoff, -:math:`r_{\rm out}` is the outer distance cutoff, :math:`\theta_c` is +where :math:`r_\mathrm{in}` is the inner spline distance cutoff, +:math:`r_\mathrm{out}` is the outer distance cutoff, :math:`\theta_c` is the angle cutoff, and :math:`n` is the power of the cosine of the angle :math:`\theta`. @@ -189,8 +189,8 @@ follows: * :math:`\epsilon` (energy units) * :math:`\sigma` (distance units) * *n* = exponent in formula above -* distance cutoff :math:`r_{\rm in}` (distance units) -* distance cutoff :math:`r_{\rm out}` (distance units) +* distance cutoff :math:`r_\mathrm{in}` (distance units) +* distance cutoff :math:`r_\mathrm{out}` (distance units) * angle cutoff (degrees) For the *hbond/dreiding/morse* style the list of coefficients is as @@ -202,7 +202,7 @@ follows: * :math:`\alpha` (1/distance units) * :math:`r_0` (distance units) * *n* = exponent in formula above -* distance cutoff :math:`r_{\rm in}` (distance units) +* distance cutoff :math:`r_\mathrm{in}` (distance units) * distance cutoff :math:`r_{out}` (distance units) * angle cutoff (degrees) diff --git a/doc/src/pair_ilp_graphene_hbn.rst b/doc/src/pair_ilp_graphene_hbn.rst index 36e971ef62..7fa7d6800f 100644 --- a/doc/src/pair_ilp_graphene_hbn.rst +++ b/doc/src/pair_ilp_graphene_hbn.rst @@ -44,14 +44,14 @@ in :ref:`(Kolmogorov) `. .. math:: E = & \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\ - V_{ij} = & {\rm Tap}(r_{ij})\left \{ e^{-\alpha (r_{ij}/\beta -1)} + V_{ij} = & \mathrm{Tap}(r_{ij})\left \{ e^{-\alpha (r_{ij}/\beta -1)} \left [ \epsilon + f(\rho_{ij}) + f(\rho_{ji})\right ] - \frac{1}{1+e^{-d\left [ \left ( r_{ij}/\left (s_R \cdot r^{eff} \right ) \right )-1 \right ]}} \cdot \frac{C_6}{r^6_{ij}} \right \}\\ \rho_{ij}^2 = & r_{ij}^2 - ({\bf r}_{ij} \cdot {\bf n}_i)^2 \\ \rho_{ji}^2 = & r_{ij}^2 - ({\bf r}_{ij} \cdot {\bf n}_j)^2 \\ f(\rho) = & C e^{ -( \rho / \delta )^2 } \\ - {\rm Tap}(r_{ij}) = & 20\left ( \frac{r_{ij}}{R_{cut}} \right )^7 - + \mathrm{Tap}(r_{ij}) = & 20\left ( \frac{r_{ij}}{R_{cut}} \right )^7 - 70\left ( \frac{r_{ij}}{R_{cut}} \right )^6 + 84\left ( \frac{r_{ij}}{R_{cut}} \right )^5 - 35\left ( \frac{r_{ij}}{R_{cut}} \right )^4 + 1 diff --git a/doc/src/pair_ilp_tmd.rst b/doc/src/pair_ilp_tmd.rst index 575bafdc91..133e5f9093 100644 --- a/doc/src/pair_ilp_tmd.rst +++ b/doc/src/pair_ilp_tmd.rst @@ -41,14 +41,14 @@ as described in :ref:`(Ouyang7) ` and :ref:`(Jiang) `. .. math:: E = & \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\ - V_{ij} = & {\rm Tap}(r_{ij})\left \{ e^{-\alpha (r_{ij}/\beta -1)} + V_{ij} = & \mathrm{Tap}(r_{ij})\left \{ e^{-\alpha (r_{ij}/\beta -1)} \left [ \epsilon + f(\rho_{ij}) + f(\rho_{ji})\right ] - \frac{1}{1+e^{-d\left [ \left ( r_{ij}/\left (s_R \cdot r^{eff} \right ) \right )-1 \right ]}} \cdot \frac{C_6}{r^6_{ij}} \right \}\\ \rho_{ij}^2 = & r_{ij}^2 - ({\bf r}_{ij} \cdot {\bf n}_i)^2 \\ \rho_{ji}^2 = & r_{ij}^2 - ({\bf r}_{ij} \cdot {\bf n}_j)^2 \\ f(\rho) = & C e^{ -( \rho / \delta )^2 } \\ - {\rm Tap}(r_{ij}) = & 20\left ( \frac{r_{ij}}{R_{cut}} \right )^7 - + \mathrm{Tap}(r_{ij}) = & 20\left ( \frac{r_{ij}}{R_{cut}} \right )^7 - 70\left ( \frac{r_{ij}}{R_{cut}} \right )^6 + 84\left ( \frac{r_{ij}}{R_{cut}} \right )^5 - 35\left ( \frac{r_{ij}}{R_{cut}} \right )^4 + 1 diff --git a/doc/src/pair_lj_cut_coul.rst b/doc/src/pair_lj_cut_coul.rst index aa5f7a2620..da39ac1645 100644 --- a/doc/src/pair_lj_cut_coul.rst +++ b/doc/src/pair_lj_cut_coul.rst @@ -194,9 +194,9 @@ summation method, described in :ref:`Wolf `, given by: .. math:: E_i = \frac{1}{2} \sum_{j \neq i} - \frac{q_i q_j {\rm erfc}(\alpha r_{ij})}{r_{ij}} + + \frac{q_i q_j \mathrm{erfc}(\alpha r_{ij})}{r_{ij}} + \frac{1}{2} \sum_{j \neq i} - \frac{q_i q_j {\rm erf}(\alpha r_{ij})}{r_{ij}} \qquad r < r_c + \frac{q_i q_j \mathrm{erf}(\alpha r_{ij})}{r_{ij}} \qquad r < r_c where :math:`\alpha` is the damping parameter, and erfc() is the complementary error-function terms. This potential is essentially a diff --git a/doc/src/pair_mesodpd.rst b/doc/src/pair_mesodpd.rst index 6674b013ba..269701ee27 100644 --- a/doc/src/pair_mesodpd.rst +++ b/doc/src/pair_mesodpd.rst @@ -200,7 +200,7 @@ force :math:`F_{ij}^C` are expressed as \mathbf{F}_{ij}^{D} & = -\gamma {\omega_{D}}(r_{ij})(\mathbf{e}_{ij} \cdot \mathbf{v}_{ij})\mathbf{e}_{ij} \\ \mathbf{F}_{ij}^{R} & = \sigma {\omega_{R}}(r_{ij}){\xi_{ij}}\Delta t^{-1/2} \mathbf{e}_{ij} \\ \omega_{C}(r) & = 1 - r/r_c \\ - \omega_{D}(r) & = \omega^2_{R}(r) = (1-r/r_c)^{\rm power_f} \\ + \omega_{D}(r) & = \omega^2_{R}(r) = (1-r/r_c)^\mathrm{power_f} \\ \sigma^2 = 2\gamma k_B T The concentration flux between two tDPD particles includes the Fickian @@ -211,7 +211,7 @@ by Q_{ij}^D & = -\kappa_{ij} w_{DC}(r_{ij}) \left( C_i - C_j \right) \\ Q_{ij}^R & = \epsilon_{ij}\left( C_i + C_j \right) w_{RC}(r_{ij}) \xi_{ij} \\ - w_{DC}(r_{ij}) & =w^2_{RC}(r_{ij}) = (1 - r/r_{cc})^{\rm power_{cc}} \\ + w_{DC}(r_{ij}) & =w^2_{RC}(r_{ij}) = (1 - r/r_{cc})^\mathrm{power_{cc}} \\ \epsilon_{ij}^2 & = m_s^2\kappa_{ij}\rho where the parameters kappa and epsilon determine the strength of the diff --git a/doc/src/pair_mgpt.rst b/doc/src/pair_mgpt.rst index 92bf9cd738..13a4bcb079 100644 --- a/doc/src/pair_mgpt.rst +++ b/doc/src/pair_mgpt.rst @@ -33,7 +33,7 @@ elemental bulk material in the form .. math:: - E_{\rm tot}({\bf R}_1 \ldots {\bf R}_N) = NE_{\rm vol}(\Omega ) + E_\mathrm{tot}({\bf R}_1 \ldots {\bf R}_N) = NE_\mathrm{vol}(\Omega ) + \frac{1}{2} \sum _{i,j} \mbox{}^\prime \ v_2(ij;\Omega ) + \frac{1}{6} \sum _{i,j,k} \mbox{}^\prime \ v_3(ijk;\Omega ) + \frac{1}{24} \sum _{i,j,k,l} \mbox{}^\prime \ v_4(ijkl;\Omega ) diff --git a/doc/src/pair_saip_metal.rst b/doc/src/pair_saip_metal.rst index ed011894c9..098edff916 100644 --- a/doc/src/pair_saip_metal.rst +++ b/doc/src/pair_saip_metal.rst @@ -41,14 +41,14 @@ potential (ILP) potential for hetero-junctions formed with hexagonal .. math:: E = & \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\ - V_{ij} = & {\rm Tap}(r_{ij})\left \{ e^{-\alpha (r_{ij}/\beta -1)} + V_{ij} = & \mathrm{Tap}(r_{ij})\left \{ e^{-\alpha (r_{ij}/\beta -1)} \left [ \epsilon + f(\rho_{ij}) + f(\rho_{ji})\right ] - \frac{1}{1+e^{-d\left [ \left ( r_{ij}/\left (s_R \cdot r^{eff} \right ) \right )-1 \right ]}} \cdot \frac{C_6}{r^6_{ij}} \right \}\\ \rho_{ij}^2 = & r_{ij}^2 - ({\bf r}_{ij} \cdot {\bf n}_i)^2 \\ \rho_{ji}^2 = & r_{ij}^2 - ({\bf r}_{ij} \cdot {\bf n}_j)^2 \\ f(\rho) = & C e^{ -( \rho / \delta )^2 } \\ - {\rm Tap}(r_{ij}) = & 20\left ( \frac{r_{ij}}{R_{cut}} \right )^7 - + \mathrm{Tap}(r_{ij}) = & 20\left ( \frac{r_{ij}}{R_{cut}} \right )^7 - 70\left ( \frac{r_{ij}}{R_{cut}} \right )^6 + 84\left ( \frac{r_{ij}}{R_{cut}} \right )^5 - 35\left ( \frac{r_{ij}}{R_{cut}} \right )^4 + 1 diff --git a/doc/src/pair_spin_dipole.rst b/doc/src/pair_spin_dipole.rst index c38bba03ae..faa2bc7461 100644 --- a/doc/src/pair_spin_dipole.rst +++ b/doc/src/pair_spin_dipole.rst @@ -43,7 +43,7 @@ vector omega and mechanical force between particles I and J. .. math:: - \mathcal{H}_{\rm long} & = + \mathcal{H}_\mathrm{long} & = -\frac{\mu_{0} \left( \mu_B\right)^2}{4\pi} \sum_{i,j,i\neq j}^{N} \frac{g_i g_j}{r_{ij}^3} diff --git a/doc/src/pair_spin_dmi.rst b/doc/src/pair_spin_dmi.rst index 282da39ff7..bb98c72d84 100644 --- a/doc/src/pair_spin_dmi.rst +++ b/doc/src/pair_spin_dmi.rst @@ -52,7 +52,7 @@ particle i: .. math:: \vec{\omega}_i = -\frac{1}{\hbar} \sum_{j}^{Neighb} \vec{s}_{j}\times \left(\vec{e}_{ij}\times \vec{D} \right) - ~~{\rm and}~~ + ~~\mathrm{and}~~ \vec{F}_i = -\sum_{j}^{Neighb} \frac{1}{r_{ij}} \vec{D} \times \left( \vec{s}_{i}\times \vec{s}_{j} \right) More details about the derivation of these torques/forces are reported in diff --git a/doc/src/pair_spin_exchange.rst b/doc/src/pair_spin_exchange.rst index 553af72983..a922c45a8d 100644 --- a/doc/src/pair_spin_exchange.rst +++ b/doc/src/pair_spin_exchange.rst @@ -94,7 +94,7 @@ submitted to a force :math:`\vec{F}_{i}` for spin-lattice calculations (see \vec{\omega}_{i} = \frac{1}{\hbar} \sum_{j}^{Neighb} {J} \left(r_{ij} \right)\,\vec{s}_{j} - ~~{\rm and}~~ + ~~\mathrm{and}~~ \vec{F}_{i} = \sum_{j}^{Neighb} \frac{\partial {J} \left(r_{ij} \right)}{ \partial r_{ij}} \left( \vec{s}_{i}\cdot \vec{s}_{j} \right) \vec{e}_{ij} diff --git a/doc/utils/sphinx-config/conf.py.in b/doc/utils/sphinx-config/conf.py.in index 073143a7e9..12e5c57f78 100644 --- a/doc/utils/sphinx-config/conf.py.in +++ b/doc/utils/sphinx-config/conf.py.in @@ -288,7 +288,7 @@ rst_prolog = r""" .. only:: html - :math:`\renewcommand{\AA}{\text{Å}}` + :math:`\renewcommand{\AA}{\textup{\r{A}}` .. role:: lammps(code) :language: LAMMPS diff --git a/tools/lammps-gui/org.lammps.lammps-gui.yml b/tools/lammps-gui/org.lammps.lammps-gui.yml index a16ef5fdee..f88ea55bb2 100644 --- a/tools/lammps-gui/org.lammps.lammps-gui.yml +++ b/tools/lammps-gui/org.lammps.lammps-gui.yml @@ -110,5 +110,5 @@ modules: - -D BUILD_WHAM=yes sources: - type: git - url: https://github.com/lammps/lammps.git - branch: release + url: https://github.com/akohlmey/lammps.git + branch: collected-small-fixes From 6d6fce7866e39fa508d818246f3daa0d2249f9e4 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 12 Mar 2025 20:36:01 -0400 Subject: [PATCH 081/113] provide explanation for "variable evaluated before simulation box is defined" --- doc/src/Errors_details.rst | 58 +++++++++++++++++++++++++++++++++++++- src/variable.cpp | 18 ++++++++---- 2 files changed, 69 insertions(+), 7 deletions(-) diff --git a/doc/src/Errors_details.rst b/doc/src/Errors_details.rst index 8a8e00184a..147d5c927f 100644 --- a/doc/src/Errors_details.rst +++ b/doc/src/Errors_details.rst @@ -210,6 +210,29 @@ disabled by using the :ref:`-nb or -nonbuf ` command-line flag. This is most often needed when debugging crashing multi-replica calculations. +.. _hint12: + +Errors before or after the simulation box is created +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +As critical step in a LAMMPS input is when the simulation box is +defined, either with a :doc:`create_box command `, a +:doc:`read_data command `, or a :doc:`read_restart command +`. After this step, certain settings are locked in (e.g. +units, or number of atom, bond, angle, dihedral, improper types) and +cannot be changed after that. Consequently, commands that change such +settings (e.g. :doc:`units `) are only allowed before the box is +defined. Very few commands can be used before and after, like +:doc:`pair_style ` (but not :doc:`pair_coeff `). +Most LAMMPS commands must be used after the simulation box is created. + +Consequently, LAMMPS will stop with an error, if a command is used in +the wrong place. This is not always obvious. So you can expand an index +or string style :doc:`variable ` anywhere in the input, but +equal style (or similar) variables only, if they do not reference +anything that is only allowed after the box is defined (e.g. a compute +reference or fix reference, or a thermo keyword). + ------ .. _err0001: @@ -613,7 +636,7 @@ or not. .. _err0029: System is not charge neutral, net charge = ... --------------------------------------------------- +---------------------------------------------- the sum of charges in the system is not zero. When a system is not charge-neutral, methods that evolve/manipulate per-atom charges, evaluate @@ -645,3 +668,36 @@ severity of these artifacts depends on the magnitude of total charge, system size, and methods used. Before running simulations or calculations for systems with non-zero net charge, users should test for artifacts and convergence of properties. + +.. _err0030: + +Variable evaluation before simulation box is defined +---------------------------------------------------- + +This error happens, when trying to expand or use an equal- or atom-style +variable (or an equivalent style), where the expression contains a +reference to something (e.g. a compute reference, a property of an atom, +or a thermo keyword) that is not allowed to be used before the +simulation box is defined. See the paragraph on :ref:`errors before or +after the simulation box is created ` for additional +information. + +.. _err0031: + +Invalid thermo keyword 'X' in variable formula +---------------------------------------------- + +This error message is often misleading. It is caused when evaluating a +:doc:`variable command ` expression and LAMMPS comes across a +string that it does not recognize. LAMMPS first checks if a string is a +reference to a compute, fix, custom property, or another variable by +looking at the first 2-3 characters (and if it is, it checks whether the +referenced item exists). Next LAMMPS checks if the string matches one +of the available functions or constants. If that fails, LAMMPS will +assume that this string is a :doc:`thermo keyword ` and +let the code for printing thermodynamic output return the corresponding +value. However, if this fails too, since the string is not a thermo +keyword, LAMMPS stops with the 'Invalid thermo keyword' error. But it +is also possible, that there is just a typo in the name of a valid +variable function. Thus it is recommended to check the failing variable +expression very carefully. diff --git a/src/variable.cpp b/src/variable.cpp index e0c0ae35ee..19a9a0a855 100644 --- a/src/variable.cpp +++ b/src/variable.cpp @@ -1547,7 +1547,8 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) if (utils::strmatch(word,"^[Cc]_")) { if (domain->box_exist == 0) - print_var_error(FLERR,"Variable evaluation before simulation box is defined",ivar); + print_var_error(FLERR,"Variable evaluation before simulation box is defined" + + utils::errorurl(30),ivar); // uppercase used to access of peratom data by equal-style var @@ -1824,7 +1825,8 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) } else if (utils::strmatch(word,"^[fF]_")) { if (domain->box_exist == 0) - print_var_error(FLERR,"Variable evaluation before simulation box is defined",ivar); + print_var_error(FLERR,"Variable evaluation before simulation box is defined" + + utils::errorurl(30),ivar); // uppercase used to force access of // global vector vs global scalar, and global array vs global vector @@ -2227,7 +2229,8 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) } else if (utils::strmatch(word,"^[id]2?_")) { if (domain->box_exist == 0) - print_var_error(FLERR,"Variable evaluation before simulation box is defined",ivar); + print_var_error(FLERR,"Variable evaluation before simulation box is defined" + + utils::errorurl(30),ivar); int index_custom,type_custom,cols_custom; if (word[1] == '2') index_custom = atom->find_custom(word+3,type_custom,cols_custom); @@ -2361,7 +2364,8 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) } else if (str[i] == '[') { if (domain->box_exist == 0) - print_var_error(FLERR,"Variable evaluation before simulation box is defined",ivar); + print_var_error(FLERR,"Variable evaluation before simulation box is defined" + + utils::errorurl(30),ivar); ptr = &str[i]; tagint id = int_between_brackets(ptr,1); @@ -2375,7 +2379,8 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) } else if (is_atom_vector(word)) { if (domain->box_exist == 0) - print_var_error(FLERR,"Variable evaluation before simulation box is defined",ivar); + print_var_error(FLERR,"Variable evaluation before simulation box is defined" + + utils::errorurl(30),ivar); atom_vector(word,tree,treestack,ntreestack); @@ -2398,7 +2403,8 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) } else { if (domain->box_exist == 0) - print_var_error(FLERR,"Variable evaluation before simulation box is defined",ivar); + print_var_error(FLERR,"Variable evaluation before simulation box is defined" + + utils::errorurl(30),ivar); int flag = output->thermo->evaluate_keyword(word,&value1); if (flag) From 33ac6c88368bf748e1a0a7892785acfa9d8212a4 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 12 Mar 2025 22:33:07 -0400 Subject: [PATCH 082/113] address several issues related to variables and improve error messages --- doc/src/Errors_details.rst | 53 ++++- src/variable.cpp | 458 +++++++++++++++++++------------------ 2 files changed, 280 insertions(+), 231 deletions(-) diff --git a/doc/src/Errors_details.rst b/doc/src/Errors_details.rst index 147d5c927f..44b038d29d 100644 --- a/doc/src/Errors_details.rst +++ b/doc/src/Errors_details.rst @@ -450,17 +450,31 @@ sufficient information to easily reproduce it. Substitution for illegal variable --------------------------------- -A variable in an input script was not able to be parsed by LAMMPS on read-in. -LAMMPS has a few different accepted formats for variables, as detailed in the -:doc:`variable ` doc page. One cause for this error beyond simple -typos is missing brackets, for example when changing a variable definition from -a single letter (which does not require brackets) to one with multiple letters, -for example ``variable a equal 1.0`` (which can be evaluated later as ``$a`` or -``${a}``) to ``variable a0 equal 1.0`` (which can only be evaluated as -``${a0}``). Another potential source off this error may be invalid command line -variables used when launching LAMMPS from an interactive shell or shell scripts. -Users with harder-to-track variable errors might also find reading :doc:`Section -5.2. Parsing rules for input scripts` helpful. +A variable in an input script or a variable expression was not found in +the list of valid variables. The most common reason for this is a typo +somewhere in the input file and the expression uses an invalid variable +name. The second most common reason is to omit the curly braces for a +direct variable with a name that is not a single letter. Example: + +.. code-block:: LAMMPS + + variable cutoff index 10.0 + pair_style lj/cut ${cutoff} # this is correct + pair_style lj/cut $cutoff # this is incorrect, LAMMPS looks for 'c' instead of 'cutoff' + variable c index 5.0 # if $c is defined, LAMMPS subsitutes only '$c' and reads: 5utoff + +Another potential source of this error may be invalid command line +variables (-var or -v argument) used when launching LAMMPS from an +interactive shell or shell scripts. An uncommon source for this error +is the :doc:`next command `: with an index style variable +definition a list of values can be provided and LAMMPS will advance to +the next in the list with the :doc:`next command`. If there is no +remaining element in the list, LAMMPS will delete the variable and any +following expansion or reference attempt with trigger the error. + +Users with harder-to-track variable errors might also find reading +:doc:`Section 5.2. Parsing rules for input scripts` +helpful. .. _err0015: @@ -487,6 +501,23 @@ Most likely, one or more atoms have been blown out of the simulation box to a great distance or a fix (like fix deform or a barostat) has excessively grown the simulation box. +.. _err0020: + +Variable formula X is accessed out-of-range +------------------------------------------- + +When accessing an individual element of a global vector or array provided +by a compute or fix, or data from a specific atom, and index in square +brackets ("[ ]") must be provided and must be in a valid range. While +LAMMPS is written in C++ these indices start at 1 (i.e. similar to Fortran), +so any value smaller than 1 will trigger this error. But also too large +values can cause this error, specifically for computes or fixes where +the number of rows or columns can change or in simulations where the +number of atoms changes. Since this kind of error frequently happens +with rather complex expressions, it is recommended to test these with +small test systems, where the values can be tracked with output files +for all relevant properties for every step. + .. _err0021: Incorrect args for pair coefficients (also bond/angle/dihedral/improper coefficients) diff --git a/src/variable.cpp b/src/variable.cpp index 19a9a0a855..d34331a847 100644 --- a/src/variable.cpp +++ b/src/variable.cpp @@ -60,13 +60,15 @@ static constexpr int MAXFUNCARG = 6; // must match enumerator in variable.h const std::vector Variable::varstyles = { - "index", "loop", "world", "universe", "uloop", "string", "getenv", - "file", "atomfile", "format", "equal", "atom", "vector", "python", - "timer", "internal", "(unknown)"}; + "index", "loop", "world", "universe", "uloop", "string", "getenv", "file", "atomfile", + "format", "equal", "atom", "vector", "python", "timer", "internal", "(unknown)"}; -static inline double MYROUND(double a) { return ((a - floor(a)) >= 0.5) ? ceil(a) : floor(a); } +static inline double MYROUND(double a) +{ + return ((a - floor(a)) >= 0.5) ? ceil(a) : floor(a); +} -enum{ARG,OP}; +enum { ARG, OP }; // customize by adding a function // if add before XOR: @@ -83,14 +85,14 @@ enum{DONE,ADD,SUBTRACT,MULTIPLY,DIVIDE,CARAT,MODULO,UNARY, // customize by adding a special function -enum{SUM,XMIN,XMAX,AVE,TRAP,SLOPE,SORT,RSORT,NOVECTOR}; +enum { SUM, XMIN, XMAX, AVE, TRAP, SLOPE, SORT, RSORT, NOVECTOR }; static constexpr double BIG = 1.0e20; // INT64_MAX cannot be represented with a double. reduce to avoid overflow when casting back #if defined(LAMMPS_SMALLBIG) || defined(LAMMPS_BIGBIG) -static constexpr double MAXBIGINT_DOUBLE = (double) (MAXBIGINT-512); +static constexpr double MAXBIGINT_DOUBLE = (double) (MAXBIGINT - 512); #else static constexpr double MAXBIGINT_DOUBLE = (double) MAXBIGINT; #endif @@ -99,21 +101,14 @@ static constexpr double MAXBIGINT_DOUBLE = (double) MAXBIGINT; // if needed (cf. 'version') initialize in Variable class constructor. static std::unordered_map constants = { - {"PI", MY_PI }, - {"version", -1 }, - {"yes", 1 }, - {"no", 0 }, - {"on", 1 }, - {"off", 0 }, - {"true", 1 }, - {"false", 0 } -}; + {"PI", MY_PI}, {"version", -1}, {"yes", 1}, {"no", 0}, + {"on", 1}, {"off", 0}, {"true", 1}, {"false", 0}}; /* ---------------------------------------------------------------------- */ Variable::Variable(LAMMPS *lmp) : Pointers(lmp) { - MPI_Comm_rank(world,&me); + MPI_Comm_rank(world, &me); nvar = maxvar = 0; names = nullptr; @@ -155,8 +150,10 @@ Variable::~Variable() for (int i = 0; i < nvar; i++) { delete[] names[i]; delete reader[i]; - if (style[i] == LOOP || style[i] == ULOOP) delete[] data[i][0]; - else for (int j = 0; j < num[i]; j++) delete[] data[i][j]; + if (style[i] == LOOP || style[i] == ULOOP) + delete[] data[i][0]; + else + for (int j = 0; j < num[i]; j++) delete[] data[i][j]; delete[] data[i]; if (style[i] == VECTOR) memory->destroy(vecs[i].values); } @@ -174,7 +171,6 @@ Variable::~Variable() delete randomequal; delete randomatom; - } /* ---------------------------------------------------------------------- @@ -190,16 +186,17 @@ void Variable::set(int narg, char **arg) // DELETE // doesn't matter if variable no longer exists - if (strcmp(arg[1],"delete") == 0) { - if (narg != 2) - error->all(FLERR,"Illegal variable delete command: expected 2 arguments but found {}", narg); + if (strcmp(arg[1], "delete") == 0) { + if (narg > 2) + error->all(FLERR, 2, "Illegal variable delete command: expected 2 arguments but found {}", + narg); if (find(arg[0]) >= 0) remove(find(arg[0])); return; - // INDEX - // num = listed args, which = 1st value, data = copied args + // INDEX + // num = listed args, which = 1st value, data = copied args - } else if (strcmp(arg[1],"index") == 0) { + } else if (strcmp(arg[1], "index") == 0) { if (narg < 3) utils::missing_cmd_args(FLERR, "variable index", error); if (find(arg[0]) >= 0) return; if (nvar == maxvar) grow(); @@ -207,132 +204,138 @@ void Variable::set(int narg, char **arg) num[nvar] = narg - 2; which[nvar] = 0; pad[nvar] = 0; - data[nvar] = new char*[num[nvar]]; - copy(num[nvar],&arg[2],data[nvar]); + data[nvar] = new char *[num[nvar]]; + copy(num[nvar], &arg[2], data[nvar]); - // LOOP - // 1 arg + pad: num = N, which = 1st value, data = single string - // 2 args + pad: num = N2, which = N1, data = single string + // LOOP + // 1 arg + pad: num = N, which = 1st value, data = single string + // 2 args + pad: num = N2, which = N1, data = single string - } else if (strcmp(arg[1],"loop") == 0) { + } else if (strcmp(arg[1], "loop") == 0) { if (narg < 3) utils::missing_cmd_args(FLERR, "variable loop", error); if (find(arg[0]) >= 0) return; if (nvar == maxvar) grow(); style[nvar] = LOOP; - int nfirst = 0,nlast = 0; - if (narg == 3 || (narg == 4 && strcmp(arg[3],"pad") == 0)) { + int nfirst = 0, nlast = 0; + if (narg == 3 || (narg == 4 && strcmp(arg[3], "pad") == 0)) { nfirst = 1; - nlast = utils::inumeric(FLERR,arg[2],false,lmp); - if (nlast <= 0) error->all(FLERR, "Invalid variable loop argument: {}", nlast); - if (narg == 4 && strcmp(arg[3],"pad") == 0) { - pad[nvar] = fmt::format("{}",nlast).size(); - } else pad[nvar] = 0; - } else if (narg == 4 || (narg == 5 && strcmp(arg[4],"pad") == 0)) { - nfirst = utils::inumeric(FLERR,arg[2],false,lmp); - nlast = utils::inumeric(FLERR,arg[3],false,lmp); + nlast = utils::inumeric(FLERR, arg[2], false, lmp); + if (nlast <= 0) error->all(FLERR, 2, "Invalid variable loop argument: {}", nlast); + if (narg == 4 && strcmp(arg[3], "pad") == 0) { + pad[nvar] = fmt::format("{}", nlast).size(); + } else + pad[nvar] = 0; + } else if (narg == 4 || (narg == 5 && strcmp(arg[4], "pad") == 0)) { + nfirst = utils::inumeric(FLERR, arg[2], false, lmp); + nlast = utils::inumeric(FLERR, arg[3], false, lmp); if (nfirst > nlast || nlast < 0) - error->all(FLERR,"Illegal variable loop command: {} > {}", nfirst,nlast); - if (narg == 5 && strcmp(arg[4],"pad") == 0) { - pad[nvar] = fmt::format("{}",nlast).size(); - } else pad[nvar] = 0; - } else error->all(FLERR,"Illegal variable loop command: too many arguments"); + error->all(FLERR, 2, "Illegal variable loop command: {} > {}", nfirst, nlast); + if (narg == 5 && strcmp(arg[4], "pad") == 0) { + pad[nvar] = fmt::format("{}", nlast).size(); + } else + pad[nvar] = 0; + } else + error->all(FLERR, narg - 1, "Illegal variable loop command: too many arguments"); num[nvar] = nlast; - which[nvar] = nfirst-1; - data[nvar] = new char*[1]; + which[nvar] = nfirst - 1; + data[nvar] = new char *[1]; data[nvar][0] = nullptr; - // WORLD - // num = listed args, which = partition this proc is in, data = copied args - // error check that num = # of worlds in universe + // WORLD + // num = listed args, which = partition this proc is in, data = copied args + // error check that num = # of worlds in universe - } else if (strcmp(arg[1],"world") == 0) { + } else if (strcmp(arg[1], "world") == 0) { if (narg < 3) utils::missing_cmd_args(FLERR, "variable world", error); if (find(arg[0]) >= 0) return; if (nvar == maxvar) grow(); style[nvar] = WORLD; num[nvar] = narg - 2; if (num[nvar] != universe->nworlds) - error->all(FLERR,"World variable count doesn't match # of partitions"); + error->all(FLERR, narg - 1, "World variable count {} doesn't match # of partitions {}", + narg - 2, universe->nworlds); which[nvar] = universe->iworld; pad[nvar] = 0; - data[nvar] = new char*[num[nvar]]; - copy(num[nvar],&arg[2],data[nvar]); + data[nvar] = new char *[num[nvar]]; + copy(num[nvar], &arg[2], data[nvar]); - // UNIVERSE and ULOOP - // for UNIVERSE: num = listed args, data = copied args - // for ULOOP: num = N, data = single string - // which = partition this proc is in - // universe proc 0 creates lock file - // error check that all other universe/uloop variables are same length + // UNIVERSE and ULOOP + // for UNIVERSE: num = listed args, data = copied args + // for ULOOP: num = N, data = single string + // which = partition this proc is in + // universe proc 0 creates lock file + // error check that all other universe/uloop variables are same length - } else if (strcmp(arg[1],"universe") == 0 || strcmp(arg[1],"uloop") == 0) { - if (strcmp(arg[1],"universe") == 0) { + } else if (strcmp(arg[1], "universe") == 0 || strcmp(arg[1], "uloop") == 0) { + if (strcmp(arg[1], "universe") == 0) { if (narg < 3) utils::missing_cmd_args(FLERR, "variable universe", error); if (find(arg[0]) >= 0) return; if (nvar == maxvar) grow(); style[nvar] = UNIVERSE; num[nvar] = narg - 2; pad[nvar] = 0; - data[nvar] = new char*[num[nvar]]; - copy(num[nvar],&arg[2],data[nvar]); - } else if (strcmp(arg[1],"uloop") == 0) { + data[nvar] = new char *[num[nvar]]; + copy(num[nvar], &arg[2], data[nvar]); + } else if (strcmp(arg[1], "uloop") == 0) { if (narg < 3 || narg > 4) - error->all(FLERR,"Illegal variable command: expected 3 or 4 arguments but found {}: {}", + error->all(FLERR, 1, "Illegal variable command: expected 3 or 4 arguments but found {}: {}", narg, utils::errorurl(3)); - if (narg == 4 && strcmp(arg[3],"pad") != 0) - error->all(FLERR, "Invalid variable uloop argument: {}", arg[3]); + if (narg == 4 && strcmp(arg[3], "pad") != 0) + error->all(FLERR, 3, "Invalid variable uloop argument: {}", arg[3]); if (find(arg[0]) >= 0) return; if (nvar == maxvar) grow(); style[nvar] = ULOOP; - num[nvar] = utils::inumeric(FLERR,arg[2],false,lmp); - data[nvar] = new char*[1]; + num[nvar] = utils::inumeric(FLERR, arg[2], false, lmp); + data[nvar] = new char *[1]; data[nvar][0] = nullptr; - if (narg == 4) pad[nvar] = std::to_string(num[nvar]).size(); - else pad[nvar] = 0; + if (narg == 4) + pad[nvar] = std::to_string(num[nvar]).size(); + else + pad[nvar] = 0; } if (num[nvar] < universe->nworlds) - error->all(FLERR,"Universe/uloop variable count < # of partitions"); + error->all(FLERR, 2, "Universe/uloop variable count {} < # of partitions {}", num[nvar], + universe->nworlds); which[nvar] = universe->iworld; if (universe->me == 0) { - FILE *fp = fopen("tmp.lammps.variable","w"); + FILE *fp = fopen("tmp.lammps.variable", "w"); if (fp == nullptr) - error->one(FLERR,"Cannot open temporary file for world counter: " + utils::getsyserror()); - fprintf(fp,"%d\n",universe->nworlds); + error->one(FLERR, "Cannot open temporary file for world counter: " + utils::getsyserror()); + fprintf(fp, "%d\n", universe->nworlds); fclose(fp); fp = nullptr; } for (int jvar = 0; jvar < nvar; jvar++) - if (num[jvar] && (style[jvar] == UNIVERSE || style[jvar] == ULOOP) && - num[nvar] != num[jvar]) - error->all(FLERR,"All universe/uloop variables must have same # of values"); + if (num[jvar] && (style[jvar] == UNIVERSE || style[jvar] == ULOOP) && num[nvar] != num[jvar]) + error->all(FLERR, "All universe/uloop variables must have same # of values"); - // STRING - // replace pre-existing var if also style STRING (allows it to be reset) - // num = 1, which = 1st value - // data = 1 value, string to eval + // STRING + // replace pre-existing var if also style STRING (allows it to be reset) + // num = 1, which = 1st value + // data = 1 value, string to eval - } else if (strcmp(arg[1],"string") == 0) { + } else if (strcmp(arg[1], "string") == 0) { if (narg != 3) - error->all(FLERR,"Illegal variable command: expected 3 arguments but found {}{}", - narg, utils::errorurl(3)); + error->all(FLERR, "Illegal variable command: expected 3 arguments but found {}{}", narg, + utils::errorurl(3)); int maxcopy = strlen(arg[2]) + 1; int maxwork = maxcopy; - auto scopy = (char *) memory->smalloc(maxcopy,"var:string/copy"); - auto work = (char *) memory->smalloc(maxwork,"var:string/work"); - strcpy(scopy,arg[2]); - input->substitute(scopy,work,maxcopy,maxwork,1); + auto scopy = (char *) memory->smalloc(maxcopy, "var:string/copy"); + auto work = (char *) memory->smalloc(maxwork, "var:string/work"); + strcpy(scopy, arg[2]); + input->substitute(scopy, work, maxcopy, maxwork, 1); memory->sfree(work); int ivar = find(arg[0]); if (ivar >= 0) { if (style[ivar] != STRING) - error->all(FLERR,"Cannot redefine variable as a different style"); + error->all(FLERR, 1, "Cannot redefine variable {} as a different style", arg[0]); delete[] data[ivar][0]; - copy(1,&scopy,data[ivar]); + copy(1, &scopy, data[ivar]); replaceflag = 1; } else { if (nvar == maxvar) grow(); @@ -340,23 +343,23 @@ void Variable::set(int narg, char **arg) num[nvar] = 1; which[nvar] = 0; pad[nvar] = 0; - data[nvar] = new char*[num[nvar]]; - copy(1,&scopy,data[nvar]); + data[nvar] = new char *[num[nvar]]; + copy(1, &scopy, data[nvar]); } memory->sfree(scopy); - // GETENV - // remove pre-existing var if also style GETENV (allows it to be reset) - // num = 1, which = 1st value - // data = 1 value, string to eval + // GETENV + // remove pre-existing var if also style GETENV (allows it to be reset) + // num = 1, which = 1st value + // data = 1 value, string to eval - } else if (strcmp(arg[1],"getenv") == 0) { + } else if (strcmp(arg[1], "getenv") == 0) { if (narg != 3) - error->all(FLERR,"Illegal variable command: expected 3 arguments but found {}{}", - narg, utils::errorurl(3)); + error->all(FLERR, "Illegal variable command: expected 3 arguments but found {}{}", narg, + utils::errorurl(3)); if (find(arg[0]) >= 0) { if (style[find(arg[0])] != GETENV) - error->all(FLERR,"Cannot redefine variable as a different style"); + error->all(FLERR, 1, "Cannot redefine variable {} as a different style", arg[0]); remove(find(arg[0])); } if (nvar == maxvar) grow(); @@ -364,63 +367,62 @@ void Variable::set(int narg, char **arg) num[nvar] = 2; which[nvar] = 0; pad[nvar] = 0; - data[nvar] = new char*[num[nvar]]; + data[nvar] = new char *[num[nvar]]; data[nvar][0] = utils::strdup(arg[2]); data[nvar][1] = utils::strdup("(undefined)"); - // SCALARFILE for strings or numbers - // which = 1st value - // data = 1 value, string to eval + // SCALARFILE for strings or numbers + // which = 1st value + // data = 1 value, string to eval - } else if (strcmp(arg[1],"file") == 0) { + } else if (strcmp(arg[1], "file") == 0) { if (narg != 3) - error->all(FLERR,"Illegal variable command: expected 3 arguments but found {}{}", - narg, utils::errorurl(3)); + error->all(FLERR, "Illegal variable command: expected 3 arguments but found {}{}", narg, + utils::errorurl(3)); if (find(arg[0]) >= 0) return; if (nvar == maxvar) grow(); style[nvar] = SCALARFILE; num[nvar] = 1; which[nvar] = 0; pad[nvar] = 0; - data[nvar] = new char*[num[nvar]]; + data[nvar] = new char *[num[nvar]]; data[nvar][0] = new char[MAXLINE]; - reader[nvar] = new VarReader(lmp,arg[0],arg[2],SCALARFILE); + reader[nvar] = new VarReader(lmp, arg[0], arg[2], SCALARFILE); int flag = reader[nvar]->read_scalar(data[nvar][0]); - if (flag) - error->all(FLERR,"File variable {} could not read value from {}", arg[0], arg[2]); + if (flag) error->all(FLERR, "File variable {} could not read value from {}", arg[0], arg[2]); - // ATOMFILE for numbers - // which = 1st value - // data = nullptr + // ATOMFILE for numbers + // which = 1st value + // data = nullptr - } else if (strcmp(arg[1],"atomfile") == 0) { + } else if (strcmp(arg[1], "atomfile") == 0) { if (narg != 3) - error->all(FLERR,"Illegal variable command: expected 3 arguments but found {}{}", - narg, utils::errorurl(3)); + error->all(FLERR, "Illegal variable command: expected 3 arguments but found {}{}", narg, + utils::errorurl(3)); if (find(arg[0]) >= 0) return; if (nvar == maxvar) grow(); style[nvar] = ATOMFILE; num[nvar] = 1; which[nvar] = 0; pad[nvar] = 0; - data[nvar] = new char*[num[nvar]]; + data[nvar] = new char *[num[nvar]]; data[nvar][0] = nullptr; - reader[nvar] = new VarReader(lmp,arg[0],arg[2],ATOMFILE); + reader[nvar] = new VarReader(lmp, arg[0], arg[2], ATOMFILE); int flag = reader[nvar]->read_peratom(); if (flag) - error->all(FLERR,"Atomfile variable {} could not read values from {}", arg[0], arg[2]); + error->all(FLERR, "Atomfile variable {} could not read values from {}", arg[0], arg[2]); - // FORMAT - // num = 3, which = 1st value - // data = 3 values - // 1st is name of variable to eval, 2nd is format string, - // 3rd is filled on retrieval + // FORMAT + // num = 3, which = 1st value + // data = 3 values + // 1st is name of variable to eval, 2nd is format string, + // 3rd is filled on retrieval - } else if (strcmp(arg[1],"format") == 0) { + } else if (strcmp(arg[1], "format") == 0) { constexpr char validfmt[] = "^% ?-?[0-9]*\\.?[0-9]*[efgEFG]$"; if (narg != 4) - error->all(FLERR,"Illegal variable command: expected 4 arguments but found {}{}", - narg, utils::errorurl(3)); + error->all(FLERR, "Illegal variable command: expected 4 arguments but found {}{}", narg, + utils::errorurl(3)); int ivar = find(arg[0]); int jvar = find(arg[2]); if (jvar < 0) @@ -429,9 +431,9 @@ void Variable::set(int narg, char **arg) error->all(FLERR, "Variable {}: format variable {} has incompatible style", arg[0], arg[2]); if (ivar >= 0) { if (style[ivar] != FORMAT) - error->all(FLERR,"Cannot redefine variable as a different style"); + error->all(FLERR, 1, "Cannot redefine variable {} as a different style", arg[0]); if (!utils::strmatch(arg[3], validfmt)) - error->all(FLERR,"Incorrect conversion in format string"); + error->all(FLERR, "Incorrect conversion in format string"); delete[] data[ivar][0]; delete[] data[ivar][1]; data[ivar][0] = utils::strdup(arg[2]); @@ -444,19 +446,19 @@ void Variable::set(int narg, char **arg) which[nvar] = 0; pad[nvar] = 0; if (!utils::strmatch(arg[3], validfmt)) - error->all(FLERR,"Incorrect conversion in format string"); - data[nvar] = new char*[num[nvar]]; - copy(2,&arg[2],data[nvar]); + error->all(FLERR, "Incorrect conversion in format string"); + data[nvar] = new char *[num[nvar]]; + copy(2, &arg[2], data[nvar]); data[nvar][2] = new char[VALUELENGTH]; - strcpy(data[nvar][2],"(undefined)"); + strcpy(data[nvar][2], "(undefined)"); } - // EQUAL - // replace pre-existing var if also style EQUAL (allows it to be reset) - // num = 2, which = 1st value - // data = 2 values, 1st is string to eval, 2nd is filled on retrieval + // EQUAL + // replace pre-existing var if also style EQUAL (allows it to be reset) + // num = 2, which = 1st value + // data = 2 values, 1st is string to eval, 2nd is filled on retrieval - } else if (strcmp(arg[1],"equal") == 0) { + } else if (strcmp(arg[1], "equal") == 0) { if (narg < 3) utils::missing_cmd_args(FLERR, "variable equal", error); // combine excess arguments into single string with a blank as separator @@ -469,7 +471,7 @@ void Variable::set(int narg, char **arg) int ivar = find(arg[0]); if (ivar >= 0) { if (style[ivar] != EQUAL) - error->all(FLERR,"Cannot redefine variable as a different style"); + error->all(FLERR, 1, "Cannot redefine variable {} as a different style", arg[0]); delete[] data[ivar][0]; data[ivar][0] = utils::strdup(combined); replaceflag = 1; @@ -479,18 +481,18 @@ void Variable::set(int narg, char **arg) num[nvar] = 2; which[nvar] = 0; pad[nvar] = 0; - data[nvar] = new char*[num[nvar]]; + data[nvar] = new char *[num[nvar]]; data[nvar][0] = utils::strdup(combined); data[nvar][1] = new char[VALUELENGTH]; - strcpy(data[nvar][1],"(undefined)"); + strcpy(data[nvar][1], "(undefined)"); } - // ATOM - // replace pre-existing var if also style ATOM (allows it to be reset) - // num = 1, which = 1st value - // data = 1 value, string to eval + // ATOM + // replace pre-existing var if also style ATOM (allows it to be reset) + // num = 1, which = 1st value + // data = 1 value, string to eval - } else if (strcmp(arg[1],"atom") == 0) { + } else if (strcmp(arg[1], "atom") == 0) { if (narg < 3) utils::missing_cmd_args(FLERR, "variable atom", error); // combine excess arguments into single string with a blank as separator @@ -503,7 +505,7 @@ void Variable::set(int narg, char **arg) int ivar = find(arg[0]); if (ivar >= 0) { if (style[ivar] != ATOM) - error->all(FLERR,"Cannot redefine variable as a different style"); + error->all(FLERR, 1, "Cannot redefine variable {} as a different style", arg[0]); delete[] data[ivar][0]; data[ivar][0] = utils::strdup(combined); replaceflag = 1; @@ -513,18 +515,18 @@ void Variable::set(int narg, char **arg) num[nvar] = 1; which[nvar] = 0; pad[nvar] = 0; - data[nvar] = new char*[num[nvar]]; + data[nvar] = new char *[num[nvar]]; data[nvar][0] = utils::strdup(combined); } - // VECTOR - // replace pre-existing var if also style VECTOR (allows it to be reset) - // num = 2, which = 1st value - // data = 2 values, 1st is string to eval, 2nd is formatted output string [1,2,3] - // if formula string is [value,value,...] then - // immediately store it as N-length vector and set dynamic flag to 0 + // VECTOR + // replace pre-existing var if also style VECTOR (allows it to be reset) + // num = 2, which = 1st value + // data = 2 values, 1st is string to eval, 2nd is formatted output string [1,2,3] + // if formula string is [value,value,...] then + // immediately store it as N-length vector and set dynamic flag to 0 - } else if (strcmp(arg[1],"vector") == 0) { + } else if (strcmp(arg[1], "vector") == 0) { if (narg < 3) utils::missing_cmd_args(FLERR, "variable atom", error); // combine excess arguments into single string with a blank as separator @@ -537,7 +539,7 @@ void Variable::set(int narg, char **arg) int ivar = find(arg[0]); if (ivar >= 0) { if (style[ivar] != VECTOR) - error->all(FLERR,"Cannot redefine variable as a different style"); + error->all(FLERR, 1, "Cannot redefine variable {} as a different style", arg[0]); delete[] data[ivar][0]; delete[] data[ivar][1]; data[ivar][0] = utils::strdup(combined); @@ -545,9 +547,9 @@ void Variable::set(int narg, char **arg) vecs[ivar].dynamic = 1; else { vecs[ivar].dynamic = 0; - parse_vector(ivar,data[ivar][0]); - std::vector vec(vecs[ivar].values,vecs[ivar].values + vecs[ivar].n); - data[ivar][1] = utils::strdup(fmt::format("[{}]", fmt::join(vec,","))); + parse_vector(ivar, data[ivar][0]); + std::vector vec(vecs[ivar].values, vecs[ivar].values + vecs[ivar].n); + data[ivar][1] = utils::strdup(fmt::format("[{}]", fmt::join(vec, ","))); } replaceflag = 1; } else { @@ -556,34 +558,33 @@ void Variable::set(int narg, char **arg) num[nvar] = 2; which[nvar] = 0; pad[nvar] = 0; - data[nvar] = new char*[num[nvar]]; + data[nvar] = new char *[num[nvar]]; data[nvar][0] = utils::strdup(combined); if (data[nvar][0][0] != '[') { vecs[nvar].dynamic = 1; data[nvar][1] = nullptr; } else { vecs[nvar].dynamic = 0; - parse_vector(nvar,data[nvar][0]); - std::vector vec(vecs[nvar].values,vecs[nvar].values + vecs[nvar].n); - data[nvar][1] = utils::strdup(fmt::format("[{}]", fmt::join(vec,","))); + parse_vector(nvar, data[nvar][0]); + std::vector vec(vecs[nvar].values, vecs[nvar].values + vecs[nvar].n); + data[nvar][1] = utils::strdup(fmt::format("[{}]", fmt::join(vec, ","))); } } - // PYTHON - // replace pre-existing var if also style PYTHON (allows it to be reset) - // num = 2, which = 1st value - // data = 2 values, 1st is Python func to invoke, 2nd is filled by invoke + // PYTHON + // replace pre-existing var if also style PYTHON (allows it to be reset) + // num = 2, which = 1st value + // data = 2 values, 1st is Python func to invoke, 2nd is filled by invoke - } else if (strcmp(arg[1],"python") == 0) { + } else if (strcmp(arg[1], "python") == 0) { if (narg != 3) - error->all(FLERR,"Illegal variable command: expected 3 arguments but found {}{}", - narg, utils::errorurl(3)); - if (!python->is_enabled()) - error->all(FLERR,"LAMMPS is not built with Python embedded"); + error->all(FLERR, "Illegal variable command: expected 3 arguments but found {}{}", narg, + utils::errorurl(3)); + if (!python->is_enabled()) error->all(FLERR, "LAMMPS is not built with Python embedded"); int ivar = find(arg[0]); if (ivar >= 0) { if (style[ivar] != PYTHON) - error->all(FLERR,"Cannot redefine variable as a different style"); + error->all(FLERR, 1, "Cannot redefine variable {} as a different style", arg[0]); delete[] data[ivar][0]; data[ivar][0] = utils::strdup(arg[2]); replaceflag = 1; @@ -593,24 +594,25 @@ void Variable::set(int narg, char **arg) num[nvar] = 2; which[nvar] = 1; pad[nvar] = 0; - data[nvar] = new char*[num[nvar]]; + data[nvar] = new char *[num[nvar]]; data[nvar][0] = utils::strdup(arg[2]); data[nvar][1] = new char[VALUELENGTH]; - strcpy(data[nvar][1],"(undefined)"); + strcpy(data[nvar][1], "(undefined)"); } - // TIMER - // stores current walltime as a timestamp in seconds - // replace pre-existing var if also style TIMER (allows reset with current time) - // num = 1, for string representation of dvalue, set by retrieve() - // dvalue = numeric initialization via platform::walltime() + // TIMER + // stores current walltime as a timestamp in seconds + // replace pre-existing var if also style TIMER (allows reset with current time) + // num = 1, for string representation of dvalue, set by retrieve() + // dvalue = numeric initialization via platform::walltime() - } else if (strcmp(arg[1],"timer") == 0) { - if (narg != 2) error->all(FLERR,"Illegal variable command: expected 2 arguments but found {}", narg); + } else if (strcmp(arg[1], "timer") == 0) { + if (narg != 2) + error->all(FLERR, "Illegal variable command: expected 2 arguments but found {}", narg); int ivar = find(arg[0]); if (ivar >= 0) { if (style[ivar] != TIMER) - error->all(FLERR,"Cannot redefine variable as a different style"); + error->all(FLERR, 1, "Cannot redefine variable {} as a different style", arg[0]); dvalue[ivar] = platform::walltime(); replaceflag = 1; } else { @@ -619,25 +621,25 @@ void Variable::set(int narg, char **arg) num[nvar] = 1; which[nvar] = 0; pad[nvar] = 0; - data[nvar] = new char*[num[nvar]]; + data[nvar] = new char *[num[nvar]]; data[nvar][0] = new char[VALUELENGTH]; dvalue[nvar] = platform::walltime(); } - // INTERNAL - // replace pre-existing var if also style INTERNAL (allows it to be reset) - // num = 1, for string representation of dvalue, set by retrieve() - // dvalue = numeric initialization from 2nd arg, reset by internal_set() + // INTERNAL + // replace pre-existing var if also style INTERNAL (allows it to be reset) + // num = 1, for string representation of dvalue, set by retrieve() + // dvalue = numeric initialization from 2nd arg, reset by internal_set() - } else if (strcmp(arg[1],"internal") == 0) { + } else if (strcmp(arg[1], "internal") == 0) { if (narg != 3) - error->all(FLERR,"Illegal variable command: expected 3 arguments but found {}{}", - narg, utils::errorurl(3)); + error->all(FLERR, "Illegal variable command: expected 3 arguments but found {}{}", narg, + utils::errorurl(3)); int ivar = find(arg[0]); if (ivar >= 0) { if (style[ivar] != INTERNAL) - error->all(FLERR,"Cannot redefine variable as a different style"); - dvalue[nvar] = utils::numeric(FLERR,arg[2],false,lmp); + error->all(FLERR, 1, "Cannot redefine variable {} as a different style", arg[0]); + dvalue[nvar] = utils::numeric(FLERR, arg[2], false, lmp); replaceflag = 1; } else { if (nvar == maxvar) grow(); @@ -645,14 +647,15 @@ void Variable::set(int narg, char **arg) num[nvar] = 1; which[nvar] = 0; pad[nvar] = 0; - data[nvar] = new char*[num[nvar]]; + data[nvar] = new char *[num[nvar]]; data[nvar][0] = new char[VALUELENGTH]; - dvalue[nvar] = utils::numeric(FLERR,arg[2],false,lmp); + dvalue[nvar] = utils::numeric(FLERR, arg[2], false, lmp); } - // unrecognized variable style + // unrecognized variable style - } else error->all(FLERR,"Unknown variable style: {}", arg[1]); + } else + error->all(FLERR, 1, "Unknown variable style: {}", arg[1]); // set name of variable, if not replacing one flagged with replaceflag // name must be all alphanumeric chars or underscores @@ -660,7 +663,7 @@ void Variable::set(int narg, char **arg) if (replaceflag) return; if (!utils::is_id(arg[0])) - error->all(FLERR,"Variable name '{}' must have only letters, numbers, or underscores",arg[0]); + error->all(FLERR, "Variable name '{}' must have only letters, numbers, or underscores", arg[0]); names[nvar] = utils::strdup(arg[0]); nvar++; } @@ -723,7 +726,7 @@ int Variable::next(int narg, char **arg) { int ivar; - if (narg == 0) error->all(FLERR,"Illegal next command"); + if (narg == 0) utils::missing_cmd_args(FLERR, "next", error); // check that variables exist and are all the same style // exception: UNIVERSE and ULOOP variables can be mixed in same next command @@ -731,7 +734,7 @@ int Variable::next(int narg, char **arg) for (int iarg = 0; iarg < narg; iarg++) { ivar = find(arg[iarg]); if (ivar < 0) - error->all(FLERR,"Invalid variable '{}' in next command",arg[iarg]); + error->all(FLERR, iarg, "Invalid variable '{}' in next command",arg[iarg]); if (style[ivar] == ULOOP && style[find(arg[0])] == UNIVERSE) continue; else if (style[ivar] == UNIVERSE && style[find(arg[0])] == ULOOP) continue; else if (style[ivar] != style[find(arg[0])]) @@ -746,7 +749,8 @@ int Variable::next(int narg, char **arg) istyle == WORLD || istyle == GETENV || istyle == ATOM || istyle == VECTOR || istyle == FORMAT || istyle == PYTHON || istyle == TIMER || istyle == INTERNAL) - error->all(FLERR,"Invalid variable style with next command"); + error->all(FLERR, Error::ARGZERO, "Variable {} has invalid style {} for next command", + arg[0], varstyles[istyle]); // if istyle = UNIVERSE or ULOOP, ensure all such variables are incremented @@ -1619,7 +1623,8 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) // to allow for computes with size_vector_variable == 1 if (index1 > compute->size_vector) - print_var_error(FLERR,"Variable formula compute vector is accessed out-of-range",ivar,0); + print_var_error(FLERR,"Variable formula compute vector is accessed out-of-range" + + utils::errorurl(20), ivar, 0); value1 = compute->vector[index1-1]; argstack[nargstack++] = value1; @@ -1631,7 +1636,8 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) if (!compute->array_flag) print_var_error(FLERR,"Mismatched compute in variable formula",ivar); if (index2 > compute->size_array_cols) - print_var_error(FLERR,"Variable formula compute array is accessed out-of-range",ivar,0); + print_var_error(FLERR,"Variable formula compute array is accessed out-of-range" + + utils::errorurl(20), ivar, 0); if (!compute->is_initialized()) print_var_error(FLERR,"Variable formula compute cannot be invoked before " "initialization by a run",ivar); @@ -1644,7 +1650,8 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) // to allow for computes with size_array_rows_variable == 1 if (index1 > compute->size_array_rows) - print_var_error(FLERR,"Variable formula compute array is accessed out-of-range",ivar,0); + print_var_error(FLERR,"Variable formula compute array is accessed out-of-range" + + utils::errorurl(20), ivar, 0); value1 = compute->array[index1-1][index2-1]; argstack[nargstack++] = value1; @@ -1677,7 +1684,8 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) if (!compute->size_peratom_cols) print_var_error(FLERR,"Mismatched compute in variable formula",ivar); if (index2 > compute->size_peratom_cols) - print_var_error(FLERR,"Variable formula compute array is accessed out-of-range",ivar,0); + print_var_error(FLERR,"Variable formula compute array is accessed out-of-range" + + utils::errorurl(20), ivar,0); if (!compute->is_initialized()) print_var_error(FLERR,"Variable formula compute cannot be invoked before " "initialization by a run",ivar); @@ -1739,7 +1747,8 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) print_var_error(FLERR,"Variable formula compute cannot be invoked before " "initialization by a run",ivar); if (index1 > compute->size_array_cols) - print_var_error(FLERR,"Variable formula compute array is accessed out-of-range",ivar,0); + print_var_error(FLERR,"Variable formula compute array is accessed out-of-range" + + utils::errorurl(20), ivar,0); if (!(compute->invoked_flag & Compute::INVOKED_ARRAY)) { compute->compute_array(); compute->invoked_flag |= Compute::INVOKED_ARRAY; @@ -1797,7 +1806,8 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) if (!compute->size_peratom_cols) print_var_error(FLERR,"Mismatched compute in variable formula",ivar); if (index1 > compute->size_peratom_cols) - print_var_error(FLERR,"Variable formula compute array is accessed out-of-range",ivar,0); + print_var_error(FLERR,"Variable formula compute array is accessed out-of-range" + + utils::errorurl(20), ivar,0); if (!compute->is_initialized()) print_var_error(FLERR,"Variable formula compute cannot be invoked before " "initialization by a run",ivar); @@ -1882,7 +1892,8 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) if (!fix->vector_flag) print_var_error(FLERR,"Mismatched fix in variable formula",ivar); if (index1 > fix->size_vector && fix->size_vector_variable == 0) - print_var_error(FLERR,"Variable formula fix vector is accessed out-of-range",ivar,0); + print_var_error(FLERR,"Variable formula fix vector is accessed out-of-range" + + utils::errorurl(20), ivar,0); if (update->whichflag > 0 && update->ntimestep % fix->global_freq) print_var_error(FLERR,"Fix in variable not computed at a compatible time",ivar); @@ -1900,9 +1911,11 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) if (!fix->array_flag) print_var_error(FLERR,"Mismatched fix in variable formula",ivar); if (index1 > fix->size_array_rows && fix->size_array_rows_variable == 0) - print_var_error(FLERR,"Variable formula fix array is accessed out-of-range",ivar,0); + print_var_error(FLERR,"Variable formula fix array is accessed out-of-range" + + utils::errorurl(20), ivar,0); if (index2 > fix->size_array_cols) - print_var_error(FLERR,"Variable formula fix array is accessed out-of-range",ivar,0); + print_var_error(FLERR,"Variable formula fix array is accessed out-of-range" + + utils::errorurl(20), ivar,0); if (update->whichflag > 0 && update->ntimestep % fix->global_freq) print_var_error(FLERR,"Fix in variable not computed at a compatible time",ivar); @@ -1937,7 +1950,8 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) if (!fix->size_peratom_cols) print_var_error(FLERR,"Mismatched fix in variable formula",ivar); if (index2 > fix->size_peratom_cols) - print_var_error(FLERR,"Variable formula fix array is accessed out-of-range",ivar,0); + print_var_error(FLERR,"Variable formula fix array is accessed out-of-range" + + utils::errorurl(20), ivar,0); if (update->whichflag > 0 && update->ntimestep % fix->peratom_freq) print_var_error(FLERR,"Fix in variable not computed at a compatible time",ivar); @@ -1991,7 +2005,8 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) if (fix->size_array_rows == 0) print_var_error(FLERR,"Variable formula fix array is zero length",ivar); if (index1 > fix->size_array_cols) - print_var_error(FLERR,"Variable formula fix array is accessed out-of-range",ivar,0); + print_var_error(FLERR,"Variable formula fix array is accessed out-of-range" + + utils::errorurl(20), ivar,0); if (update->whichflag > 0 && update->ntimestep % fix->global_freq) print_var_error(FLERR,"Fix in variable not computed at a compatible time",ivar); @@ -2043,7 +2058,8 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) if (!fix->size_peratom_cols) print_var_error(FLERR,"Mismatched fix in variable formula",ivar); if (index1 > fix->size_peratom_cols) - print_var_error(FLERR,"Variable formula fix array is accessed out-of-range",ivar,0); + print_var_error(FLERR,"Variable formula fix array is accessed out-of-range" + + utils::errorurl(20), ivar,0); if (update->whichflag > 0 && update->ntimestep % fix->peratom_freq) print_var_error(FLERR,"Fix in variable not computed at compatible time",ivar); @@ -4480,7 +4496,8 @@ int Variable::special_function(const std::string &word, char *contents, Tree **t nstride = 1; } else if (index && compute->array_flag) { if (index > compute->size_array_cols) - print_var_error(FLERR,"Variable formula compute array is accessed out-of-range",ivar,0); + print_var_error(FLERR,"Variable formula compute array is accessed out-of-range" + + utils::errorurl(20), ivar,0); if (!compute->is_initialized()) print_var_error(FLERR,"Variable formula compute cannot be invoked before " "initialization by a run",ivar); @@ -4520,7 +4537,8 @@ int Variable::special_function(const std::string &word, char *contents, Tree **t nstride = 1; } else if (index && fix->array_flag) { if (index > fix->size_array_cols) - print_var_error(FLERR,"Variable formula fix array is accessed out-of-range",ivar); + print_var_error(FLERR,"Variable formula fix array is accessed out-of-range" + + utils::errorurl(20), ivar); if (update->whichflag > 0 && update->ntimestep % fix->global_freq) print_var_error(FLERR,"Fix in variable not computed at compatible time",ivar); nvec = fix->size_array_rows; From f158b5195ec241442cc1c48f8e5bf51b1f35c699 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 12 Mar 2025 22:51:29 -0400 Subject: [PATCH 083/113] add explanation for "did not assign all atoms" --- doc/src/Errors_details.rst | 20 ++++++++++++++++++++ src/read_data.cpp | 14 +++++++++----- src/read_restart.cpp | 3 ++- src/replicate.cpp | 3 ++- 4 files changed, 33 insertions(+), 7 deletions(-) diff --git a/doc/src/Errors_details.rst b/doc/src/Errors_details.rst index 44b038d29d..d9b77cfe2a 100644 --- a/doc/src/Errors_details.rst +++ b/doc/src/Errors_details.rst @@ -490,6 +490,26 @@ fill space. This error can be avoided using the generally slower :doc:`nsq neighbor style ` or by increasing the size of the smallest box lengths. +.. _err0016: + +Did not assign all atoms correctly +---------------------------------- + +This error happens most commonly, when :doc:`reading a data file ` +under :doc:`non-periodic boundary conditions`. Only atoms with +positions **inside** the simulation box will be read and thus any atoms +outside the box will be skipped and the total atom count will not match, +which triggers the error. This does not happen with periodic boundary +conditions where atoms outside the principal box will be "wrapped" into +the principal box and their image flags set accordingly. + +Similar errors can happen with the :doc:`replicate command` or +the :doc:`read_restart command`. In these cases the cause +may be a problematic geometry, an insufficient communication cutoff or +a bug in the LAMMPS source code. In these cases it is advisable to set +up :ref:`small test case ` for testing and debugging. This will +be required in case you need to get help from a LAMMPS developer. + .. _err0017: Domain too large for neighbor bins diff --git a/src/read_data.cpp b/src/read_data.cpp index 29696bd62d..02fd6ed7db 100644 --- a/src/read_data.cpp +++ b/src/read_data.cpp @@ -526,7 +526,8 @@ void ReadData::command(int narg, char **arg) if (tilt_flag) triclinic = 1; } else { if (xloxhi_flag || yloyhi_flag || zlozhi_flag || tilt_flag) - error->all(FLERR,"Read_data header cannot specify simulation box lo/hi/tilt and ABC vectors"); + error->all(FLERR, + "Read_data header cannot specify simulation box lo/hi/tilt and ABC vectors"); triclinic = triclinic_general = 1; } @@ -538,7 +539,8 @@ void ReadData::command(int narg, char **arg) error->all(FLERR, "Read_data zlo/zhi for 2d simulation must straddle 0.0"); } else if (triclinic_general == 1) { if (cvec[0] != 0.0 || cvec[1] != 0.0 || cvec[2] != 1.0 || abc_origin[2] != -0.5) - error->all(FLERR,"Read_data cvec and/or abc_origin is invalid for " + error->all(FLERR, + "Read_data cvec and/or abc_origin is invalid for " "2d simulation with general triclinic box"); } } @@ -672,7 +674,8 @@ void ReadData::command(int narg, char **arg) int flag_all; MPI_Allreduce(&iflag, &flag_all, 1, MPI_INT, MPI_SUM, world); if ((flag_all > 0) && (comm->me == 0)) - error->warning(FLERR, "Non-zero image flags with growing box can produce bad coordinates"); + error->warning(FLERR, + "Non-zero image flags with growing box can produce bad coordinates"); } } @@ -1170,7 +1173,8 @@ void ReadData::command(int narg, char **arg) bigint nblocal = atom->nlocal; MPI_Allreduce(&nblocal, &natoms, 1, MPI_LMP_BIGINT, MPI_SUM, world); if (natoms != atom->natoms) - error->all(FLERR, "Read_data shrink wrap did not assign all atoms correctly"); + error->all(FLERR, Error::NOLASTLINE, + "Read_data shrink wrap did not assign all atoms correctly" + utils::errorurl(16)); } // restore old styles, when reading with nocoeff flag given @@ -1559,7 +1563,7 @@ void ReadData::atoms() if (me == 0) utils::logmesg(lmp, " {} atoms\n", nassign); - if (sum != atom->natoms) error->all(FLERR, "Did not assign all atoms correctly"); + if (sum != atom->natoms) error->all(FLERR, "Did not assign all atoms correctly" + errorurl(16)); // check that atom IDs are valid diff --git a/src/read_restart.cpp b/src/read_restart.cpp index 615dd4b4b0..a7d16c55e2 100644 --- a/src/read_restart.cpp +++ b/src/read_restart.cpp @@ -441,7 +441,8 @@ void ReadRestart::command(int narg, char **arg) utils::logmesg(lmp," {} atoms\n",natoms); if (natoms != atom->natoms) - error->all(FLERR,"Did not assign all restart atoms correctly"); + error->all(FLERR, Error::NOLASTLINE, "Did not assign all restart atoms correctly" + +utils::errorurl(16)); if ((atom->molecular == Atom::TEMPLATE) && (me == 0)) { std::string mesg; diff --git a/src/replicate.cpp b/src/replicate.cpp index 15c477faa6..97a7569f64 100644 --- a/src/replicate.cpp +++ b/src/replicate.cpp @@ -404,7 +404,8 @@ void Replicate::command(int narg, char **arg) } if (natoms != atom->natoms) - error->all(FLERR,"Replicate did not assign all atoms correctly"); + error->all(FLERR, Error::NOLASTLINE, "Replicate did not assign all atoms correctly" + + utils::errorurl(16)); if (me == 0) { const char *molstyle = ""; From fd06c20a6a98376fb6a386804e9610c409003088 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 12 Mar 2025 22:58:33 -0400 Subject: [PATCH 084/113] fix copy-n-paste error --- src/read_data.cpp | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/read_data.cpp b/src/read_data.cpp index 02fd6ed7db..8d97b11243 100644 --- a/src/read_data.cpp +++ b/src/read_data.cpp @@ -1563,7 +1563,8 @@ void ReadData::atoms() if (me == 0) utils::logmesg(lmp, " {} atoms\n", nassign); - if (sum != atom->natoms) error->all(FLERR, "Did not assign all atoms correctly" + errorurl(16)); + if (sum != atom->natoms) + error->all(FLERR, "Did not assign all atoms correctly" + utils::errorurl(16)); // check that atom IDs are valid From a8924955752af8a9630a3c5bdb2f4022490f4008 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 13 Mar 2025 02:59:43 -0400 Subject: [PATCH 085/113] revert unintended commit --- tools/lammps-gui/org.lammps.lammps-gui.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tools/lammps-gui/org.lammps.lammps-gui.yml b/tools/lammps-gui/org.lammps.lammps-gui.yml index f88ea55bb2..a16ef5fdee 100644 --- a/tools/lammps-gui/org.lammps.lammps-gui.yml +++ b/tools/lammps-gui/org.lammps.lammps-gui.yml @@ -110,5 +110,5 @@ modules: - -D BUILD_WHAM=yes sources: - type: git - url: https://github.com/akohlmey/lammps.git - branch: collected-small-fixes + url: https://github.com/lammps/lammps.git + branch: release From 933f618eb4aaaa53922d35055d376f10f22c1fd6 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 13 Mar 2025 03:57:41 -0400 Subject: [PATCH 086/113] update .gitignore --- src/.gitignore | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/src/.gitignore b/src/.gitignore index 910a584354..a2f7da0400 100644 --- a/src/.gitignore +++ b/src/.gitignore @@ -1661,10 +1661,14 @@ /fix_pimd.h /fix_pimd_langevin.cpp /fix_pimd_langevin.h +/fix_pimd_langevin_bosonic.cpp +/fix_pimd_langevin_bosonic.h /fix_alchemy.cpp /fix_alchemy.h /fix_pimd_nvt.cpp /fix_pimd_nvt.h +/fix_pimd_nvt_bosonic.cpp +/fix_pimd_nvt_bosonic.h /fix_qbmsst.cpp /fix_qbmsst.h /fix_qtb.cpp From 71c8c2aaa2d2f4905f06d9bc2aa2e251d9cb5c17 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 13 Mar 2025 03:58:12 -0400 Subject: [PATCH 087/113] improve error messages --- src/REPLICA/fix_pimd_langevin.cpp | 85 ++++++++++++++++++------------- src/REPLICA/fix_pimd_nvt.cpp | 26 ++++++---- 2 files changed, 65 insertions(+), 46 deletions(-) diff --git a/src/REPLICA/fix_pimd_langevin.cpp b/src/REPLICA/fix_pimd_langevin.cpp index 037af71990..a7ca71e080 100644 --- a/src/REPLICA/fix_pimd_langevin.cpp +++ b/src/REPLICA/fix_pimd_langevin.cpp @@ -113,7 +113,8 @@ FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) : int seed = -1; - if (domain->dimension != 3) error->universe_all(FLERR, "Fix pimd/langevin requires a 3d system"); + if (domain->dimension != 3) + error->universe_all(FLERR, fmt::format("Fix {} requires a 3d system", style)); for (int i = 0; i < 6; i++) { p_flag[i] = 0; @@ -127,7 +128,7 @@ FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) : else if (strcmp(arg[i + 1], "pimd") == 0) method = PIMD; else - error->universe_all(FLERR, "Unknown method parameter for fix pimd/langevin"); + error->universe_all(FLERR, fmt::format("Unknown method parameter for fix {}", style)); } else if (strcmp(arg[i], "integrator") == 0) { if (strcmp(arg[i + 1], "obabo") == 0) integrator = OBABO; @@ -135,8 +136,9 @@ FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) : integrator = BAOAB; else error->universe_all(FLERR, - "Unknown integrator parameter for fix pimd/langevin. Only obabo and " - "baoab integrators are supported!"); + fmt::format("Unknown integrator parameter for fix {}. Only obabo and " + "baoab integrators are supported!", + style)); } else if (strcmp(arg[i], "ensemble") == 0) { if (strcmp(arg[i + 1], "nve") == 0) { ensemble = NVE; @@ -156,15 +158,16 @@ FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) : pstat_flag = 1; } else error->universe_all(FLERR, - "Unknown ensemble parameter for fix pimd/langevin. Only nve, nvt, nph, " - "and npt ensembles are supported!"); + fmt::format("Unknown ensemble parameter for fix {}. Only nve, nvt, " + "nph, and npt ensembles are supported!", + style)); } else if (strcmp(arg[i], "fmass") == 0) { fmass = utils::numeric(FLERR, arg[i + 1], false, lmp); if (fmass < 0.0 || fmass > np) - error->universe_all(FLERR, "Invalid fmass value for fix pimd/langevin"); + error->universe_all(FLERR, fmt::format("Invalid fmass value for fix {}", style)); } else if (strcmp(arg[i], "sp") == 0) { sp = utils::numeric(FLERR, arg[i + 1], false, lmp); - if (sp < 0.0) error->universe_all(FLERR, "Invalid sp value for fix pimd/langevin"); + if (sp < 0.0) error->universe_all(FLERR, fmt::format("Invalid sp value for fix {}", style)); } else if (strcmp(arg[i], "fmmode") == 0) { if (strcmp(arg[i + 1], "physical") == 0) fmmode = PHYSICAL; @@ -172,8 +175,9 @@ FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) : fmmode = NORMAL; else error->universe_all(FLERR, - "Unknown fictitious mass mode for fix pimd/langevin. Only physical " - "mass and normal mode mass are supported!"); + fmt::format("Unknown fictitious mass mode for fix {}. Only physical " + "mass and normal mode mass are supported!", + style)); } else if (strcmp(arg[i], "scale") == 0) { if (method == PIMD) error->universe_all( @@ -182,10 +186,11 @@ FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) : "scale parameter if you do want to use method pimd."); pilescale = utils::numeric(FLERR, arg[i + 1], false, lmp); if (pilescale < 0.0) - error->universe_all(FLERR, "Invalid PILE_L scale value for fix pimd/langevin"); + error->universe_all(FLERR, fmt::format("Invalid PILE_L scale value for fix {}", style)); } else if (strcmp(arg[i], "temp") == 0) { temp = utils::numeric(FLERR, arg[i + 1], false, lmp); - if (temp < 0.0) error->universe_all(FLERR, "Invalid temp value for fix pimd/langevin"); + if (temp < 0.0) + error->universe_all(FLERR, fmt::format("Invalid temp value for fix {}", style)); } else if (strcmp(arg[i], "lj") == 0) { lj_epsilon = utils::numeric(FLERR, arg[i + 1], false, lmp); lj_sigma = utils::numeric(FLERR, arg[i + 2], false, lmp); @@ -207,7 +212,7 @@ FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) : } else if (strcmp(arg[i + 1], "BZP") == 0) { barostat = BZP; } else - error->universe_all(FLERR, "Unknown barostat parameter for fix pimd/langevin"); + error->universe_all(FLERR, fmt::format("Unknown barostat parameter for fix {}", style)); } else if (strcmp(arg[i], "iso") == 0) { pstyle = ISO; p_flag[0] = p_flag[1] = p_flag[2] = 1; @@ -237,7 +242,8 @@ FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) : pdim++; } else if (strcmp(arg[i], "taup") == 0) { tau_p = utils::numeric(FLERR, arg[i + 1], false, lmp); - if (tau_p <= 0.0) error->universe_all(FLERR, "Invalid tau_p value for fix pimd/langevin"); + if (tau_p <= 0.0) + error->universe_all(FLERR, fmt::format("Invalid tau_p value for fix {}", style)); } else if (strcmp(arg[i], "fixcom") == 0) { if (strcmp(arg[i + 1], "yes") == 0) removecomflag = 1; @@ -403,6 +409,7 @@ FixPIMDLangevin::~FixPIMDLangevin() memory->destroy(tagsend); memory->destroy(tagrecv); memory->destroy(bufbeads); + MPI_Comm_free(&rootworld); } /* ---------------------------------------------------------------------- */ @@ -422,10 +429,10 @@ int FixPIMDLangevin::setmask() void FixPIMDLangevin::init() { if (atom->map_style == Atom::MAP_NONE) - error->all(FLERR, "Fix pimd/langevin requires an atom map, see atom_modify"); + error->all(FLERR, fmt::format("Fix {} requires an atom map, see atom_modify", style)); if (universe->me == 0 && universe->uscreen) - fprintf(universe->uscreen, "Fix pimd/langevin: initializing Path-Integral ...\n"); + utils::print(universe->uscreen, "Fix {}: initializing Path-Integral ...\n", style); // prepare the constants @@ -448,8 +455,8 @@ void FixPIMDLangevin::init() fbond = _fbond * force->mvv2e; if ((universe->me == 0) && (universe->uscreen)) - fprintf(universe->uscreen, - "Fix pimd/langevin: -P/(beta^2 * hbar^2) = %20.7lE (kcal/mol/A^2)\n\n", fbond); + utils::print(universe->uscreen, "Fix {}: -P/(beta^2 * hbar^2) = {:20.7e} (kcal/mol/A^2)\n\n", + style, fbond); if (integrator == OBABO) { dtf = 0.5 * update->dt * force->ftm2v; @@ -462,7 +469,7 @@ void FixPIMDLangevin::init() dtv2 = dtv * dtv; dtv3 = THIRD * dtv2 * dtv * force->ftm2v; } else { - error->universe_all(FLERR, "Unknown integrator parameter for fix pimd/langevin"); + error->universe_all(FLERR, fmt::format("Unknown integrator parameter for fix {}", style)); } comm_init(); @@ -525,7 +532,8 @@ void FixPIMDLangevin::setup(int vflag) } else { error->universe_all( FLERR, - "Unknown method parameter for fix pimd/langevin. Only nmpimd and pimd are supported!"); + fmt::format("Unknown method parameter for fix {}. Only nmpimd and pimd are supported!", + style)); } collect_xc(); compute_spring_energy(); @@ -587,7 +595,8 @@ void FixPIMDLangevin::initial_integrate(int /*vflag*/) } else { error->universe_all( FLERR, - "Unknown method parameter for fix pimd/langevin. Only nmpimd and pimd are supported!"); + fmt::format("Unknown method parameter for fix {}. Only nmpimd and pimd are supported!", + style)); } } else if (integrator == BAOAB) { if (pstat_flag) { @@ -609,7 +618,8 @@ void FixPIMDLangevin::initial_integrate(int /*vflag*/) } else { error->universe_all( FLERR, - "Unknown method parameter for fix pimd/langevin. Only nmpimd and pimd are supported!"); + fmt::format("Unknown method parameter for fix {}. Only nmpimd and pimd are supported!", + style)); } if (tstat_flag) { o_step(); @@ -624,12 +634,14 @@ void FixPIMDLangevin::initial_integrate(int /*vflag*/) } else { error->universe_all( FLERR, - "Unknown method parameter for fix pimd/langevin. Only nmpimd and pimd are supported!"); + fmt::format("Unknown method parameter for fix {}. Only nmpimd and pimd are supported!", + style)); } } else { error->universe_all(FLERR, - "Unknown integrator parameter for fix pimd/langevin. Only obabo and baoab " - "integrators are supported!"); + fmt::format("Unknown integrator parameter for fix {}. Only obabo and baoab " + "integrators are supported!", + style)); } collect_xc(); @@ -671,7 +683,7 @@ void FixPIMDLangevin::final_integrate() } else if (integrator == BAOAB) { } else { - error->universe_all(FLERR, "Unknown integrator parameter for fix pimd/langevin"); + error->universe_all(FLERR, fmt::format("Unknown integrator parameter for fix {}", style)); } } @@ -1045,8 +1057,9 @@ void FixPIMDLangevin::langevin_init() c1 = exp(-gamma * update->dt); else error->universe_all(FLERR, - "Unknown integrator parameter for fix pimd/langevin. Only obabo and " - "baoab integrators are supported!"); + fmt::format("Unknown integrator parameter for fix {}. Only obabo and baoab " + "integrators are supported!", + style)); c2 = sqrt(1.0 - c1 * c1); // note that c1 and c2 here only works for the centroid mode. @@ -1068,8 +1081,9 @@ void FixPIMDLangevin::langevin_init() c1_k[i] = exp(-1.0 * update->dt / tau_k[i]); else error->universe_all(FLERR, - "Unknown integrator parameter for fix pimd/langevin. Only obabo and " - "baoab integrators are supported!"); + fmt::format("Unknown integrator parameter for fix {}. Only obabo and " + "baoab integrators are supported!", + style)); c2_k[i] = sqrt(1.0 - c1_k[i] * c1_k[i]); } for (int i = 0; i < np; i++) { @@ -1420,7 +1434,9 @@ void FixPIMDLangevin::remove_com_motion() } } } else { - error->all(FLERR, "Unknown method for fix pimd/langevin. Only nmpimd and pimd are supported!"); + error->all( + FLERR, + fmt::format("Unknown method for fix {}. Only nmpimd and pimd are supported!", style)); } } @@ -1551,7 +1567,8 @@ void FixPIMDLangevin::compute_spring_energy() } else { error->universe_all( FLERR, - "Unknown method parameter for fix pimd/langevin. Only nmpimd and pimd are supported!"); + fmt::format("Unknown method parameter for fix {}. Only nmpimd and pimd are supported!", + style)); } } @@ -1613,9 +1630,7 @@ void FixPIMDLangevin::compute_p_cv() } else if (method == PIMD) { p_cv = THIRD * inv_volume * ((2.0 * totke / np - centroid_vir) * force->nktv2p + vir) / np; } else { - error->universe_all( - FLERR, - "Unknown method parameter for fix pimd/langevin. Only nmpimd and pimd are supported!"); + error->universe_all(FLERR, fmt::format("Unknown method parameter for fix {}. Only nmpimd and pimd are supported!", style)); } } diff --git a/src/REPLICA/fix_pimd_nvt.cpp b/src/REPLICA/fix_pimd_nvt.cpp index 09c2258c17..d11bc34337 100644 --- a/src/REPLICA/fix_pimd_nvt.cpp +++ b/src/REPLICA/fix_pimd_nvt.cpp @@ -89,26 +89,28 @@ FixPIMDNVT::FixPIMDNVT(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg) method = CMD; else error->universe_all( - FLERR, fmt::format("Unknown method parameter {} for fix pimd/nvt", arg[i + 1])); + FLERR, fmt::format("Unknown method parameter {} for fix {}", arg[i + 1], style)); } else if (strcmp(arg[i], "fmass") == 0) { fmass = utils::numeric(FLERR, arg[i + 1], false, lmp); if ((fmass < 0.0) || (fmass > np)) - error->universe_all(FLERR, fmt::format("Invalid fmass value {} for fix pimd/nvt", fmass)); + error->universe_all(FLERR, fmt::format("Invalid fmass value {} for fix {}", fmass, style)); } else if (strcmp(arg[i], "sp") == 0) { sp = utils::numeric(FLERR, arg[i + 1], false, lmp); - if (sp < 0.0) error->universe_all(FLERR, "Invalid sp value for fix pimd/nvt"); + if (sp < 0.0) error->universe_all(FLERR, fmt::format("Invalid sp value for fix {}", style)); } else if (strcmp(arg[i], "temp") == 0) { nhc_temp = utils::numeric(FLERR, arg[i + 1], false, lmp); - if (nhc_temp < 0.0) error->universe_all(FLERR, "Invalid temp value for fix pimd/nvt"); + if (nhc_temp < 0.0) + error->universe_all(FLERR, fmt::format("Invalid temp value for fix {}", style)); } else if (strcmp(arg[i], "nhc") == 0) { nhc_nchain = utils::inumeric(FLERR, arg[i + 1], false, lmp); - if (nhc_nchain < 2) error->universe_all(FLERR, "Invalid nhc value for fix pimd/nvt"); + if (nhc_nchain < 2) + error->universe_all(FLERR, fmt::format("Invalid nhc value for fix {}", style)); } else - error->universe_all(FLERR, fmt::format("Unknown keyword {} for fix pimd/nvt", arg[i])); + error->universe_all(FLERR, fmt::format("Unknown keyword {} for fix {}", arg[i], style)); } if (strcmp(update->unit_style, "lj") == 0) - error->all(FLERR, "Fix pimd/nvt does not support lj units"); + error->all(FLERR, fmt::format("Fix {} does not support lj units", style)); /* Initiation */ @@ -187,10 +189,10 @@ int FixPIMDNVT::setmask() void FixPIMDNVT::init() { if (atom->map_style == Atom::MAP_NONE) - error->universe_all(FLERR, "Fix pimd/nvt requires an atom map, see atom_modify"); + error->universe_all(FLERR, fmt::format("Fix {} requires an atom map, see atom_modify", style)); if (universe->me == 0 && universe->uscreen) - fprintf(universe->uscreen, "Fix pimd/nvt initializing Path-Integral ...\n"); + utils::print(universe->uscreen, "Fix {} initializing Path-Integral ...\n", style); // prepare the constants @@ -539,13 +541,15 @@ void FixPIMDNVT::nmpimd_transform(double **src, double **des, double *vector) /* ---------------------------------------------------------------------- */ -void FixPIMDNVT::pre_spring_force_estimators(){ +void FixPIMDNVT::pre_spring_force_estimators() +{ vir_estimator(); } /* ---------------------------------------------------------------------- */ -void FixPIMDNVT::vir_estimator() { +void FixPIMDNVT::vir_estimator() +{ double **x = atom->x; double **f = atom->f; int nlocal = atom->nlocal; From 0812d3c772f79dcabae67f61b2683a4fba78b028 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 13 Mar 2025 03:58:33 -0400 Subject: [PATCH 088/113] must use delete[] on array allocated with new --- src/REPLICA/fix_pimd_langevin_bosonic.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/REPLICA/fix_pimd_langevin_bosonic.cpp b/src/REPLICA/fix_pimd_langevin_bosonic.cpp index 140dd1afc5..2b554f67c3 100644 --- a/src/REPLICA/fix_pimd_langevin_bosonic.cpp +++ b/src/REPLICA/fix_pimd_langevin_bosonic.cpp @@ -98,7 +98,7 @@ FixPIMDBLangevin::~FixPIMDBLangevin() { memory->destroy(f_tag_order); for (int i = 0; i < filtered_narg; ++i) delete[] filtered_args[i]; - memory->destroy(filtered_args); + delete[] filtered_args; delete bosonic_exchange; } From 009a7b19163c2ff73188ad41e0576e264c038c95 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 13 Mar 2025 03:58:51 -0400 Subject: [PATCH 089/113] print detailed version string also for multi-replica runs --- src/lammps.cpp | 14 ++++++++++---- 1 file changed, 10 insertions(+), 4 deletions(-) diff --git a/src/lammps.cpp b/src/lammps.cpp index cecad6e870..575ef2575c 100644 --- a/src/lammps.cpp +++ b/src/lammps.cpp @@ -645,18 +645,24 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) : } // screen and logfile messages for universe and world + std::string update_string = UPDATE_STRING; + if (has_git_info() && ((update_string == " - Development") + || (update_string == " - Maintenance"))) + update_string += fmt::format(" - {}", git_descriptor()); if ((universe->me == 0) && (!helpflag)) { - constexpr char fmt[] = "LAMMPS ({})\nRunning on {} partitions of processors\n"; + + constexpr char fmt[] = "LAMMPS ({}{})\nRunning on {} partitions of processors\n"; if (universe->uscreen) - utils::print(universe->uscreen,fmt,version,universe->nworlds); + utils::print(universe->uscreen, fmt, version, update_string, universe->nworlds); if (universe->ulogfile) - utils::print(universe->ulogfile,fmt,version,universe->nworlds); + utils::print(universe->ulogfile, fmt, version, update_string, universe->nworlds); } if ((me == 0) && (!helpflag)) - utils::logmesg(this,"LAMMPS ({})\nProcessor partition = {}\n", version, universe->iworld); + utils::logmesg(this,"LAMMPS ({}{})\nProcessor partition = {}\n", version, + update_string, universe->iworld); } // check consistency of datatype settings in lmptype.h From 8c9e1fe6a2f7fb41ed0d1bd30e038cfcd408d6cc Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 13 Mar 2025 03:59:50 -0400 Subject: [PATCH 090/113] update pimd/*/bosonic examples --- .../harmonic_trap_langevin/log.13Mar2025.g++ | 2 ++ .../{log.lammps.0 => log.13Mar2025.g++.0} | 24 ++++++++++-------- .../{log.lammps.1 => log.13Mar2025.g++.1} | 24 ++++++++++-------- .../{log.lammps.2 => log.13Mar2025.g++.2} | 24 ++++++++++-------- .../{log.lammps.3 => log.13Mar2025.g++.3} | 24 ++++++++++-------- .../harmonic_trap_nvt/log.13Mar2025.g++ | 2 ++ .../{log.lammps.0 => log.13Mar2025.g++.0} | 25 ++++++++++--------- .../{log.lammps.1 => log.13Mar2025.g++.1} | 25 ++++++++++--------- .../{log.lammps.2 => log.13Mar2025.g++.2} | 25 ++++++++++--------- .../{log.lammps.3 => log.13Mar2025.g++.3} | 25 ++++++++++--------- 10 files changed, 108 insertions(+), 92 deletions(-) create mode 100644 examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/log.13Mar2025.g++ rename examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/{log.lammps.0 => log.13Mar2025.g++.0} (93%) rename examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/{log.lammps.1 => log.13Mar2025.g++.1} (92%) rename examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/{log.lammps.2 => log.13Mar2025.g++.2} (92%) rename examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/{log.lammps.3 => log.13Mar2025.g++.3} (92%) create mode 100644 examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/log.13Mar2025.g++ rename examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/{log.lammps.0 => log.13Mar2025.g++.0} (92%) rename examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/{log.lammps.1 => log.13Mar2025.g++.1} (92%) rename examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/{log.lammps.2 => log.13Mar2025.g++.2} (92%) rename examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/{log.lammps.3 => log.13Mar2025.g++.3} (92%) diff --git a/examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/log.13Mar2025.g++ b/examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/log.13Mar2025.g++ new file mode 100644 index 0000000000..3d91f7ea87 --- /dev/null +++ b/examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/log.13Mar2025.g++ @@ -0,0 +1,2 @@ +LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-344-g0a4a2f6deb-modified) +Running on 4 partitions of processors diff --git a/examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/log.lammps.0 b/examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/log.13Mar2025.g++.0 similarity index 93% rename from examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/log.lammps.0 rename to examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/log.13Mar2025.g++.0 index 2e5f1b0225..cb5c5c236a 100644 --- a/examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/log.lammps.0 +++ b/examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/log.13Mar2025.g++.0 @@ -1,5 +1,6 @@ -LAMMPS (4 Feb 2025) +LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-344-g0a4a2f6deb-modified) Processor partition = 0 + using 1 OpenMP thread(s) per MPI task # Units and dimensions units electron dimension 3 @@ -103,8 +104,8 @@ Initializing PI Langevin equation thermostat... 3 9.11206647e-03 5.00000000e+01 9.95012479e-01 9.97505201e-02 PILE_L thermostat successfully initialized! -WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2444) -WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:212) +WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2444) +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:212) Per MPI rank memory allocation (min/avg/max) = 2.801 | 2.801 | 2.801 Mbytes Step PotEng v_virial v_prim_kinetic 0 0 1.3661449e-08 0.0009918329 @@ -208,20 +209,20 @@ Per MPI rank memory allocation (min/avg/max) = 2.801 | 2.801 | 2.801 Mbytes 98 9.2042324e-06 1.780703e-05 0.00083221292 99 9.5058078e-06 1.8141862e-05 0.00082913227 100 9.8087647e-06 1.8457846e-05 0.00082619877 -Loop time of 0.122922 on 1 procs for 100 steps with 3 atoms +Loop time of 0.00116399 on 1 procs for 100 steps with 3 atoms -Performance: 35144210.362 fs/day, 0.000 hours/fs, 813.523 timesteps/s, 2.441 katom-step/s -70.1% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 3711359336.904 fs/day, 0.000 hours/fs, 85911.096 timesteps/s, 257.733 katom-step/s +89.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 1.1593e-05 | 1.1593e-05 | 1.1593e-05 | 0.0 | 0.01 -Comm | 9.2183e-05 | 9.2183e-05 | 9.2183e-05 | 0.0 | 0.07 -Output | 0.023243 | 0.023243 | 0.023243 | 0.0 | 18.91 -Modify | 0.099386 | 0.099386 | 0.099386 | 0.0 | 80.85 -Other | | 0.0001896 | | | 0.15 +Neigh | 1.292e-06 | 1.292e-06 | 1.292e-06 | 0.0 | 0.11 +Comm | 1.2305e-05 | 1.2305e-05 | 1.2305e-05 | 0.0 | 1.06 +Output | 0.00018105 | 0.00018105 | 0.00018105 | 0.0 | 15.55 +Modify | 0.00090255 | 0.00090255 | 0.00090255 | 0.0 | 77.54 +Other | | 6.68e-05 | | | 5.74 Nlocal: 3 ave 3 max 3 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -234,3 +235,4 @@ Total # of neighbors = 0 Ave neighs/atom = 0 Neighbor list builds = 33 Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/log.lammps.1 b/examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/log.13Mar2025.g++.1 similarity index 92% rename from examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/log.lammps.1 rename to examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/log.13Mar2025.g++.1 index a00ac90be8..a170220ef0 100644 --- a/examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/log.lammps.1 +++ b/examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/log.13Mar2025.g++.1 @@ -1,5 +1,6 @@ -LAMMPS (4 Feb 2025) +LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-344-g0a4a2f6deb-modified) Processor partition = 1 + using 1 OpenMP thread(s) per MPI task # Units and dimensions units electron dimension 3 @@ -95,8 +96,8 @@ thermo_style custom step pe v_virial v_prim_kinetic thermo 1 run 100 -WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2444) -WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:212) +WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2444) +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:212) Per MPI rank memory allocation (min/avg/max) = 2.801 | 2.801 | 2.801 Mbytes Step PotEng v_virial v_prim_kinetic 0 0 1.3661449e-08 0.0009918329 @@ -200,20 +201,20 @@ Per MPI rank memory allocation (min/avg/max) = 2.801 | 2.801 | 2.801 Mbytes 98 2.5769956e-05 1.780703e-05 0.00083221292 99 2.624134e-05 1.8141862e-05 0.00082913227 100 2.6731735e-05 1.8457846e-05 0.00082619877 -Loop time of 0.122878 on 1 procs for 100 steps with 3 atoms +Loop time of 0.0011782 on 1 procs for 100 steps with 3 atoms -Performance: 35156789.883 fs/day, 0.000 hours/fs, 813.815 timesteps/s, 2.441 katom-step/s -46.7% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 3666606971.137 fs/day, 0.000 hours/fs, 84875.161 timesteps/s, 254.625 katom-step/s +88.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 1.9787e-05 | 1.9787e-05 | 1.9787e-05 | 0.0 | 0.02 -Comm | 9.2033e-05 | 9.2033e-05 | 9.2033e-05 | 0.0 | 0.07 -Output | 0.0022584 | 0.0022584 | 0.0022584 | 0.0 | 1.84 -Modify | 0.12033 | 0.12033 | 0.12033 | 0.0 | 97.93 -Other | | 0.0001755 | | | 0.14 +Neigh | 1.773e-06 | 1.773e-06 | 1.773e-06 | 0.0 | 0.15 +Comm | 1.4979e-05 | 1.4979e-05 | 1.4979e-05 | 0.0 | 1.27 +Output | 0.00021888 | 0.00021888 | 0.00021888 | 0.0 | 18.58 +Modify | 0.00086503 | 0.00086503 | 0.00086503 | 0.0 | 73.42 +Other | | 7.754e-05 | | | 6.58 Nlocal: 3 ave 3 max 3 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -226,3 +227,4 @@ Total # of neighbors = 0 Ave neighs/atom = 0 Neighbor list builds = 44 Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/log.lammps.2 b/examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/log.13Mar2025.g++.2 similarity index 92% rename from examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/log.lammps.2 rename to examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/log.13Mar2025.g++.2 index 9cc0033c8a..cb5b5a1a95 100644 --- a/examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/log.lammps.2 +++ b/examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/log.13Mar2025.g++.2 @@ -1,5 +1,6 @@ -LAMMPS (4 Feb 2025) +LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-344-g0a4a2f6deb-modified) Processor partition = 2 + using 1 OpenMP thread(s) per MPI task # Units and dimensions units electron dimension 3 @@ -95,8 +96,8 @@ thermo_style custom step pe v_virial v_prim_kinetic thermo 1 run 100 -WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2444) -WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:212) +WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2444) +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:212) Per MPI rank memory allocation (min/avg/max) = 2.801 | 2.801 | 2.801 Mbytes Step PotEng v_virial v_prim_kinetic 0 0 1.3661449e-08 0.0009918329 @@ -200,20 +201,20 @@ Per MPI rank memory allocation (min/avg/max) = 2.801 | 2.801 | 2.801 Mbytes 98 1.8568337e-05 1.780703e-05 0.00083221292 99 1.9188379e-05 1.8141862e-05 0.00082913227 100 1.9789011e-05 1.8457846e-05 0.00082619877 -Loop time of 0.112003 on 1 procs for 100 steps with 3 atoms +Loop time of 0.00116163 on 1 procs for 100 steps with 3 atoms -Performance: 38570373.396 fs/day, 0.000 hours/fs, 892.833 timesteps/s, 2.678 katom-step/s -52.7% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 3718915419.639 fs/day, 0.000 hours/fs, 86086.005 timesteps/s, 258.258 katom-step/s +89.6% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 1.4356e-05 | 1.4356e-05 | 1.4356e-05 | 0.0 | 0.01 -Comm | 9.7936e-05 | 9.7936e-05 | 9.7936e-05 | 0.0 | 0.09 -Output | 0.0017373 | 0.0017373 | 0.0017373 | 0.0 | 1.55 -Modify | 0.10997 | 0.10997 | 0.10997 | 0.0 | 98.19 -Other | | 0.0001804 | | | 0.16 +Neigh | 1.582e-06 | 1.582e-06 | 1.582e-06 | 0.0 | 0.14 +Comm | 1.3306e-05 | 1.3306e-05 | 1.3306e-05 | 0.0 | 1.15 +Output | 0.00017996 | 0.00017996 | 0.00017996 | 0.0 | 15.49 +Modify | 0.00090771 | 0.00090771 | 0.00090771 | 0.0 | 78.14 +Other | | 5.907e-05 | | | 5.09 Nlocal: 3 ave 3 max 3 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -226,3 +227,4 @@ Total # of neighbors = 0 Ave neighs/atom = 0 Neighbor list builds = 41 Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/log.lammps.3 b/examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/log.13Mar2025.g++.3 similarity index 92% rename from examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/log.lammps.3 rename to examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/log.13Mar2025.g++.3 index 941334c25c..a587bfd3af 100644 --- a/examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/log.lammps.3 +++ b/examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/log.13Mar2025.g++.3 @@ -1,5 +1,6 @@ -LAMMPS (4 Feb 2025) +LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-344-g0a4a2f6deb-modified) Processor partition = 3 + using 1 OpenMP thread(s) per MPI task # Units and dimensions units electron dimension 3 @@ -95,8 +96,8 @@ thermo_style custom step pe v_virial v_prim_kinetic thermo 1 run 100 -WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2444) -WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:212) +WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2444) +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:212) Per MPI rank memory allocation (min/avg/max) = 2.801 | 2.801 | 2.801 Mbytes Step PotEng v_virial v_prim_kinetic 0 0 1.3661449e-08 0.0009918329 @@ -200,20 +201,20 @@ Per MPI rank memory allocation (min/avg/max) = 2.801 | 2.801 | 2.801 Mbytes 98 2.5288512e-05 1.780703e-05 0.00083221292 99 2.5384836e-05 1.8141862e-05 0.00082913227 100 2.5401412e-05 1.8457846e-05 0.00082619877 -Loop time of 0.122921 on 1 procs for 100 steps with 3 atoms +Loop time of 0.00116067 on 1 procs for 100 steps with 3 atoms -Performance: 35144393.915 fs/day, 0.000 hours/fs, 813.528 timesteps/s, 2.441 katom-step/s -88.8% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 3721997782.310 fs/day, 0.000 hours/fs, 86157.356 timesteps/s, 258.472 katom-step/s +88.3% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 1.5885e-05 | 1.5885e-05 | 1.5885e-05 | 0.0 | 0.01 -Comm | 9.4707e-05 | 9.4707e-05 | 9.4707e-05 | 0.0 | 0.08 -Output | 0.0027076 | 0.0027076 | 0.0027076 | 0.0 | 2.20 -Modify | 0.11993 | 0.11993 | 0.11993 | 0.0 | 97.57 -Other | | 0.0001738 | | | 0.14 +Neigh | 1.441e-06 | 1.441e-06 | 1.441e-06 | 0.0 | 0.12 +Comm | 1.2111e-05 | 1.2111e-05 | 1.2111e-05 | 0.0 | 1.04 +Output | 0.00018148 | 0.00018148 | 0.00018148 | 0.0 | 15.64 +Modify | 0.0009054 | 0.0009054 | 0.0009054 | 0.0 | 78.01 +Other | | 6.023e-05 | | | 5.19 Nlocal: 3 ave 3 max 3 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -226,3 +227,4 @@ Total # of neighbors = 0 Ave neighs/atom = 0 Neighbor list builds = 42 Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/log.13Mar2025.g++ b/examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/log.13Mar2025.g++ new file mode 100644 index 0000000000..3d91f7ea87 --- /dev/null +++ b/examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/log.13Mar2025.g++ @@ -0,0 +1,2 @@ +LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-344-g0a4a2f6deb-modified) +Running on 4 partitions of processors diff --git a/examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/log.lammps.0 b/examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/log.13Mar2025.g++.0 similarity index 92% rename from examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/log.lammps.0 rename to examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/log.13Mar2025.g++.0 index bf46982da6..460e1cf198 100644 --- a/examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/log.lammps.0 +++ b/examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/log.13Mar2025.g++.0 @@ -1,5 +1,6 @@ -LAMMPS (4 Feb 2025) +LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-344-g0a4a2f6deb-modified) Processor partition = 0 + using 1 OpenMP thread(s) per MPI task # Units and dimensions units electron dimension 3 @@ -99,11 +100,11 @@ thermo_style custom step pe v_virial v_prim_kinetic thermo 1 run 100 -WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) Fix pimd/nvt -P/(beta^2 * hbar^2) = -2.2139311e-05 (kcal/mol/A^2) -WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2444) -WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:212) +WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2444) +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:212) Per MPI rank memory allocation (min/avg/max) = 9.176 | 9.176 | 9.176 Mbytes Step PotEng v_virial v_prim_kinetic 0 0 0 0.00024794798 @@ -207,20 +208,20 @@ Per MPI rank memory allocation (min/avg/max) = 9.176 | 9.176 | 9.176 Mbytes 98 7.4842314e-06 1.8940408e-06 0.0002348915 99 7.622805e-06 1.9289045e-06 0.00023466684 100 7.76221e-06 1.9639756e-06 0.00023444136 -Loop time of 0.00940749 on 1 procs for 100 steps with 3 atoms +Loop time of 0.00193128 on 1 procs for 100 steps with 3 atoms -Performance: 459208566.791 fs/day, 0.000 hours/fs, 10629.828 timesteps/s, 31.889 katom-step/s -90.3% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 2236858456.568 fs/day, 0.000 hours/fs, 51779.131 timesteps/s, 155.337 katom-step/s +36.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 8.466e-06 | 8.466e-06 | 8.466e-06 | 0.0 | 0.09 -Comm | 7.8365e-05 | 7.8365e-05 | 7.8365e-05 | 0.0 | 0.83 -Output | 0.0012482 | 0.0012482 | 0.0012482 | 0.0 | 13.27 -Modify | 0.0079193 | 0.0079193 | 0.0079193 | 0.0 | 84.18 -Other | | 0.0001532 | | | 1.63 +Neigh | 1.454e-06 | 1.454e-06 | 1.454e-06 | 0.0 | 0.08 +Comm | 2.3033e-05 | 2.3033e-05 | 2.3033e-05 | 0.0 | 1.19 +Output | 0.00030824 | 0.00030824 | 0.00030824 | 0.0 | 15.96 +Modify | 0.001541 | 0.001541 | 0.001541 | 0.0 | 79.79 +Other | | 5.754e-05 | | | 2.98 Nlocal: 3 ave 3 max 3 min Histogram: 1 0 0 0 0 0 0 0 0 0 diff --git a/examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/log.lammps.1 b/examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/log.13Mar2025.g++.1 similarity index 92% rename from examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/log.lammps.1 rename to examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/log.13Mar2025.g++.1 index f129f10c09..7e01637f3d 100644 --- a/examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/log.lammps.1 +++ b/examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/log.13Mar2025.g++.1 @@ -1,5 +1,6 @@ -LAMMPS (4 Feb 2025) +LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-344-g0a4a2f6deb-modified) Processor partition = 1 + using 1 OpenMP thread(s) per MPI task # Units and dimensions units electron dimension 3 @@ -99,9 +100,9 @@ thermo_style custom step pe v_virial v_prim_kinetic thermo 1 run 100 -WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) -WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2444) -WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:212) +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2444) +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:212) Per MPI rank memory allocation (min/avg/max) = 9.176 | 9.176 | 9.176 Mbytes Step PotEng v_virial v_prim_kinetic 0 0 0 0.00024796164 @@ -205,20 +206,20 @@ Per MPI rank memory allocation (min/avg/max) = 9.176 | 9.176 | 9.176 Mbytes 98 7.3002707e-06 1.8531354e-06 0.00024148118 99 7.4315008e-06 1.88617e-06 0.00024137268 100 7.563358e-06 1.9193596e-06 0.00024126398 -Loop time of 0.00941353 on 1 procs for 100 steps with 3 atoms +Loop time of 0.00190888 on 1 procs for 100 steps with 3 atoms -Performance: 458913876.206 fs/day, 0.000 hours/fs, 10623.006 timesteps/s, 31.869 katom-step/s -50.9% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 2263110719.025 fs/day, 0.000 hours/fs, 52386.822 timesteps/s, 157.160 katom-step/s +0.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 8.215e-06 | 8.215e-06 | 8.215e-06 | 0.0 | 0.09 -Comm | 7.7692e-05 | 7.7692e-05 | 7.7692e-05 | 0.0 | 0.83 -Output | 0.0047662 | 0.0047662 | 0.0047662 | 0.0 | 50.63 -Modify | 0.004407 | 0.004407 | 0.004407 | 0.0 | 46.82 -Other | | 0.0001545 | | | 1.64 +Neigh | 2.774e-06 | 2.774e-06 | 2.774e-06 | 0.0 | 0.15 +Comm | 2.3215e-05 | 2.3215e-05 | 2.3215e-05 | 0.0 | 1.22 +Output | 0.00042246 | 0.00042246 | 0.00042246 | 0.0 | 22.13 +Modify | 0.0013744 | 0.0013744 | 0.0013744 | 0.0 | 72.00 +Other | | 8.601e-05 | | | 4.51 Nlocal: 3 ave 3 max 3 min Histogram: 1 0 0 0 0 0 0 0 0 0 diff --git a/examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/log.lammps.2 b/examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/log.13Mar2025.g++.2 similarity index 92% rename from examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/log.lammps.2 rename to examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/log.13Mar2025.g++.2 index 074acc9d50..9540baaf27 100644 --- a/examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/log.lammps.2 +++ b/examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/log.13Mar2025.g++.2 @@ -1,5 +1,6 @@ -LAMMPS (4 Feb 2025) +LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-344-g0a4a2f6deb-modified) Processor partition = 2 + using 1 OpenMP thread(s) per MPI task # Units and dimensions units electron dimension 3 @@ -99,9 +100,9 @@ thermo_style custom step pe v_virial v_prim_kinetic thermo 1 run 100 -WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) -WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2444) -WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:212) +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2444) +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:212) Per MPI rank memory allocation (min/avg/max) = 9.176 | 9.176 | 9.176 Mbytes Step PotEng v_virial v_prim_kinetic 0 0 0 0.00024796164 @@ -205,20 +206,20 @@ Per MPI rank memory allocation (min/avg/max) = 9.176 | 9.176 | 9.176 Mbytes 98 7.1356907e-06 1.7335027e-06 0.0002297417 99 7.2605738e-06 1.7643404e-06 0.00022943234 100 7.3859169e-06 1.7952968e-06 0.00022912226 -Loop time of 0.00941372 on 1 procs for 100 steps with 3 atoms +Loop time of 0.00195857 on 1 procs for 100 steps with 3 atoms -Performance: 458904516.311 fs/day, 0.000 hours/fs, 10622.790 timesteps/s, 31.868 katom-step/s -24.7% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 2205688634.372 fs/day, 0.000 hours/fs, 51057.607 timesteps/s, 153.173 katom-step/s +39.2% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 8.785e-06 | 8.785e-06 | 8.785e-06 | 0.0 | 0.09 -Comm | 7.9921e-05 | 7.9921e-05 | 7.9921e-05 | 0.0 | 0.85 -Output | 0.0071119 | 0.0071119 | 0.0071119 | 0.0 | 75.55 -Modify | 0.0020558 | 0.0020558 | 0.0020558 | 0.0 | 21.84 -Other | | 0.0001572 | | | 1.67 +Neigh | 1.602e-06 | 1.602e-06 | 1.602e-06 | 0.0 | 0.08 +Comm | 1.6951e-05 | 1.6951e-05 | 1.6951e-05 | 0.0 | 0.87 +Output | 0.00032627 | 0.00032627 | 0.00032627 | 0.0 | 16.66 +Modify | 0.0015486 | 0.0015486 | 0.0015486 | 0.0 | 79.07 +Other | | 6.514e-05 | | | 3.33 Nlocal: 3 ave 3 max 3 min Histogram: 1 0 0 0 0 0 0 0 0 0 diff --git a/examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/log.lammps.3 b/examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/log.13Mar2025.g++.3 similarity index 92% rename from examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/log.lammps.3 rename to examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/log.13Mar2025.g++.3 index edebd7096c..de7655776f 100644 --- a/examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/log.lammps.3 +++ b/examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/log.13Mar2025.g++.3 @@ -1,5 +1,6 @@ -LAMMPS (4 Feb 2025) +LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-344-g0a4a2f6deb-modified) Processor partition = 3 + using 1 OpenMP thread(s) per MPI task # Units and dimensions units electron dimension 3 @@ -99,9 +100,9 @@ thermo_style custom step pe v_virial v_prim_kinetic thermo 1 run 100 -WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) -WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2444) -WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:212) +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2444) +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:212) Per MPI rank memory allocation (min/avg/max) = 9.176 | 9.176 | 9.176 Mbytes Step PotEng v_virial v_prim_kinetic 0 0 0 0.00024796164 @@ -205,20 +206,20 @@ Per MPI rank memory allocation (min/avg/max) = 9.176 | 9.176 | 9.176 Mbytes 98 7.2937187e-06 1.8407787e-06 0.00023702765 99 7.4250201e-06 1.8736806e-06 0.00023685186 100 7.5569619e-06 1.9067398e-06 0.00023667607 -Loop time of 0.00939597 on 1 procs for 100 steps with 3 atoms +Loop time of 0.00197094 on 1 procs for 100 steps with 3 atoms -Performance: 459771778.655 fs/day, 0.000 hours/fs, 10642.865 timesteps/s, 31.929 katom-step/s -25.2% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 2191851993.165 fs/day, 0.000 hours/fs, 50737.315 timesteps/s, 152.212 katom-step/s +37.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 8.404e-06 | 8.404e-06 | 8.404e-06 | 0.0 | 0.09 -Comm | 8.6872e-05 | 8.6872e-05 | 8.6872e-05 | 0.0 | 0.92 -Output | 0.0071309 | 0.0071309 | 0.0071309 | 0.0 | 75.89 -Modify | 0.0020085 | 0.0020085 | 0.0020085 | 0.0 | 21.38 -Other | | 0.0001612 | | | 1.72 +Neigh | 1.652e-06 | 1.652e-06 | 1.652e-06 | 0.0 | 0.08 +Comm | 1.7965e-05 | 1.7965e-05 | 1.7965e-05 | 0.0 | 0.91 +Output | 0.00036011 | 0.00036011 | 0.00036011 | 0.0 | 18.27 +Modify | 0.0015231 | 0.0015231 | 0.0015231 | 0.0 | 77.28 +Other | | 6.806e-05 | | | 3.45 Nlocal: 3 ave 3 max 3 min Histogram: 1 0 0 0 0 0 0 0 0 0 From a1c0d93953c460963c7efdb528394abbf7c2a15c Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 13 Mar 2025 04:15:16 -0400 Subject: [PATCH 091/113] limit to 1 processor per partition --- src/REPLICA/fix_pimd_langevin_bosonic.cpp | 6 ++++-- src/REPLICA/fix_pimd_nvt_bosonic.cpp | 4 ++++ 2 files changed, 8 insertions(+), 2 deletions(-) diff --git a/src/REPLICA/fix_pimd_langevin_bosonic.cpp b/src/REPLICA/fix_pimd_langevin_bosonic.cpp index 2b554f67c3..77ac05636d 100644 --- a/src/REPLICA/fix_pimd_langevin_bosonic.cpp +++ b/src/REPLICA/fix_pimd_langevin_bosonic.cpp @@ -86,10 +86,12 @@ FixPIMDBLangevin::FixPIMDBLangevin(LAMMPS *lmp, int narg, char **arg) : } method = PIMD; - size_vector = 6; - memory->create(f_tag_order, nbosons, 3, "FixPIMDBLangevin:f_tag_order"); + + if (cmode != SINGLE_PROC) + error->universe_all(FLERR, + fmt::format("Fix {} only supports a single processor per bead", style)); } /* ---------------------------------------------------------------------- */ diff --git a/src/REPLICA/fix_pimd_nvt_bosonic.cpp b/src/REPLICA/fix_pimd_nvt_bosonic.cpp index 1458a4b72f..02b6ed014d 100644 --- a/src/REPLICA/fix_pimd_nvt_bosonic.cpp +++ b/src/REPLICA/fix_pimd_nvt_bosonic.cpp @@ -26,6 +26,7 @@ #include "bosonic_exchange.h" #include "atom.h" +#include "comm.h" #include "error.h" #include "force.h" #include "universe.h" @@ -46,6 +47,9 @@ FixPIMDBNVT::FixPIMDBNVT(LAMMPS *lmp, int narg, char **arg) : FixPIMDNVT(lmp, na error->universe_all(FLERR, "Method not supported in fix pimdb/nvt; only methods PIMD and NMPIMD"); } + if (comm->nprocs != 1) + error->universe_all(FLERR, + fmt::format("Fix {} only supports a single processor per bead", style)); } /* ---------------------------------------------------------------------- */ From b53449ff1047fc1d3c409b4aad44853da576b741 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 13 Mar 2025 04:15:41 -0400 Subject: [PATCH 092/113] free communicator only if not NULL --- src/REPLICA/fix_pimd_langevin.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/REPLICA/fix_pimd_langevin.cpp b/src/REPLICA/fix_pimd_langevin.cpp index a7ca71e080..b1ebc86aea 100644 --- a/src/REPLICA/fix_pimd_langevin.cpp +++ b/src/REPLICA/fix_pimd_langevin.cpp @@ -409,7 +409,7 @@ FixPIMDLangevin::~FixPIMDLangevin() memory->destroy(tagsend); memory->destroy(tagrecv); memory->destroy(bufbeads); - MPI_Comm_free(&rootworld); + if (rootworld != MPI_COMM_NULL) MPI_Comm_free(&rootworld); } /* ---------------------------------------------------------------------- */ From c449bed8145cc7d51b9bf09d77b6342a2fa4cb7f Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 13 Mar 2025 04:15:49 -0400 Subject: [PATCH 093/113] apply clang-format --- src/REPLICA/fix_pimd_langevin.cpp | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/src/REPLICA/fix_pimd_langevin.cpp b/src/REPLICA/fix_pimd_langevin.cpp index b1ebc86aea..6a18b48376 100644 --- a/src/REPLICA/fix_pimd_langevin.cpp +++ b/src/REPLICA/fix_pimd_langevin.cpp @@ -1568,7 +1568,7 @@ void FixPIMDLangevin::compute_spring_energy() error->universe_all( FLERR, fmt::format("Unknown method parameter for fix {}. Only nmpimd and pimd are supported!", - style)); + style)); } } @@ -1630,7 +1630,10 @@ void FixPIMDLangevin::compute_p_cv() } else if (method == PIMD) { p_cv = THIRD * inv_volume * ((2.0 * totke / np - centroid_vir) * force->nktv2p + vir) / np; } else { - error->universe_all(FLERR, fmt::format("Unknown method parameter for fix {}. Only nmpimd and pimd are supported!", style)); + error->universe_all( + FLERR, + fmt::format("Unknown method parameter for fix {}. Only nmpimd and pimd are supported!", + style)); } } From 0f10741f71bc2c8fdfca5add95199271065c6530 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 13 Mar 2025 04:38:58 -0400 Subject: [PATCH 094/113] update tests for variable commands --- src/variable.cpp | 18 +++++++++--------- unittest/commands/test_variables.cpp | 22 ++++++++++++---------- 2 files changed, 21 insertions(+), 19 deletions(-) diff --git a/src/variable.cpp b/src/variable.cpp index d34331a847..5ca3dbc2fb 100644 --- a/src/variable.cpp +++ b/src/variable.cpp @@ -333,7 +333,7 @@ void Variable::set(int narg, char **arg) int ivar = find(arg[0]); if (ivar >= 0) { if (style[ivar] != STRING) - error->all(FLERR, 1, "Cannot redefine variable {} as a different style", arg[0]); + error->all(FLERR, 1, "Cannot redefine variable {} with a different style", arg[0]); delete[] data[ivar][0]; copy(1, &scopy, data[ivar]); replaceflag = 1; @@ -359,7 +359,7 @@ void Variable::set(int narg, char **arg) utils::errorurl(3)); if (find(arg[0]) >= 0) { if (style[find(arg[0])] != GETENV) - error->all(FLERR, 1, "Cannot redefine variable {} as a different style", arg[0]); + error->all(FLERR, 1, "Cannot redefine variable {} with a different style", arg[0]); remove(find(arg[0])); } if (nvar == maxvar) grow(); @@ -431,7 +431,7 @@ void Variable::set(int narg, char **arg) error->all(FLERR, "Variable {}: format variable {} has incompatible style", arg[0], arg[2]); if (ivar >= 0) { if (style[ivar] != FORMAT) - error->all(FLERR, 1, "Cannot redefine variable {} as a different style", arg[0]); + error->all(FLERR, 1, "Cannot redefine variable {} with a different style", arg[0]); if (!utils::strmatch(arg[3], validfmt)) error->all(FLERR, "Incorrect conversion in format string"); delete[] data[ivar][0]; @@ -471,7 +471,7 @@ void Variable::set(int narg, char **arg) int ivar = find(arg[0]); if (ivar >= 0) { if (style[ivar] != EQUAL) - error->all(FLERR, 1, "Cannot redefine variable {} as a different style", arg[0]); + error->all(FLERR, 1, "Cannot redefine variable {} with a different style", arg[0]); delete[] data[ivar][0]; data[ivar][0] = utils::strdup(combined); replaceflag = 1; @@ -505,7 +505,7 @@ void Variable::set(int narg, char **arg) int ivar = find(arg[0]); if (ivar >= 0) { if (style[ivar] != ATOM) - error->all(FLERR, 1, "Cannot redefine variable {} as a different style", arg[0]); + error->all(FLERR, 1, "Cannot redefine variable {} with a different style", arg[0]); delete[] data[ivar][0]; data[ivar][0] = utils::strdup(combined); replaceflag = 1; @@ -539,7 +539,7 @@ void Variable::set(int narg, char **arg) int ivar = find(arg[0]); if (ivar >= 0) { if (style[ivar] != VECTOR) - error->all(FLERR, 1, "Cannot redefine variable {} as a different style", arg[0]); + error->all(FLERR, 1, "Cannot redefine variable {} with a different style", arg[0]); delete[] data[ivar][0]; delete[] data[ivar][1]; data[ivar][0] = utils::strdup(combined); @@ -584,7 +584,7 @@ void Variable::set(int narg, char **arg) int ivar = find(arg[0]); if (ivar >= 0) { if (style[ivar] != PYTHON) - error->all(FLERR, 1, "Cannot redefine variable {} as a different style", arg[0]); + error->all(FLERR, 1, "Cannot redefine variable {} with a different style", arg[0]); delete[] data[ivar][0]; data[ivar][0] = utils::strdup(arg[2]); replaceflag = 1; @@ -612,7 +612,7 @@ void Variable::set(int narg, char **arg) int ivar = find(arg[0]); if (ivar >= 0) { if (style[ivar] != TIMER) - error->all(FLERR, 1, "Cannot redefine variable {} as a different style", arg[0]); + error->all(FLERR, 1, "Cannot redefine variable {} with a different style", arg[0]); dvalue[ivar] = platform::walltime(); replaceflag = 1; } else { @@ -638,7 +638,7 @@ void Variable::set(int narg, char **arg) int ivar = find(arg[0]); if (ivar >= 0) { if (style[ivar] != INTERNAL) - error->all(FLERR, 1, "Cannot redefine variable {} as a different style", arg[0]); + error->all(FLERR, 1, "Cannot redefine variable {} with a different style", arg[0]); dvalue[nvar] = utils::numeric(FLERR, arg[2], false, lmp); replaceflag = 1; } else { diff --git a/unittest/commands/test_variables.cpp b/unittest/commands/test_variables.cpp index 0d8d28426c..d05e751a2f 100644 --- a/unittest/commands/test_variables.cpp +++ b/unittest/commands/test_variables.cpp @@ -207,19 +207,19 @@ TEST_F(VariableTest, CreateDelete) command("variable dummy loop -1");); TEST_FAILURE(".*ERROR: Illegal variable loop command.*", command("variable dummy loop 10 1");); TEST_FAILURE(".*ERROR: Unknown variable style: xxx.*", command("variable dummy xxxx");); - TEST_FAILURE(".*ERROR: Cannot redefine variable as a different style.*", + TEST_FAILURE(".*ERROR: Cannot redefine variable two with a different style.*", command("variable two string xxx");); - TEST_FAILURE(".*ERROR: Cannot redefine variable as a different style.*", + TEST_FAILURE(".*ERROR: Cannot redefine variable two with a different style.*", command("variable two getenv xxx");); - TEST_FAILURE(".*ERROR: Cannot redefine variable as a different style.*", + TEST_FAILURE(".*ERROR: Cannot redefine variable one with a different style.*", command("variable one equal 2");); - TEST_FAILURE(".*ERROR: Cannot redefine variable as a different style.*", + TEST_FAILURE(".*ERROR: Cannot redefine variable one with a different style.*", command("variable one internal 2");); TEST_FAILURE(".*ERROR: Cannot use atomfile-style variable unless an atom map exists.*", command("variable eleven atomfile test_variable.atomfile");); TEST_FAILURE(".*ERROR on proc 0: Cannot open file variable nine1 file test_variable.xxx.*", command("variable nine1 file test_variable.xxx");); - TEST_FAILURE(".*ERROR: World variable count doesn't match # of partitions.*", + TEST_FAILURE(".*ERROR: World variable count 2 doesn't match # of partitions.*", command("variable ten10 world xxx xxx");); TEST_FAILURE(".*ERROR: All universe/uloop variables must have same # of values.*", command("variable ten6 uloop 2");); @@ -291,9 +291,9 @@ TEST_F(VariableTest, AtomicSystem) ASSERT_DOUBLE_EQ(variable->compute_equal("1.5+3.25"), 4.75); ASSERT_DOUBLE_EQ(variable->compute_equal("-2.5*1.5"), -3.75); - TEST_FAILURE(".*ERROR: Cannot redefine variable as a different style.*", + TEST_FAILURE(".*ERROR: Cannot redefine variable one with a different style.*", command("variable one atom x");); - TEST_FAILURE(".*ERROR: Cannot redefine variable as a different style.*", + TEST_FAILURE(".*ERROR: Cannot redefine variable id with a different style.*", command("variable id vector f_press");); TEST_FAILURE(".*ERROR on proc 0: Cannot open atomfile variable ten1 file test_variable.xxx.*", command("variable ten1 atomfile test_variable.xxx");); @@ -341,7 +341,8 @@ TEST_F(VariableTest, Expressions) command("variable ten8 equal 1|^0"); command("variable ten9 equal v_one-v_ten9"); command("variable ten10 internal 100.0"); - command("variable ten11 equal (1 != 1)+(2 < 1)+(2<=1)+(1>2)+(1>=2)+(1&&0)+(0||0)+(1|^1)+10^0"); + command( + "variable ten11 equal (1 != 1)+(2 < 1)+(2<=1)+(1>2)+(1>=2)+(1&&0)+(0||0)+(1|^1)+10^0"); command("variable ten12 equal yes+no+on+off+true+false"); command("variable err1 equal v_one/v_ten7"); command("variable err2 equal v_one%v_ten7"); @@ -626,7 +627,8 @@ TEST_F(VariableTest, NextCommand) TEST_FAILURE(".*ERROR: Illegal next command.*", command("next");); TEST_FAILURE(".*ERROR: Invalid variable 'xxx' in next command.*", command("next xxx");); - TEST_FAILURE(".*ERROR: Invalid variable style with next command.*", command("next two");); + TEST_FAILURE(".*ERROR: Variable two has invalid style equal for next command.*", + command("next two");); TEST_FAILURE(".*ERROR: All variables in next command must have same style.*", command("next five four");); } @@ -792,7 +794,7 @@ TEST_F(VariableTest, Format) command("variable f1idx format yyy %8.4f");); TEST_FAILURE(".*ERROR: Variable f1three: format variable three does not exist.*", variable->retrieve("f1three");); - TEST_FAILURE(".*ERROR: Cannot redefine variable as a different style.*", + TEST_FAILURE(".*ERROR: Cannot redefine variable f2one with a different style.*", command("variable f2one equal 0.5");); TEST_FAILURE(".*ERROR: Illegal variable command.*", command("variable xxx format \"xxx\"");); TEST_FAILURE(".*ERROR: Incorrect conversion in format string.*", From 9d70c8b8ae979b06306052520defc85f04951e0e Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 13 Mar 2025 05:31:41 -0400 Subject: [PATCH 095/113] provide error information for two more cases --- doc/src/Errors_details.rst | 73 +++++++++++++++++++++++++++++++++--- src/REAXFF/reaxff_forces.cpp | 9 ++++- src/molecule.cpp | 8 ++-- src/utils.cpp | 8 ++-- 4 files changed, 82 insertions(+), 16 deletions(-) diff --git a/doc/src/Errors_details.rst b/doc/src/Errors_details.rst index d9b77cfe2a..a6028117e9 100644 --- a/doc/src/Errors_details.rst +++ b/doc/src/Errors_details.rst @@ -521,6 +521,47 @@ Most likely, one or more atoms have been blown out of the simulation box to a great distance or a fix (like fix deform or a barostat) has excessively grown the simulation box. +.. _err0018: + +Step X: (h)bondchk failed +------------------------- + +This error is a consequence of the heuristic memory allocations for +buffers of the regular ReaxFF version. In ReaxFF simulation the lists +of bonds and hydrogen bonds can change due to chemical reactions. The +default approach, however, assumes that these changes are not very +large, so it allocates buffers for the current system setup plus a +safety margin. This can be adjusted with the :doc:`safezone, mincap, +and minhbonds settings of pair style `, but only to some +extent. When equilibrating a new system, or simulating a sparse system +in parallel, this can be difficult to control and become wasteful. A +simple workaround is often to break a simulation down in multiple +chunks. A better approach, however, is to compile and use the KOKKOS +package version of ReaxFF (you don't need a GPU for that, but can also +compile it in serial or OpenMP mode), which uses are much more robust +memory allocation approach. + +.. _err0019: + +Numeric index X is out of bounds +-------------------------------- + +This error most commonly happens, when setting force field coefficients +with either the :doc:`pair_coeff `, the :doc:`bond_coeff +`, the :doc:`angle_coeff `, the +:doc:`dihedral_coeff `, or the :doc:`improper_coeff +` command. These commands accept type labels, +explicit numbers and wildcards for ranges of numbers. If the numeric +value of any of these is outside the valid range (defined by the number +of corresponding types), LAMMPS will stop with this error. Also +a few other commands and styles allow ranges of numbers and check +using the same method and thus print the same kind of error. + +The cause is almost always a typo in the input or a logic error +when defining the values or ranges. So one needs to carefully +review the input. Along with the error, LAMMPS will print the +valid range as a hint. + .. _err0020: Variable formula X is accessed out-of-range @@ -613,20 +654,40 @@ Another cause is requesting a quantity on a timestep that is not a thermo or dump output timestep. This can often be remedied by increasing the frequency of thermo or dump output. +.. _err0023: + +Molecule auto special bond generation overflow +---------------------------------------------- + +In order to correctly apply the :doc:`special_bonds ` +settings (also known as "exclusions"), LAMMPS needs to maintain for each +atom a list of atoms that are connected to this atom either with a bond +or are connected to a bonded atom. The purpose is to either remove or +tag those pairs of atoms in the neighbor list. This information is stored with individual +atoms and thus the maximum number of such "special" neighbors is set +when the simulation box is created. When reading (relative) geometry +and topology of a 'molecule' from a :doc:`molecule file `, +LAMMPS will build the list of such "special" for the molecule atom +(if not given in the molecule file explicitly). The error is triggered +when the resulting list is too long for the space reserved when +creating the simulation box. The solution is to increase the +corresponding setting. Overestimating this value will only consume +more memory, and is thus a safe choice. + .. _err0024: Molecule topology/atom exceeds system topology/atom --------------------------------------------------- -LAMMPS uses :doc:`domain decomposition ` to distribute data -(i.e. atoms) across the MPI processes in parallel runs. This includes topology -data, that is data about bonds, angles, dihedrals, impropers and :doc:`"special" -neighbors `. +LAMMPS uses :doc:`domain decomposition ` to +distribute data (i.e. atoms) across the MPI processes in parallel +runs. This includes topology data, that is data about bonds, angles, +dihedrals, impropers and :doc:`"special" neighbors `. This information is stored with either one or all atoms involved in such a topology entry (which of the two option applies depends on the :doc:`newton ` setting for bonds. When reading a data file, -LAMMPS analyzes the requirements for this file and then the values -are "locked in" and cannot be extended. +LAMMPS analyzes the requirements for this file and then the values are +"locked in" and cannot be extended. So loading a molecule file that requires more of the topology per atom storage or adding a data file with such needs will lead to an error. To diff --git a/src/REAXFF/reaxff_forces.cpp b/src/REAXFF/reaxff_forces.cpp index 274799c30c..26702bea05 100644 --- a/src/REAXFF/reaxff_forces.cpp +++ b/src/REAXFF/reaxff_forces.cpp @@ -31,6 +31,9 @@ #include #include "error.h" +#include "utils.h" + +using LAMMPS_NS::utils::errorurl; namespace ReaxFF { @@ -95,7 +98,8 @@ namespace ReaxFF { if (End_Index(i, bonds) > comp) system->error_ptr->one(FLERR, fmt::format("step {}: bondchk failed: " - "i={} end(i)={} str(i+1)={}\n", + "i={} end(i)={} str(i+1)={}\n" + + errorurl(18), step,i,End_Index(i,bonds),comp)); } } @@ -117,7 +121,8 @@ namespace ReaxFF { if (End_Index(Hindex, hbonds) > comp) system->error_ptr->one(FLERR, fmt::format("step {}: hbondchk failed: " - "H={} end(H)={} str(H+1)={}\n", + "H={} end(H)={} str(H+1)={}\n" + + errorurl(18), step, Hindex,End_Index(Hindex,hbonds),comp)); } } diff --git a/src/molecule.cpp b/src/molecule.cpp index ab793ab534..318e2a1e0f 100644 --- a/src/molecule.cpp +++ b/src/molecule.cpp @@ -1554,7 +1554,7 @@ void Molecule::special_generate() nspecial[i][0]++; nspecial[atom2][0]++; if (count[i] >= atom->maxspecial || count[atom2] >= atom->maxspecial) - error->all(FLERR, fileiarg, "Molecule auto special bond generation overflow"); + error->all(FLERR, fileiarg, "Molecule auto special bond generation overflow" + utils::errorurl(23)); tmpspecial[i][count[i]++] = atom2 + 1; tmpspecial[atom2][count[atom2]++] = i + 1; } @@ -1566,7 +1566,7 @@ void Molecule::special_generate() atom1 = i; atom2 = bond_atom[i][j]; if (count[atom1] >= atom->maxspecial) - error->all(FLERR, fileiarg, "Molecule auto special bond generation overflow"); + error->all(FLERR, fileiarg, "Molecule auto special bond generation overflow" + utils::errorurl(23)); tmpspecial[i][count[atom1]++] = atom2; } } @@ -1589,7 +1589,7 @@ void Molecule::special_generate() } if (!dedup) { if (count[i] >= atom->maxspecial) - error->all(FLERR, fileiarg, "Molecule auto special bond generation overflow"); + error->all(FLERR, fileiarg, "Molecule auto special bond generation overflow" + utils::errorurl(23)); tmpspecial[i][count[i]++] = tmpspecial[tmpspecial[i][m] - 1][j]; nspecial[i][1]++; } @@ -1613,7 +1613,7 @@ void Molecule::special_generate() } if (!dedup) { if (count[i] >= atom->maxspecial) - error->all(FLERR, fileiarg, "Molecule auto special bond generation overflow"); + error->all(FLERR, fileiarg, "Molecule auto special bond generation overflow" + utils::errorurl(23)); tmpspecial[i][count[i]++] = tmpspecial[tmpspecial[i][m] - 1][j]; nspecial[i][2]++; } diff --git a/src/utils.cpp b/src/utils.cpp index 74c615fd04..8ab757ac44 100644 --- a/src/utils.cpp +++ b/src/utils.cpp @@ -807,13 +807,13 @@ void utils::bounds(const char *file, int line, const std::string &str, if (error) { if ((nlo <= 0) || (nhi <= 0)) error->all(file, line, failed, "Invalid range string: {}", str); - + constexpr char fmt[] = "Numeric index {} is out of bounds ({}-{}){}"; if (nlo < nmin) - error->all(file, line, failed, "Numeric index {} is out of bounds ({}-{})", nlo, nmin, nmax); + error->all(file, line, failed, fmt, nlo, nmin, nmax, errorurl(19)); else if (nhi > nmax) - error->all(file, line, failed, "Numeric index {} is out of bounds ({}-{})", nhi, nmin, nmax); + error->all(file, line, failed, fmt, nhi, nmin, nmax, errorurl(19)); else if (nlo > nhi) - error->all(file, line, failed, "Numeric index {} is out of bounds ({}-{})", nlo, nmin, nhi); + error->all(file, line, failed, fmt, nlo, nmin, nhi, errorurl(19)); } } From bfdfd322df510ac85b32f3d48b148cd36406d53d Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 13 Mar 2025 05:41:32 -0400 Subject: [PATCH 096/113] make compatible with C++20 and later --- src/REAXFF/reaxff_forces.cpp | 14 ++++++-------- 1 file changed, 6 insertions(+), 8 deletions(-) diff --git a/src/REAXFF/reaxff_forces.cpp b/src/REAXFF/reaxff_forces.cpp index 26702bea05..a12779fd1b 100644 --- a/src/REAXFF/reaxff_forces.cpp +++ b/src/REAXFF/reaxff_forces.cpp @@ -97,10 +97,9 @@ namespace ReaxFF { else comp = bonds->num_intrs; if (End_Index(i, bonds) > comp) - system->error_ptr->one(FLERR, fmt::format("step {}: bondchk failed: " - "i={} end(i)={} str(i+1)={}\n" - + errorurl(18), - step,i,End_Index(i,bonds),comp)); + system->error_ptr->one(FLERR, fmt::format("step {}: bondchk failed: i={} end(i)={} " + "str(i+1)={}{}", step, i ,End_Index(i,bonds), + comp, errorurl(18))); } } @@ -120,10 +119,9 @@ namespace ReaxFF { else comp = hbonds->num_intrs; if (End_Index(Hindex, hbonds) > comp) - system->error_ptr->one(FLERR, fmt::format("step {}: hbondchk failed: " - "H={} end(H)={} str(H+1)={}\n" - + errorurl(18), - step, Hindex,End_Index(Hindex,hbonds),comp)); + system->error_ptr->one(FLERR, fmt::format("step {}: hbondchk failed: H={} end(H)={} " + "str(H+1)={}{}", step, Hindex, + End_Index(Hindex,hbonds),comp,errorurl(18))); } } } From 889f91763f119a61aa3ccc4471700bf2a8cd8c1f Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 13 Mar 2025 09:36:58 -0400 Subject: [PATCH 097/113] explain image flag related errors and warnings --- doc/src/Errors_details.rst | 37 +++++++++++++++++++++++++++++++++++++ src/domain.cpp | 12 +++++++----- 2 files changed, 44 insertions(+), 5 deletions(-) diff --git a/doc/src/Errors_details.rst b/doc/src/Errors_details.rst index a6028117e9..8248ecdd10 100644 --- a/doc/src/Errors_details.rst +++ b/doc/src/Errors_details.rst @@ -476,6 +476,21 @@ Users with harder-to-track variable errors might also find reading :doc:`Section 5.2. Parsing rules for input scripts` helpful. +.. _err0014: + +Bond atom missing in image check or box size check +-------------------------------------------------- + +This can be either an error or a warning depending on your +:doc:`thermo_modify settings `. It is flagged in a part +of the LAMMPS code where it updates the domain decomposition and before +it builds the neighbor lists. It checks that both atoms of a bond are +within the communication cutoff of a subdomain. It is usually caused by +atoms moving too fast (see the :ref:`paragraph on fast moving atoms +`), or by the :doc:`communication cutoff being too +small `, or by waiting too long for doing :doc:`sub-domain +and neighbor list updates `. + .. _err0015: Cannot use neighbor bins - box size \<\< cutoff @@ -726,6 +741,28 @@ atom type. Thus it would not be required to have a Masses section and the included data would be ignored. LAMMPS prints this warning to inform about this case. +.. _err0027: + +Inconsistent image flags +------------------------ + +This warning happens when the distance between the *unwrapped* x-, y-, +or z-components of the coordinates of a bond is larger than half the box +with periodic boundaries or larger than the box with non-periodic +boundaries. It means that the positions and image flags have become +inconsistent. LAMMPS will still compute bonded interactions based on +the closest periodic images of the atoms and thus in most cases the +results will be correct. Nevertheless, it is good practice to update +the system so that the message does not appear. It will help with +future manipulations of the system. + +There is one case where this warning *must* appear: when you have a +chain of connected bonds that pass through the entire box and connect +back to the first atom in the chain through periodic boundaries, +i.e. some kind of "infinite polymer". In that case, the bond image +flags *must* be inconsistent for the one bond that reaches back to the +beginning of the chain. + .. _err0028: diff --git a/src/domain.cpp b/src/domain.cpp index 0b1bbf2c77..31350482bd 100644 --- a/src/domain.cpp +++ b/src/domain.cpp @@ -1028,7 +1028,8 @@ void Domain::image_check() if (k == -1) { nmissing++; if (lostbond == Thermo::ERROR) - error->one(FLERR,"Bond atom missing in image check"); + error->one(FLERR, Error::NOLASTLINE, + "Bond atom missing in image check" + utils::errorurl(14)); continue; } @@ -1048,13 +1049,13 @@ void Domain::image_check() int flagall; MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_MAX,world); if (flagall && comm->me == 0) - error->warning(FLERR,"Inconsistent image flags"); + error->warning(FLERR,"Inconsistent image flags" + utils::errorurl(27)); if (lostbond == Thermo::WARN) { int all; MPI_Allreduce(&nmissing,&all,1,MPI_INT,MPI_SUM,world); if (all && comm->me == 0) - error->warning(FLERR,"Bond atom missing in image check"); + error->warning(FLERR, "Bond atom missing in image check" + utils::errorurl(14)); } memory->destroy(unwrap); @@ -1127,7 +1128,8 @@ void Domain::box_too_small_check() if (k == -1) { nmissing++; if (lostbond == Thermo::ERROR) - error->one(FLERR,"Bond atom missing in box size check"); + error->one(FLERR, Error::NOLASTLINE, + "Bond atom missing in box size check" + utils::errorurl(14)); continue; } @@ -1144,7 +1146,7 @@ void Domain::box_too_small_check() int all; MPI_Allreduce(&nmissing,&all,1,MPI_INT,MPI_SUM,world); if (all && comm->me == 0) - error->warning(FLERR,"Bond atom missing in box size check"); + error->warning(FLERR,"Bond atom missing in box size check" + utils::errorurl(14)); } double maxbondall; From 34b3dd9ebd4c5bd1088091862f5f8deea6359965 Mon Sep 17 00:00:00 2001 From: jtclemm Date: Thu, 13 Mar 2025 11:34:09 -0600 Subject: [PATCH 098/113] Proofreading errors doc page --- doc/src/Errors_details.rst | 223 +++++++++++++++++++------------------ 1 file changed, 113 insertions(+), 110 deletions(-) diff --git a/doc/src/Errors_details.rst b/doc/src/Errors_details.rst index 8248ecdd10..ade66823d2 100644 --- a/doc/src/Errors_details.rst +++ b/doc/src/Errors_details.rst @@ -65,7 +65,7 @@ memory address is computed from an incorrect index, a memory buffer is used after it has been freed, some general memory corruption. When investigating a segmentation fault (aka segfault), it is important to determine which process is causing it; it may not always be LAMMPS. For -example, some MPI library implementation report a segmentation fault +example, some MPI library implementations report a segmentation fault from their "mpirun" or "mpiexec" command when the application has been terminated unexpectedly. @@ -75,13 +75,13 @@ simulation settings. For time critical code paths, LAMMPS will assume the user has chosen the settings carefully and will not make any checks to avoid to avoid performance penalties. -A crucial step in resolving segmentation faults is to identify the exact -location in the code where this happens. Please see `Errors_debug` for +A crucial step in resolving a segmentation fault is to identify the exact +location in the code where it happens. Please see `Errors_debug` for a couple of examples showing how to do this on a Linux machine. With -this information, a simple way to reproduce the segmentation fault, and -the information about the :doc:`exact LAMMPS version ` -and platform you are running on, you can contact the LAMMPS developers -or post in the LAMMPS forum to get assistance. +this information -- a simple way to reproduce the segmentation fault and +the exact :doc:`LAMMPS version ` and platform you are +running on -- you can contact the LAMMPS developers or post in the LAMMPS +forum to get assistance. .. _hint05: @@ -91,10 +91,10 @@ Fast moving atoms Fast moving atoms may be "lost" or "missing" when their velocity becomes so large that they can cross a sub-domain within one timestep. This often happens when atoms are too close, but atoms may also "move" too -fast from sub-domain to sub-domain if the box changes rapidly, e.g. when +fast from sub-domain to sub-domain if the box changes rapidly. E.g. when setting a large an initial box with :doc:`shrink-wrap boundary conditions ` that collapses on the first step (in this case -the solution is often using 'm' instead of 's' as boundary condition). +the solution is often using 'm' instead of 's' as a boundary condition). To reduce the impact of "close contacts", one can remove those atoms or molecules with something like :doc:`delete_atoms overlap 0.1 all all @@ -104,13 +104,14 @@ to first run a minimization (aka quench) before starting the MD. Reducing the time step can also help. Many times, one just needs to "ease" the system into a balanced state and can then switch to more aggressive settings. -The speed of atoms during an MD depends on the steepness of the +The speed of atoms during an MD run depends on the steepness of the potential function and their mass. Since the positions and velocities -of atoms are computed with finite timesteps, they choice of timestep can -be too large for a stable numeric integration of the trajectory. In -those cases using (temporarily) :doc:`fix nve/limit ` or -:doc:`fix dt/reset ` can help to avoid too large updates -or adapt the timestep according to the displacements. +of atoms are computed with finite timesteps, the timestep needs to be +small enough for stable numeric integration of the trajectory. If the timestep +is too large during initialization (or other instances of extreme dynamics), +using :doc:`fix nve/limit ` or :doc:`fix dt/reset ` +temporarily can help to avoid too large updates or adapt the timestep according +to the displacements. .. _hint06: @@ -118,9 +119,9 @@ Ignoring lost atoms ^^^^^^^^^^^^^^^^^^^ It is tempting to use the :doc:`thermo_modify lost ignore ` -to avoid that LAMMPS stops with an error on lost atoms. This setting should, however, -*only* be used when atoms *should* leave the system. In general, ignoring -a problem does not solve it. +to avoid LAMMPS aborting with an error on lost atoms. This setting should, +however, *only* be used when atoms *should* leave the system. In general, +ignoring a problem does not solve it. .. _hint07: @@ -148,14 +149,14 @@ Communication cutoff The communication cutoff determines the "overlap" between sub-domains and atoms in these regions are referred to in LAMMPS as "ghost atoms". This region has to be large enough to contain all atoms of a bond, -angle, dihedral or improper with just one atom in the actual sub-domain. +angle, dihedral, or improper with just one atom in the actual sub-domain. Typically, this cutoff is set to the largest cutoff from the :doc:`pair style(s) ` plus the :doc:`neighbor list skin distance -` and will be more than sufficient for all bonded -interactions. But if the pair style cutoff is small this may not be +` and will typically be sufficient for all bonded +interactions. But if the pair style cutoff is small, this may not be enough. LAMMPS will print a warning in this case using some heuristic -based on the equilibrium bond length, but that may not be sufficient for -cases where the force constants are small and thus bonds may be +based on the equilibrium bond length, but that still may not be sufficient +for cases where the force constants are small and thus bonds may be stretched very far. The communication cutoff can be adjusted with :doc:`comm_modify cutoff \ `, but setting this too large will waste CPU time and memory. @@ -190,7 +191,7 @@ are parameterized for other settings, most notably :doc:`ReaxFF potentials ` that use "real" units. Also, individual parameters for :doc:`pair_coeff ` commands -taken from publications or other MD software, may need to be converted +taken from publications or other MD software may need to be converted and sometimes in unexpected ways. Thus some careful checking is recommended. @@ -199,16 +200,16 @@ recommended. No error message printed ^^^^^^^^^^^^^^^^^^^^^^^^ -In some cases - especially when running in parallel with MPI - LAMMPS -may stop without displaying an error. But that does not mean, that -there was no error message, instead it is highly likely that the message -was written to a buffer and LAMMPS was aborted before the buffer was -output. Usually, output buffers are output for every line of output, -but sometimes, this is delayed until 4096 or 8192 bytes of output have -been accumulated. This buffering for screen and logfile output can be -disabled by using the :ref:`-nb or -nonbuf ` command-line flag. -This is most often needed when debugging crashing multi-replica -calculations. +In some cases -- especially when running in parallel with MPI -- LAMMPS +may stop without displaying an error. But the fact that nothing was +displayed does not mean there was not an error message. Instead it is +highly likely that the message was written to a buffer and LAMMPS was +aborted before the buffer was output. Usually, output buffers are output +for every line of output, but sometimes this is delayed until 4096 or +8192 bytes of output have been accumulated. This buffering for screen +and logfile output can be disabled by using the :ref:`-nb or -nonbuf +` command-line flag. This is most often needed when debugging +crashing multi-replica calculations. .. _hint12: @@ -227,11 +228,11 @@ defined. Very few commands can be used before and after, like Most LAMMPS commands must be used after the simulation box is created. Consequently, LAMMPS will stop with an error, if a command is used in -the wrong place. This is not always obvious. So you can expand an index -or string style :doc:`variable ` anywhere in the input, but -equal style (or similar) variables only, if they do not reference -anything that is only allowed after the box is defined (e.g. a compute -reference or fix reference, or a thermo keyword). +the wrong place. This is not always obvious. So index or string style +:doc:`variables ` can be expanded anywhere in the input, but +equal style (or similar) variables can only be expanded before the box +is defined if they do not reference anything that cannot be defined +before the box (e.g. a compute or fix reference or a thermo keyword). ------ @@ -261,8 +262,8 @@ treated as a comment. Another possibility to trigger this error is to have a keyword in the data file that corresponds to a fix (e.g. :doc:`fix cmap `) but the :doc:`read_data ` command is missing the (optional) -arguments that identify the fix and the header keyword and section -keyword or those arguments are inconsistent with the keywords in the +arguments that identify the fix and its header and section keywords. +Alternatively, those arguments are inconsistent with the keywords in the data file. .. _err0002: @@ -272,63 +273,61 @@ Incorrect format in ... section of data file This error happens when LAMMPS reads the contents of a section of a :doc:`data file ` and the number of parameters in the line -differs from what is expected. This most commonly happens, when the +differs from what is expected. This most commonly happens when the atom style is different from what is expected for a specific data file since changing the atom style usually changes the format of the line. -This error can also happen when the number of entries indicated in the +This error can also occur when the number of entries indicated in the header of a data file (e.g. the number of atoms) is larger than the number of lines provided (e.g. in the corresponding Atoms section) -and then LAMMPS will continue reading into the next section and that -would have a completely different format. +causing LAMMPS to continue reading into the next section which has +a completely different format. .. _err0003: Illegal variable command: expected X arguments but found Y ---------------------------------------------------------- -This error indicates that there are the wrong number of arguments for a -specific variable command, but a common reason for that is a variable -expression that has whitespace but is not enclosed in single or double -quotes. +This error indicates that a variable command has the wrong number of +arguments. A common reason for this is that the variable expression +has whitespace, but is not enclosed in single or double quotes. To explain, the LAMMPS input parser reads and processes lines. The resulting line is broken down into "words". Those are usually -individual commands, labels, names, values separated by whitespace (a +individual commands, labels, names, and values separated by whitespace (a space or tab character). For "words" that may contain whitespace, they have to be enclosed in single (') or double (") quotes. The parser will -then remove the outermost pair of quotes and then pass that string as +then remove the outermost pair of quotes and pass that string as "word" to the variable command. -Thus missing quotes or accidental extra whitespace will lead to the -error shown in the header because the unquoted whitespace will result -in the text being broken into more "words", i.e. the variable expression -being split. +Thus missing quotes or accidental extra whitespace will trigger this +error because the unquoted whitespace will result in the text being broken +into more "words", i.e. the variable expression being split. .. _err0004: Out of range atoms - cannot compute ... --------------------------------------- -The PPPM (and also PPPMDisp and MSM) methods require to assemble a grid +The PPPM (and also PPPMDisp and MSM) methods need to assemble a grid of electron density data derived from the (partial) charges assigned to -the atoms. This charges are smeared out across multiple grid points +the atoms. These charges are smeared out across multiple grid points (see :doc:`kspace_modify order `). When running in parallel with MPI, LAMMPS uses a :doc:`domain decomposition scheme ` where each processor manages a subset of atoms and -thus also a grid representing the density, which covers the actual -volume of the sub-domain and some extra space corresponding to the +thus also a grid representing the density. The processor's grid covers the +actual volume of the sub-domain and some extra space corresponding to the :doc:`neighbor list skin `. These are then :doc:`combined and redistributed ` for parallel processing of the long-range component of the Coulomb interaction. -The ``Out of range atoms`` error can happen, when atoms move too fast or -the neighbor list skin is too small or the neighbor lists are not -updated frequently enough. Then the smeared charges cannot be fully +The ``Out of range atoms`` error can happen when atoms move too fast, +the neighbor list skin is too small, or the neighbor lists are not +updated frequently enough. The smeared charges cannot then be fully assigned to the density grid for all atoms. LAMMPS checks for this condition and stops with an error. Most of the time, this is an -indication of a system with very high forces, most often at the -beginning of a simulation or when boundary conditions are changed. The +indication of a system with very high forces, often at the beginning +of a simulation or when boundary conditions are changed. The error becomes more likely with more MPI processes. There are multiple options to explore for avoiding the error. The best @@ -336,9 +335,9 @@ choice depends strongly on the individual system, and often a combination of changes is required. For example, more conservative MD parameter settings can be used (larger neighbor skin, shorter time step, more frequent neighbor list updates). Sometimes, it helps to revisit -the system generation and avoid close contacts when building it, or use -the :doc:`delete_atoms overlap` command to delete those -close contact atoms, or run a minimization before the MD. It can also +the system generation and avoid close contacts when building it. Otherwise +one can use the :doc:`delete_atoms overlap` command to delete +those close contact atoms or run a minimization before the MD. It can also help to temporarily use a cutoff-Coulomb pair style and no kspace style until the system has somewhat equilibrated and then switch to the long-range solver. @@ -352,17 +351,21 @@ The second atom needed to compute a particular bond (or the third or fourth atom for angle, dihedral, or improper) is missing on the indicated timestep and processor. Typically, this is because the two bonded atoms have become too far apart relative to the communication cutoff distance for ghost atoms. -Typically, the communication cutoff is set by the pair cutoff, but it can -be manually adjusted using :doc:`comm_modify ` to accommodate -larger distances between topologically connected atoms at the cost of increased -communication and more ghost atoms. However, missing bond atoms may also -indicate unstable dynamics caused the atoms blow apart such that increasing -the communication distance will not solve the underlying issue. +By default, the communication cutoff is set by the pair cutoff. However, to +accommodate larger distances between topologically connected atoms, it can +be manually adjusted using :doc:`comm_modify ` at the cost of +increased communication and more ghost atoms. However, missing bond atoms +may also indicate that there are unstable dynamics which caused the atoms +to blow apart. In this scenario, increasing the communication distance will +not solve the underlying issue. Rather, see :ref:`Fast moving atoms ` +and :ref:`Neighbor list settings ` in the general troubleshooting +section above for ideas to fix unstable dynamics. -If the simulation has open boundary conditions where atoms can leave, -potentially at different times than other atoms they are bonded to, this -error can be converted to a warning or turned off using the *lost/bond* -keyword in the :doc:`thermo_modify ` command. +If atoms are intended to be lost during a simulation (e.g. due to open boundary +conditions or :doc:`fix evaporate `) such that two bonded atoms +may be lost at different times from each other, this error can be converted to a +warning or turned off using the *lost/bond* keyword in the :doc:`thermo_modify +` command. .. _err0006: @@ -419,7 +422,7 @@ Unrecognized pair style ... is part of ... package which is not enabled in this The LAMMPS executable (binary) being used was not compiled with a package containing the specified pair style. This indicates that the executable needs to be re-built after enabling the correct package in the relevant Makefile or CMake -build directory, see :doc:`Section 3. Build LAMMPS ` for more details. +build directory. See :doc:`Section 3. Build LAMMPS ` for more details. One can check if the expected package and pair style is present in the executable by running it with the ``-help`` (or ``-h``) flag on the command line. One common oversight, especially for beginner LAMMPS users, is to enable @@ -452,9 +455,9 @@ Substitution for illegal variable A variable in an input script or a variable expression was not found in the list of valid variables. The most common reason for this is a typo -somewhere in the input file and the expression uses an invalid variable -name. The second most common reason is to omit the curly braces for a -direct variable with a name that is not a single letter. Example: +somewhere in the input file such that the expression uses an invalid variable +name. The second most common reason is omitting the curly braces for a +direct variable with a name that is not a single letter. For example: .. code-block:: LAMMPS @@ -466,11 +469,10 @@ direct variable with a name that is not a single letter. Example: Another potential source of this error may be invalid command line variables (-var or -v argument) used when launching LAMMPS from an interactive shell or shell scripts. An uncommon source for this error -is the :doc:`next command `: with an index style variable -definition a list of values can be provided and LAMMPS will advance to -the next in the list with the :doc:`next command`. If there is no -remaining element in the list, LAMMPS will delete the variable and any -following expansion or reference attempt with trigger the error. +is using the :doc:`next command ` to advance through a list of values +provided by an index style variable. If there is no remaining element in +the list, LAMMPS will delete the variable and any following expansion or +reference attempt will trigger the error. Users with harder-to-track variable errors might also find reading :doc:`Section 5.2. Parsing rules for input scripts` @@ -488,7 +490,7 @@ it builds the neighbor lists. It checks that both atoms of a bond are within the communication cutoff of a subdomain. It is usually caused by atoms moving too fast (see the :ref:`paragraph on fast moving atoms `), or by the :doc:`communication cutoff being too -small `, or by waiting too long for doing :doc:`sub-domain +small `, or by waiting too long between :doc:`sub-domain and neighbor list updates `. .. _err0015: @@ -510,7 +512,7 @@ smallest box lengths. Did not assign all atoms correctly ---------------------------------- -This error happens most commonly, when :doc:`reading a data file ` +This error happens most commonly when :doc:`reading a data file ` under :doc:`non-periodic boundary conditions`. Only atoms with positions **inside** the simulation box will be read and thus any atoms outside the box will be skipped and the total atom count will not match, @@ -520,7 +522,7 @@ the principal box and their image flags set accordingly. Similar errors can happen with the :doc:`replicate command` or the :doc:`read_restart command`. In these cases the cause -may be a problematic geometry, an insufficient communication cutoff or +may be a problematic geometry, an insufficient communication cutoff, or a bug in the LAMMPS source code. In these cases it is advisable to set up :ref:`small test case ` for testing and debugging. This will be required in case you need to get help from a LAMMPS developer. @@ -531,9 +533,9 @@ Domain too large for neighbor bins ---------------------------------- The domain has become extremely large so that neighbor bins cannot -be used. Too many neighbor bins would need to be created to fill space -Most likely, one or more atoms have been blown out of the simulation -box to a great distance or a fix (like fix deform or a barostat) has +be used. Too many neighbor bins would need to be created to fill space. +Most likely, one or more atoms have been blown a great distance out of +the simulation box or a fix (like fix deform or a barostat) has excessively grown the simulation box. .. _err0018: @@ -542,18 +544,18 @@ Step X: (h)bondchk failed ------------------------- This error is a consequence of the heuristic memory allocations for -buffers of the regular ReaxFF version. In ReaxFF simulation the lists +buffers of the regular ReaxFF version. In ReaxFF simulations, the lists of bonds and hydrogen bonds can change due to chemical reactions. The default approach, however, assumes that these changes are not very large, so it allocates buffers for the current system setup plus a safety margin. This can be adjusted with the :doc:`safezone, mincap, -and minhbonds settings of pair style `, but only to some +and minhbonds settings of the pair style `, but only to some extent. When equilibrating a new system, or simulating a sparse system in parallel, this can be difficult to control and become wasteful. A simple workaround is often to break a simulation down in multiple chunks. A better approach, however, is to compile and use the KOKKOS -package version of ReaxFF (you don't need a GPU for that, but can also -compile it in serial or OpenMP mode), which uses are much more robust +package version of ReaxFF (you do not need a GPU for that, but can also +compile it in serial or OpenMP mode), which uses a more robust memory allocation approach. .. _err0019: @@ -561,15 +563,15 @@ memory allocation approach. Numeric index X is out of bounds -------------------------------- -This error most commonly happens, when setting force field coefficients +This error most commonly happens when setting force field coefficients with either the :doc:`pair_coeff `, the :doc:`bond_coeff `, the :doc:`angle_coeff `, the :doc:`dihedral_coeff `, or the :doc:`improper_coeff ` command. These commands accept type labels, -explicit numbers and wildcards for ranges of numbers. If the numeric +explicit numbers, and wildcards for ranges of numbers. If the numeric value of any of these is outside the valid range (defined by the number -of corresponding types), LAMMPS will stop with this error. Also -a few other commands and styles allow ranges of numbers and check +of corresponding types), LAMMPS will stop with this error. A few other +commands and styles also allow ranges of numbers and check using the same method and thus print the same kind of error. The cause is almost always a typo in the input or a logic error @@ -583,7 +585,7 @@ Variable formula X is accessed out-of-range ------------------------------------------- When accessing an individual element of a global vector or array provided -by a compute or fix, or data from a specific atom, and index in square +by a compute or fix or data from a specific atom, an index in square brackets ("[ ]") must be provided and must be in a valid range. While LAMMPS is written in C++ these indices start at 1 (i.e. similar to Fortran), so any value smaller than 1 will trigger this error. But also too large @@ -592,7 +594,7 @@ the number of rows or columns can change or in simulations where the number of atoms changes. Since this kind of error frequently happens with rather complex expressions, it is recommended to test these with small test systems, where the values can be tracked with output files -for all relevant properties for every step. +for all relevant properties at every step. .. _err0021: @@ -604,8 +606,8 @@ The parameters in the :doc:`pair_coeff ` command for a specified applies when seeing this error for :doc:`bond_coeff `, :doc:`angle_coeff `, :doc:`dihedral_coeff `, or :doc:`improper_coeff ` and their respective style commands when -using the MOLECULE or EXTRA-MOLECULE packages. The cases below will describe -some ways to approach pair coefficient errors, but the same strategies will +using the MOLECULE or EXTRA-MOLECULE packages. The cases below describe +some ways to approach pair coefficient errors, but the same strategies apply to bonded systems as well. Outside of normal typos, this error can have several sources. In all cases, the @@ -676,13 +678,14 @@ Molecule auto special bond generation overflow In order to correctly apply the :doc:`special_bonds ` settings (also known as "exclusions"), LAMMPS needs to maintain for each -atom a list of atoms that are connected to this atom either with a bond -or are connected to a bonded atom. The purpose is to either remove or -tag those pairs of atoms in the neighbor list. This information is stored with individual +atom a list of atoms that are connected to this atom, either directly with +a bond or indirectly through bonding with an intermediate atom(s). The purpose +is to either remove or tag those pairs of atoms in the neighbor list. This +information is stored with individual atoms and thus the maximum number of such "special" neighbors is set when the simulation box is created. When reading (relative) geometry and topology of a 'molecule' from a :doc:`molecule file `, -LAMMPS will build the list of such "special" for the molecule atom +LAMMPS will build the list of such "special" neighbors for the molecule atom (if not given in the molecule file explicitly). The error is triggered when the resulting list is too long for the space reserved when creating the simulation box. The solution is to increase the @@ -696,11 +699,11 @@ Molecule topology/atom exceeds system topology/atom LAMMPS uses :doc:`domain decomposition ` to distribute data (i.e. atoms) across the MPI processes in parallel -runs. This includes topology data, that is data about bonds, angles, +runs. This includes topology data about bonds, angles, dihedrals, impropers and :doc:`"special" neighbors `. This information is stored with either one or all atoms involved in such a topology entry (which of the two option applies depends on the -:doc:`newton ` setting for bonds. When reading a data file, +:doc:`newton ` setting for bonds). When reading a data file, LAMMPS analyzes the requirements for this file and then the values are "locked in" and cannot be extended. From bf1a5e05fdc938d98b3e35574a3577df297d3b2b Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 13 Mar 2025 18:11:18 -0400 Subject: [PATCH 099/113] correctly flag out-of-range access for thermo data, where possible --- doc/src/Errors_details.rst | 32 +++++---- src/thermo.cpp | 143 +++++++++++++++++++++++-------------- 2 files changed, 110 insertions(+), 65 deletions(-) diff --git a/doc/src/Errors_details.rst b/doc/src/Errors_details.rst index ade66823d2..99081c2525 100644 --- a/doc/src/Errors_details.rst +++ b/doc/src/Errors_details.rst @@ -581,20 +581,26 @@ valid range as a hint. .. _err0020: -Variable formula X is accessed out-of-range -------------------------------------------- +Compute, fix, or variable is accessed out-of-range +-------------------------------------------------- -When accessing an individual element of a global vector or array provided -by a compute or fix or data from a specific atom, an index in square -brackets ("[ ]") must be provided and must be in a valid range. While -LAMMPS is written in C++ these indices start at 1 (i.e. similar to Fortran), -so any value smaller than 1 will trigger this error. But also too large -values can cause this error, specifically for computes or fixes where -the number of rows or columns can change or in simulations where the -number of atoms changes. Since this kind of error frequently happens -with rather complex expressions, it is recommended to test these with -small test systems, where the values can be tracked with output files -for all relevant properties at every step. +When accessing an individual element of a global vector or array or a +per-atom vector or array provided by a compute or fix or atom-style or +vector-style variable or data from a specific atom, an index in square +brackets ("[ ]") (or two indices) must be provided to determine which +element to access and it must be in a valid range or else LAMMPS would +access invalid data or crash with a segmentation fault. In the two most +common cases, where this data is accessed, :doc:`variable expressions +` and :doc:`thermodynamic output `, LAMMPS will +check for valid indices and stop with an error otherwise. + +While LAMMPS is written in C++ (which uses 0 based indexing) these +indices start at 1 (i.e. similar to Fortran). Any index smaller than 1 +or larger than the maximum allowed value should trigger this error. +Since this kind of error frequently happens with rather complex +expressions, it is recommended to test these with small test systems, +where the values can be tracked with output files for all relevant +properties at every step. .. _err0021: diff --git a/src/thermo.cpp b/src/thermo.cpp index f6c7ec7c0e..7e934ed985 100644 --- a/src/thermo.cpp +++ b/src/thermo.cpp @@ -1078,10 +1078,10 @@ void Thermo::parse_fields(const std::string &str) if ((argi.get_type() == ArgInfo::UNKNOWN) || (argi.get_type() == ArgInfo::NONE) || (argi.get_dim() > 2)) - error->all(FLERR, "Unknown keyword '{}' in thermo_style custom command", word); + error->all(FLERR, nfield + 1, "Unknown keyword '{}' in thermo_style custom command", word); // process zero or one or two trailing brackets - // argindex1,argindex2 = int inside each bracket pair, 0 if no bracket + // argindex1,argindex2 = int inside each bracket pair argindex1[nfield] = argi.get_index1(); argindex2[nfield] = (argi.get_dim() > 1) ? argi.get_index2() : 0; @@ -1089,63 +1089,99 @@ void Thermo::parse_fields(const std::string &str) if (argi.get_type() == ArgInfo::COMPUTE) { auto icompute = modify->get_compute_by_id(argi.get_name()); if (!icompute) - error->all(FLERR, "Could not find thermo custom compute ID: {}", argi.get_name()); - if (argindex1[nfield] == 0 && icompute->scalar_flag == 0) - error->all(FLERR, "Thermo compute does not compute scalar"); - if (argindex1[nfield] > 0 && argindex2[nfield] == 0) { - if (icompute->vector_flag == 0) - error->all(FLERR, "Thermo compute does not compute vector"); - if (argindex1[nfield] > icompute->size_vector && icompute->size_vector_variable == 0) - error->all(FLERR, "Thermo compute vector is accessed out-of-range"); - } - if (argindex1[nfield] > 0 && argindex2[nfield] > 0) { - if (icompute->array_flag == 0) error->all(FLERR, "Thermo compute does not compute array"); - if (argindex1[nfield] > icompute->size_array_rows && - icompute->size_array_rows_variable == 0) - error->all(FLERR, "Thermo compute array is accessed out-of-range"); - if (argindex2[nfield] > icompute->size_array_cols) - error->all(FLERR, "Thermo compute array is accessed out-of-range"); - } + error->all(FLERR, nfield + 1, "Could not find thermo custom compute ID: {}", + icompute->id); + if (argi.get_dim() == 0) { // scalar + if (icompute->scalar_flag == 0) + error->all(FLERR, nfield + 1, "Thermo custom compute {} does not compute a scalar", + icompute->id); + field2index[nfield] = add_compute(icompute->id, SCALAR); - if (argindex1[nfield] == 0) - field2index[nfield] = add_compute(argi.get_name(), SCALAR); - else if (argindex2[nfield] == 0) - field2index[nfield] = add_compute(argi.get_name(), VECTOR); - else - field2index[nfield] = add_compute(argi.get_name(), ARRAY); + } else if (argi.get_dim() == 1) { // vector + if (icompute->vector_flag == 0) + error->all(FLERR, nfield + 1, "Thermo custom compute {} does not compute a vector", + icompute->id); + if ((argindex1[nfield] < 1) || + ((icompute->size_vector_variable == 0) && argindex1[nfield] > icompute->size_vector)) + error->all(FLERR, nfield + 1, + "Thermo custom compute {} vector is accessed out-of-range{}", + icompute->id,utils::errorurl(20)); + field2index[nfield] = add_compute(icompute->id, VECTOR); + + } else if (argi.get_dim() == 2) { // array + if (icompute->array_flag == 0) + error->all(FLERR, nfield + 1, "Thermo custom compute {} does not compute an array", + icompute->id); + if ((argindex1[nfield] < 1) || (argindex2[nfield] < 1) || + ((icompute->size_array_rows_variable == 0) && + (argindex1[nfield] > icompute->size_array_rows)) || + (argindex2[nfield] > icompute->size_array_cols)) + error->all(FLERR, nfield + 1, + "Thermo custom compute {} array is accessed out-of-range{}", + icompute->id, utils::errorurl(20)); + field2index[nfield] = add_compute(icompute->id, ARRAY); + + } else { + error->all(FLERR, nfield + 1, "Thermo custom compute {} has unsupported format", + icompute->id); + } addfield(word.c_str(), &Thermo::compute_compute, FLOAT); } else if (argi.get_type() == ArgInfo::FIX) { auto ifix = modify->get_fix_by_id(argi.get_name()); - if (!ifix) error->all(FLERR, "Could not find thermo custom fix ID: {}", argi.get_name()); - if (argindex1[nfield] == 0 && ifix->scalar_flag == 0) - error->all(FLERR, "Thermo fix does not compute scalar"); - if (argindex1[nfield] > 0 && argindex2[nfield] == 0) { - if (ifix->vector_flag == 0) error->all(FLERR, "Thermo fix does not compute vector"); - if (argindex1[nfield] > ifix->size_vector && ifix->size_vector_variable == 0) - error->all(FLERR, "Thermo fix vector is accessed out-of-range"); - } - if (argindex1[nfield] > 0 && argindex2[nfield] > 0) { - if (ifix->array_flag == 0) error->all(FLERR, "Thermo fix does not compute array"); - if (argindex1[nfield] > ifix->size_array_rows && ifix->size_array_rows_variable == 0) - error->all(FLERR, "Thermo fix array is accessed out-of-range"); - if (argindex2[nfield] > ifix->size_array_cols) - error->all(FLERR, "Thermo fix array is accessed out-of-range"); + if (!ifix) error->all(FLERR, nfield + 1, "Could not find thermo custom fix ID: {}", + ifix->id); + if (argi.get_dim() == 0) { // scalar + if (ifix->scalar_flag == 0) + error->all(FLERR, nfield + 1, "Thermo custom fix {} does not compute a scalar", + ifix->id); + + } else if (argi.get_dim() == 1) { // vector + if (ifix->vector_flag == 0) + error->all(FLERR, nfield + 1, "Thermo custom fix {} does not compute a vector", + ifix->id); + if ((argindex1[nfield] < 1) || + ((ifix->size_vector_variable == 0) && (argindex1[nfield] > ifix->size_vector))) + error->all(FLERR, nfield + 1, "Thermo custom fix {} vector is accessed out-of-range{}", + ifix->id, utils::errorurl(20)); + + } else if (argi.get_dim() == 2) { // array + if (ifix->array_flag == 0) + error->all(FLERR, nfield + 1, "Thermo custom fix {} does not compute an array", + ifix->id); + if ((argindex1[nfield] < 1) || (argindex2[nfield] < 1) + || ((ifix->size_array_rows_variable == 0) && + (argindex1[nfield] > ifix->size_array_rows)) + || (argindex2[nfield] > ifix->size_array_cols)) + error->all(FLERR, nfield + 1, "Thermo custom fix {} array is accessed out-of-range{}", + ifix->id, utils::errorurl(20)); + } else { + error->all(FLERR, nfield + 1, "Thermo custom fix {} has unsupported format", ifix->id); } - field2index[nfield] = add_fix(argi.get_name()); + field2index[nfield] = add_fix(ifix->id); addfield(word.c_str(), &Thermo::compute_fix, FLOAT); } else if (argi.get_type() == ArgInfo::VARIABLE) { int n = input->variable->find(argi.get_name()); if (n < 0) - error->all(FLERR, "Could not find thermo custom variable name: {}", argi.get_name()); - if (argindex1[nfield] == 0 && input->variable->equalstyle(n) == 0) - error->all(FLERR, "Thermo custom variable is not equal-style variable"); - if (argindex1[nfield] && input->variable->vectorstyle(n) == 0) - error->all(FLERR, "Thermo custom variable is not vector-style variable"); - if (argindex2[nfield]) error->all(FLERR, "Thermo custom variable cannot have two indices"); - + error->all(FLERR, nfield + 1, "Could not find thermo custom variable name: {}", + argi.get_name()); + if (argi.get_dim() == 0) { + if (input->variable->equalstyle(n) == 0) + error->all(FLERR, nfield + 1, + "Thermo custom variable {} is not an equal-style variable", argi.get_name()); + } else if (argi.get_dim() == 1) { + if (input->variable->vectorstyle(n) == 0) + error->all(FLERR, nfield + 1, + "Thermo custom variable {} is not a vector-style variable", argi.get_name()); + } else if (argi.get_dim() == 2) { + error->all(FLERR, nfield + 1, "Thermo custom variable {} cannot have two indices", + argi.get_name()); + } else { + error->all(FLERR, nfield + 1, + "Thermo custom variable {} has unsupported format", argi.get_name()); + } field2index[nfield] = add_variable(argi.get_name()); addfield(word.c_str(), &Thermo::compute_variable, FLOAT); } @@ -1632,14 +1668,16 @@ void Thermo::compute_compute() int m = field2index[ifield]; Compute *compute = computes[m]; - // check for out-of-range access if vector/array is variable length + // check for upper out-of-range access if vector/array is variable length + // we already checked for other conditions when the thermo style was defined. if (compute_which[m] == SCALAR) { dvalue = compute->scalar; if (normflag && compute->extscalar) dvalue /= natoms; } else if (compute_which[m] == VECTOR) { - if (compute->size_vector_variable && argindex1[ifield] > compute->size_vector) - error->all(FLERR, "Thermo compute vector is accessed out-of-range"); + if (compute->size_vector_variable && (argindex1[ifield] > compute->size_vector)) + error->all(FLERR, Error::NOLASTLINE, + "Thermo compute vector is accessed out-of-range" + utils::errorurl(20)); dvalue = compute->vector[argindex1[ifield] - 1]; if (normflag) { if (compute->extvector == 0) @@ -1650,8 +1688,9 @@ void Thermo::compute_compute() dvalue /= natoms; } } else { - if (compute->size_array_rows_variable && argindex1[ifield] > compute->size_array_rows) - error->all(FLERR, "Thermo compute array is accessed out-of-range"); + if (compute->size_array_rows_variable && (argindex1[ifield] > compute->size_array_rows)) + error->all(FLERR, Error::NOLASTLINE, + "Thermo compute array is accessed out-of-range" + utils::errorurl(20)); dvalue = compute->array[argindex1[ifield] - 1][argindex2[ifield] - 1]; if (normflag && compute->extarray) dvalue /= natoms; } From 9da8a7f73a82b64a5c303cf89e7acc076d917d15 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 13 Mar 2025 22:05:44 -0400 Subject: [PATCH 100/113] improve error pointers and out-of-range message for dump custom --- doc/src/Errors_details.rst | 4 +- src/VTK/dump_vtk.cpp | 3 +- src/dump_custom.cpp | 169 ++++++++++++++++++++++--------------- 3 files changed, 105 insertions(+), 71 deletions(-) diff --git a/doc/src/Errors_details.rst b/doc/src/Errors_details.rst index 99081c2525..5aa24d74c8 100644 --- a/doc/src/Errors_details.rst +++ b/doc/src/Errors_details.rst @@ -581,8 +581,8 @@ valid range as a hint. .. _err0020: -Compute, fix, or variable is accessed out-of-range --------------------------------------------------- +Compute, fix, or variable vector or array is accessed out-of-range +------------------------------------------------------------------ When accessing an individual element of a global vector or array or a per-atom vector or array provided by a compute or fix or atom-style or diff --git a/src/VTK/dump_vtk.cpp b/src/VTK/dump_vtk.cpp index 634eea2264..b59ec5beba 100644 --- a/src/VTK/dump_vtk.cpp +++ b/src/VTK/dump_vtk.cpp @@ -1783,7 +1783,8 @@ int DumpVTK::parse_fields(int narg, char **arg) if (argi.get_dim() > 0 && icompute->size_peratom_cols == 0) error->all(FLERR,"Dump vtk compute {} does not calculate per-atom array",aname); if (argi.get_dim() > 0 && argi.get_index1() > icompute->size_peratom_cols) - error->all(FLERR,"Dump vtk compute {} vector is accessed out-of-range",aname); + error->all(FLERR,"Dump vtk compute {} vector is accessed out-of-range{}", + aname, utils::errorurl(20)); field2index[ATTRIBUTES+iarg] = add_compute(aname); name[ATTRIBUTES+iarg] = arg[iarg]; } diff --git a/src/dump_custom.cpp b/src/dump_custom.cpp index dd53511e09..5c86b390ac 100644 --- a/src/dump_custom.cpp +++ b/src/dump_custom.cpp @@ -1429,11 +1429,16 @@ void DumpCustom::write_lines(int n, double *mybuf) int DumpCustom::parse_fields(int narg, char **arg) { + // determine offset in list of arguments for error pointer. + int argoff = 0; + while (input && input->arg[argoff] && (strcmp(input->arg[argoff], arg[0]) != 0)) argoff++; + // customize by adding to if statement has_id = 0; for (int iarg = 0; iarg < narg; iarg++) { + int errptr = iarg + argoff; if (strcmp(arg[iarg],"id") == 0) { pack_choice[iarg] = &DumpCustom::pack_id; if (sizeof(tagint) == sizeof(smallint)) vtype[iarg] = Dump::INT; @@ -1441,7 +1446,7 @@ int DumpCustom::parse_fields(int narg, char **arg) has_id = 1; } else if (strcmp(arg[iarg],"mol") == 0) { if (!atom->molecule_flag) - error->all(FLERR,"Dumping an atom property that isn't allocated"); + error->all(FLERR, errptr, "Dumping an atom property that isn't allocated"); pack_choice[iarg] = &DumpCustom::pack_molecule; if (sizeof(tagint) == sizeof(smallint)) vtype[iarg] = Dump::INT; else vtype[iarg] = Dump::BIGINT; @@ -1541,86 +1546,86 @@ int DumpCustom::parse_fields(int narg, char **arg) } else if (strcmp(arg[iarg],"q") == 0) { if (!atom->q_flag) - error->all(FLERR,"Dumping an atom property that isn't allocated"); + error->all(FLERR, errptr, "Dumping an atom property that isn't allocated"); pack_choice[iarg] = &DumpCustom::pack_q; vtype[iarg] = Dump::DOUBLE; } else if (strcmp(arg[iarg],"mux") == 0) { if (!atom->mu_flag) - error->all(FLERR,"Dumping an atom property that isn't allocated"); + error->all(FLERR, errptr, "Dumping an atom property that isn't allocated"); pack_choice[iarg] = &DumpCustom::pack_mux; vtype[iarg] = Dump::DOUBLE; } else if (strcmp(arg[iarg],"muy") == 0) { if (!atom->mu_flag) - error->all(FLERR,"Dumping an atom property that isn't allocated"); + error->all(FLERR, errptr, "Dumping an atom property that isn't allocated"); pack_choice[iarg] = &DumpCustom::pack_muy; vtype[iarg] = Dump::DOUBLE; } else if (strcmp(arg[iarg],"muz") == 0) { if (!atom->mu_flag) - error->all(FLERR,"Dumping an atom property that isn't allocated"); + error->all(FLERR, errptr, "Dumping an atom property that isn't allocated"); pack_choice[iarg] = &DumpCustom::pack_muz; vtype[iarg] = Dump::DOUBLE; } else if (strcmp(arg[iarg],"mu") == 0) { if (!atom->mu_flag) - error->all(FLERR,"Dumping an atom property that isn't allocated"); + error->all(FLERR, errptr, "Dumping an atom property that isn't allocated"); pack_choice[iarg] = &DumpCustom::pack_mu; vtype[iarg] = Dump::DOUBLE; } else if (strcmp(arg[iarg],"radius") == 0) { if (!atom->radius_flag) - error->all(FLERR,"Dumping an atom property that isn't allocated"); + error->all(FLERR, errptr, "Dumping an atom property that isn't allocated"); pack_choice[iarg] = &DumpCustom::pack_radius; vtype[iarg] = Dump::DOUBLE; } else if (strcmp(arg[iarg],"diameter") == 0) { if (!atom->radius_flag) - error->all(FLERR,"Dumping an atom property that isn't allocated"); + error->all(FLERR, errptr, "Dumping an atom property that isn't allocated"); pack_choice[iarg] = &DumpCustom::pack_diameter; vtype[iarg] = Dump::DOUBLE; } else if (strcmp(arg[iarg],"omegax") == 0) { if (!atom->omega_flag) - error->all(FLERR,"Dumping an atom property that isn't allocated"); + error->all(FLERR, errptr, "Dumping an atom property that isn't allocated"); pack_choice[iarg] = &DumpCustom::pack_omegax; vtype[iarg] = Dump::DOUBLE; } else if (strcmp(arg[iarg],"omegay") == 0) { if (!atom->omega_flag) - error->all(FLERR,"Dumping an atom property that isn't allocated"); + error->all(FLERR, errptr, "Dumping an atom property that isn't allocated"); pack_choice[iarg] = &DumpCustom::pack_omegay; vtype[iarg] = Dump::DOUBLE; } else if (strcmp(arg[iarg],"omegaz") == 0) { if (!atom->omega_flag) - error->all(FLERR,"Dumping an atom property that isn't allocated"); + error->all(FLERR, errptr, "Dumping an atom property that isn't allocated"); pack_choice[iarg] = &DumpCustom::pack_omegaz; vtype[iarg] = Dump::DOUBLE; } else if (strcmp(arg[iarg],"angmomx") == 0) { if (!atom->angmom_flag) - error->all(FLERR,"Dumping an atom property that isn't allocated"); + error->all(FLERR, errptr, "Dumping an atom property that isn't allocated"); pack_choice[iarg] = &DumpCustom::pack_angmomx; vtype[iarg] = Dump::DOUBLE; } else if (strcmp(arg[iarg],"angmomy") == 0) { if (!atom->angmom_flag) - error->all(FLERR,"Dumping an atom property that isn't allocated"); + error->all(FLERR, errptr, "Dumping an atom property that isn't allocated"); pack_choice[iarg] = &DumpCustom::pack_angmomy; vtype[iarg] = Dump::DOUBLE; } else if (strcmp(arg[iarg],"angmomz") == 0) { if (!atom->angmom_flag) - error->all(FLERR,"Dumping an atom property that isn't allocated"); + error->all(FLERR, errptr, "Dumping an atom property that isn't allocated"); pack_choice[iarg] = &DumpCustom::pack_angmomz; vtype[iarg] = Dump::DOUBLE; } else if (strcmp(arg[iarg],"tqx") == 0) { if (!atom->torque_flag) - error->all(FLERR,"Dumping an atom property that isn't allocated"); + error->all(FLERR, errptr, "Dumping an atom property that isn't allocated"); pack_choice[iarg] = &DumpCustom::pack_tqx; vtype[iarg] = Dump::DOUBLE; } else if (strcmp(arg[iarg],"tqy") == 0) { if (!atom->torque_flag) - error->all(FLERR,"Dumping an atom property that isn't allocated"); + error->all(FLERR, errptr, "Dumping an atom property that isn't allocated"); pack_choice[iarg] = &DumpCustom::pack_tqy; vtype[iarg] = Dump::DOUBLE; } else if (strcmp(arg[iarg],"tqz") == 0) { if (!atom->torque_flag) - error->all(FLERR,"Dumping an atom property that isn't allocated"); + error->all(FLERR, errptr, "Dumping an atom property that isn't allocated"); pack_choice[iarg] = &DumpCustom::pack_tqz; vtype[iarg] = Dump::DOUBLE; @@ -1638,7 +1643,8 @@ int DumpCustom::parse_fields(int narg, char **arg) switch (argi.get_type()) { case ArgInfo::UNKNOWN: - error->all(FLERR,"Invalid attribute {} in dump {} command",arg[iarg],style); + error->all(FLERR, errptr, "Invalid attribute {} in dump {} command", + arg[iarg], style); break; case ArgInfo::NONE: @@ -1656,13 +1662,17 @@ int DumpCustom::parse_fields(int narg, char **arg) icompute = modify->get_compute_by_id(name); if (!icompute) error->all(FLERR,"Could not find dump {} compute ID: {}", style, name); if (icompute->peratom_flag == 0) - error->all(FLERR,"Dump {} compute {} does not compute per-atom info", style, name); + error->all(FLERR, errptr, "Dump {} compute {} does not compute per-atom info", + style, name); if (argi.get_dim() == 0 && icompute->size_peratom_cols > 0) - error->all(FLERR,"Dump {} compute {} does not calculate per-atom vector", style, name); + error->all(FLERR, errptr, + "Dump {} compute {} does not calculate per-atom vector", style, name); if (argi.get_dim() > 0 && icompute->size_peratom_cols == 0) - error->all(FLERR,"Dump {} compute {} does not calculate per-atom array", style, name); + error->all(FLERR, errptr, "Dump {} compute {} does not calculate per-atom array", + style, name); if (argi.get_dim() > 0 && argi.get_index1() > icompute->size_peratom_cols) - error->all(FLERR,"Dump {} compute {} vector is accessed out-of-range", style, name); + error->all(FLERR, errptr, "Dump {} compute {} vector is accessed out-of-range{}", + style, name, utils::errorurl(20)); field2index[iarg] = add_compute(name); break; @@ -1675,15 +1685,16 @@ int DumpCustom::parse_fields(int narg, char **arg) vtype[iarg] = Dump::DOUBLE; ifix = modify->get_fix_by_id(name); - if (!ifix) error->all(FLERR,"Could not find dump {} fix ID: {}", style, name); + if (!ifix) error->all(FLERR, errptr, "Could not find dump {} fix ID: {}", style, name); if (ifix->peratom_flag == 0) - error->all(FLERR,"Dump {} fix {} does not compute per-atom info", style, name); + error->all(FLERR, errptr, "Dump {} fix {} does not compute per-atom info", style, name); if (argi.get_dim() == 0 && ifix->size_peratom_cols > 0) - error->all(FLERR,"Dump {} fix {} does not compute per-atom vector", style, name); + error->all(FLERR, errptr, "Dump {} fix {} does not compute per-atom vector", style, name); if (argi.get_dim() > 0 && ifix->size_peratom_cols == 0) - error->all(FLERR,"Dump {} fix {} does not compute per-atom array", style, name); + error->all(FLERR, errptr, "Dump {} fix {} does not compute per-atom array", style, name); if (argi.get_dim() > 0 && argi.get_index1() > ifix->size_peratom_cols) - error->all(FLERR,"Dump {} fix {} vector is accessed out-of-range", style, name); + error->all(FLERR, errptr, "Dump {} fix {} vector is accessed out-of-range{}", + style, name, utils::errorurl(20)); field2index[iarg] = add_fix(name); break; @@ -1695,9 +1706,9 @@ int DumpCustom::parse_fields(int narg, char **arg) vtype[iarg] = Dump::DOUBLE; n = input->variable->find(name); - if (n < 0) error->all(FLERR,"Could not find dump {} variable name {}", style, name); + if (n < 0) error->all(FLERR, errptr, "Could not find dump {} variable name {}", style, name); if (input->variable->atomstyle(n) == 0) - error->all(FLERR,"Dump {} variable {} is not atom-style variable", style, name); + error->all(FLERR, errptr, "Dump {} variable {} is not atom-style variable", style, name); field2index[iarg] = add_variable(name); break; @@ -1711,15 +1722,18 @@ int DumpCustom::parse_fields(int narg, char **arg) n = atom->find_custom(name,flag,cols); if (n < 0) - error->all(FLERR,"Could not find custom per-atom property ID: {}", name); + error->all(FLERR, errptr, "Could not find custom per-atom property ID: {}", name); if (argindex[iarg] == 0) { if (!flag || cols) - error->all(FLERR,"Property double vector {} for dump {} does not exist", name, style); + error->all(FLERR, errptr, "Property double vector {} for dump {} does not exist", + name, style); } else { if (!flag || !cols) - error->all(FLERR,"Property double array {} for dump {} does not exist", name, style); + error->all(FLERR, errptr, "Property double array {} for dump {} does not exist", + name, style); if (argindex[iarg] > atom->dcols[n]) - error->all(FLERR,"Dump {} property array {} is accessed out-of-range", style, name); + error->all(FLERR, errptr, "Dump {} property array {} is accessed out-of-range{}", + style, name, utils::errorurl(20)); } field2index[iarg] = add_custom(name,1); @@ -1734,15 +1748,18 @@ int DumpCustom::parse_fields(int narg, char **arg) n = atom->find_custom(name,flag,cols); if (n < 0) - error->all(FLERR,"Could not find custom per-atom property ID: {}", name); + error->all(FLERR, errptr, "Could not find custom per-atom property ID: {}", name); if (argindex[iarg] == 0) { if (flag || cols) - error->all(FLERR,"Property integer vector {} for dump {} does not exist", name, style); + error->all(FLERR, errptr, "Property integer vector {} for dump {} does not exist", + name, style); } else { if (flag || !cols) - error->all(FLERR,"Property integer array {} for dump {} does not exist", name, style); + error->all(FLERR, errptr, "Property integer array {} for dump {} does not exist", + name, style); if (argindex[iarg] > atom->icols[n]) - error->all(FLERR,"Dump {} property array {} is accessed out-of-range", style, name); + error->all(FLERR, errptr, "Dump {} property array {} is accessed out-of-range{}", + style, name, utils::errorurl(20)); } field2index[iarg] = add_custom(name,0); @@ -1861,25 +1878,29 @@ int DumpCustom::add_custom(const char *id, int flag) int DumpCustom::modify_param(int narg, char **arg) { + // determine offset in list of arguments for error pointer. also handle the no match case. + int argoff = 0; + while (input && input->arg[argoff] && (strcmp(input->arg[argoff], arg[0]) != 0)) argoff++; + if (strcmp(arg[0],"region") == 0) { - if (narg < 2) error->all(FLERR,"Illegal dump_modify command"); + if (narg < 2) utils::missing_cmd_args(FLERR, "dump_modify", error); if (strcmp(arg[1],"none") == 0) { delete[] idregion; idregion = nullptr; } else { delete[] idregion; if (!domain->get_region_by_id(arg[1])) - error->all(FLERR,"Dump_modify region {} does not exist", arg[1]); + error->all(FLERR, argoff + 1, "Dump_modify region {} does not exist", arg[1]); idregion = utils::strdup(arg[1]); } return 2; } if (strcmp(arg[0],"triclinic/general") == 0) { - if (narg < 2) error->all(FLERR,"Illegal dump_modify command"); + if (narg < 2) utils::missing_cmd_args(FLERR,"dump_modify triclinic/general",error); triclinic_general = utils::logical(FLERR,arg[1],false,lmp); if (triclinic_general && !domain->triclinic_general) - error->all(FLERR,"Dump_modify triclinic/general cannot be used " + error->all(FLERR, argoff, "Dump_modify triclinic/general cannot be used " "if simulation box is not general triclinic"); return 2; } @@ -1908,7 +1929,7 @@ int DumpCustom::modify_param(int narg, char **arg) // use of &str[1] removes leading '%' from BIGINT_FORMAT string char *ptr = strchr(format_int_user,'d'); if (ptr == nullptr) - error->all(FLERR,"Dump_modify int format does not contain d character"); + error->all(FLERR, argoff + 2, "Dump_modify int format does not contain d character"); char str[8]; snprintf(str,8,"%s",BIGINT_FORMAT); *ptr = '\0'; @@ -1922,7 +1943,7 @@ int DumpCustom::modify_param(int narg, char **arg) } else { int i = utils::inumeric(FLERR,arg[1],false,lmp) - 1; if (i < 0 || i >= nfield) - error->all(FLERR,"Unknown dump_modify format ID keyword: {}", arg[1]); + error->all(FLERR, argoff + 1, "Unknown dump_modify format ID keyword: {}", arg[1]); delete[] format_column_user[i]; format_column_user[i] = utils::strdup(arg[2]); } @@ -1930,8 +1951,9 @@ int DumpCustom::modify_param(int narg, char **arg) } if (strcmp(arg[0],"element") == 0) { - if (narg < ntypes+1) - error->all(FLERR,"Number of dump_modify element names does not match number of atom types"); + if (narg < ntypes + 1) + error->all(FLERR, argoff + 1, + "Number of dump_modify element names does not match number of atom types"); for (int i = 1; i <= ntypes; i++) delete[] typenames[i]; delete[] typenames; @@ -1946,7 +1968,7 @@ int DumpCustom::modify_param(int narg, char **arg) if (narg < 2) utils::missing_cmd_args(FLERR, "dump_modify refresh", error); ArgInfo argi(arg[1],ArgInfo::COMPUTE); if ((argi.get_type() != ArgInfo::COMPUTE) || (argi.get_dim() != 0)) - error->all(FLERR,"Illegal dump_modify command"); + error->all(FLERR, argoff + 1, "Illegal dump_modify command"); if (refreshflag) error->all(FLERR,"Dump_modify can only have one refresh"); refreshflag = 1; @@ -2085,7 +2107,7 @@ int DumpCustom::modify_param(int narg, char **arg) switch (argi.get_type()) { case ArgInfo::UNKNOWN: - error->all(FLERR,"Invalid attribute in dump modify command"); + error->all(FLERR, argoff + 1, "Invalid attribute in dump modify command"); break; // compute value = c_ID @@ -2095,15 +2117,16 @@ int DumpCustom::modify_param(int narg, char **arg) thresh_array[nthresh] = COMPUTE; icompute = modify->get_compute_by_id(name); - if (!icompute) error->all(FLERR,"Could not find dump modify compute ID {}",name); + if (!icompute) + error->all(FLERR, argoff + 1, "Could not find dump modify compute ID {}",name); if (icompute->peratom_flag == 0) - error->all(FLERR,"Dump modify compute ID {} does not compute per-atom info",name); + error->all(FLERR, argoff + 1, "Dump modify compute ID {} does not compute per-atom info",name); if (argi.get_dim() == 0 && icompute->size_peratom_cols > 0) - error->all(FLERR,"Dump modify compute ID {} does not compute per-atom vector",name); + error->all(FLERR, argoff + 1, "Dump modify compute ID {} does not compute per-atom vector",name); if (argi.get_index1() > 0 && icompute->size_peratom_cols == 0) - error->all(FLERR,"Dump modify compute ID {} does not compute per-atom array",name); + error->all(FLERR, argoff + 1, "Dump modify compute ID {} does not compute per-atom array",name); if (argi.get_index1() > 0 && argi.get_index1() > icompute->size_peratom_cols) - error->all(FLERR,"Dump modify compute ID {} vector is not large enough",name); + error->all(FLERR, argoff + 1, "Dump modify compute ID {} vector is not large enough",name); field2index[nfield+nthresh] = add_compute(name); break; @@ -2115,16 +2138,19 @@ int DumpCustom::modify_param(int narg, char **arg) thresh_array[nthresh] = FIX; ifix = modify->get_fix_by_id(name); - if (!ifix) error->all(FLERR,"Could not find dump modify fix ID: {}",name); + if (!ifix) error->all(FLERR, argoff + 1, "Could not find dump modify fix ID: {}",name); if (ifix->peratom_flag == 0) - error->all(FLERR,"Dump modify fix ID {} does not compute per-atom info",name); + error->all(FLERR, argoff + 1, "Dump modify fix ID {} does not compute per-atom info", + name); if (argi.get_dim() == 0 && ifix->size_peratom_cols > 0) - error->all(FLERR,"Dump modify fix ID {} does not compute per-atom vector",name); + error->all(FLERR, argoff + 1, "Dump modify fix ID {} does not compute per-atom vector", + name); if (argi.get_index1() > 0 && ifix->size_peratom_cols == 0) - error->all(FLERR,"Dump modify fix ID {} does not compute per-atom array",name); + error->all(FLERR, argoff + 1, "Dump modify fix ID {} does not compute per-atom array", + name); if (argi.get_index1() > 0 && argi.get_index1() > ifix->size_peratom_cols) - error->all(FLERR,"Dump modify fix ID {} vector is not large enough",name); + error->all(FLERR, argoff + 1, "Dump modify fix ID {} vector is not large enough",name); field2index[nfield+nthresh] = add_fix(name); break; @@ -2134,9 +2160,10 @@ int DumpCustom::modify_param(int narg, char **arg) case ArgInfo::VARIABLE: thresh_array[nthresh] = VARIABLE; n = input->variable->find(name); - if (n < 0) error->all(FLERR,"Could not find dump modify variable name: {}", name); + if (n < 0) error->all(FLERR, argoff + 1, "Could not find dump modify variable name: {}", + name); if (input->variable->atomstyle(n) == 0) - error->all(FLERR,"Dump modify variable {} is not atom-style variable", name); + error->all(FLERR, argoff + 1, "Dump modify variable {} is not atom-style variable", name); field2index[nfield+nthresh] = add_variable(name); break; @@ -2147,16 +2174,19 @@ int DumpCustom::modify_param(int narg, char **arg) n = atom->find_custom(name,flag,cols); if (n < 0) - error->all(FLERR,"Could not find custom per-atom property ID: {}", name); + error->all(FLERR, argoff + 1, "Could not find custom per-atom property ID: {}", name); if (argindex[nfield+nthresh] == 0) { if (!flag || cols) - error->all(FLERR,"Property double vector {} for dump {} does not exist", name, style); + error->all(FLERR, argoff + 1, "Property double vector {} for dump {} does not exist", + name, style); thresh_array[nthresh] = DVEC; } else { if (!flag || !cols) - error->all(FLERR,"Property double array {} for dump {} does not exist", name, style); + error->all(FLERR, argoff + 1, "Property double array {} for dump {} does not exist", + name, style); if (argindex[nfield+nthresh] > atom->dcols[n]) - error->all(FLERR,"Dump {} property array {} is accessed out-of-range", style, name); + error->all(FLERR, argoff + 1, "Dump {} property array {} is accessed out-of-range{}", + style, name, utils::errorurl(20)); thresh_array[nthresh] = DARRAY; } @@ -2169,16 +2199,19 @@ int DumpCustom::modify_param(int narg, char **arg) n = atom->find_custom(name,flag,cols); if (n < 0) - error->all(FLERR,"Could not find custom per-atom property ID: {}", name); + error->all(FLERR, argoff + 1, "Could not find custom per-atom property ID: {}", name); if (argindex[nfield+nthresh] == 0) { if (flag || cols) - error->all(FLERR,"Property integer vector {} for dump {} does not exist", name, style); + error->all(FLERR, argoff + 1, "Property integer vector {} for dump {} does not exist", + name, style); thresh_array[nthresh] = IVEC; } else { if (flag || !cols) - error->all(FLERR,"Property integer array {} for dump {} does not exist", name, style); + error->all(FLERR, argoff + 1, "Property integer array {} for dump {} does not exist", + name, style); if (argindex[nfield+nthresh] > atom->icols[n]) - error->all(FLERR,"Dump {} property array {} is accessed out-of-range", style, name); + error->all(FLERR, argoff + 1, "Dump {} property array {} is accessed out-of-range{}", + style, name, utils::errorurl(20)); thresh_array[nthresh] = IARRAY; } @@ -2188,7 +2221,7 @@ int DumpCustom::modify_param(int narg, char **arg) // no match default: - error->all(FLERR,"Invalid dump_modify thresh attribute: {}", name); + error->all(FLERR, argoff + 1, "Invalid dump_modify thresh attribute: {}", name); break; } } From 8ff5855e4014c81687f1c8bc5a6380c2d9bbce16 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 13 Mar 2025 22:14:07 -0400 Subject: [PATCH 101/113] modernize boldface font selection in LaTeX sections --- doc/src/compute_orientorder_atom.rst | 2 +- doc/src/compute_sna_atom.rst | 4 ++-- doc/src/fix_gld.rst | 4 ++-- doc/src/fix_lb_fluid.rst | 2 +- doc/src/fix_pimd.rst | 2 +- doc/src/fix_pimd_bosonic.rst | 2 +- doc/src/pair_aip_water_2dm.rst | 4 ++-- doc/src/pair_ilp_graphene_hbn.rst | 4 ++-- doc/src/pair_ilp_tmd.rst | 6 +++--- doc/src/pair_kolmogorov_crespi_full.rst | 4 ++-- doc/src/pair_mgpt.rst | 2 +- doc/src/pair_saip_metal.rst | 8 ++++---- 12 files changed, 22 insertions(+), 22 deletions(-) diff --git a/doc/src/compute_orientorder_atom.rst b/doc/src/compute_orientorder_atom.rst index 01535aa880..08153fe496 100644 --- a/doc/src/compute_orientorder_atom.rst +++ b/doc/src/compute_orientorder_atom.rst @@ -49,7 +49,7 @@ For each atom, :math:`Q_\ell` is a real number defined as follows: .. math:: - \bar{Y}_{\ell m} = & \frac{1}{nnn}\sum_{j = 1}^{nnn} Y_{\ell m}\bigl( \theta( {\bf r}_{ij} ), \phi( {\bf r}_{ij} ) \bigr) \\ + \bar{Y}_{\ell m} = & \frac{1}{nnn}\sum_{j = 1}^{nnn} Y_{\ell m}\bigl( \theta( \mathbf{r}_{ij} ), \phi( \mathbf{r}_{ij} ) \bigr) \\ Q_\ell = & \sqrt{\frac{4 \pi}{2 \ell + 1} \sum_{m = -\ell }^{m = \ell } \bar{Y}_{\ell m} \bar{Y}^*_{\ell m}} The first equation defines the local order parameters as averages diff --git a/doc/src/compute_sna_atom.rst b/doc/src/compute_sna_atom.rst index 2572093499..d0c76dd4ca 100644 --- a/doc/src/compute_sna_atom.rst +++ b/doc/src/compute_sna_atom.rst @@ -204,7 +204,7 @@ components summed separately for each LAMMPS atom type: .. math:: - -\sum_{i' \in I} \frac{\partial {B^{i'}_{j_1,j_2,j} }}{\partial {\bf r}_i} + -\sum_{i' \in I} \frac{\partial {B^{i'}_{j_1,j_2,j} }}{\partial \mathbf{r}_i} The sum is over all atoms *i'* of atom type *I*\ . For each atom *i*, this compute evaluates the above expression for each direction, each @@ -216,7 +216,7 @@ derivatives: .. math:: - -{\bf r}_i \otimes \sum_{i' \in I} \frac{\partial {B^{i'}_{j_1,j_2,j}}}{\partial {\bf r}_i} + -\mathbf{r}_i \otimes \sum_{i' \in I} \frac{\partial {B^{i'}_{j_1,j_2,j}}}{\partial \mathbf{r}_i} Again, the sum is over all atoms *i'* of atom type *I*\ . For each atom *i*, this compute evaluates the above expression for each of the six diff --git a/doc/src/fix_gld.rst b/doc/src/fix_gld.rst index ba26f7a51b..8c24275cb4 100644 --- a/doc/src/fix_gld.rst +++ b/doc/src/fix_gld.rst @@ -60,9 +60,9 @@ With this fix active, the force on the *j*\ th atom is given as .. math:: - {\bf F}_{j}(t) = & {\bf F}^C_j(t)-\int \limits_{0}^{t} \Gamma_j(t-s) {\bf v}_j(s)~\text{d}s + {\bf F}^R_j(t) \\ + \mathbf{F}_{j}(t) = & \mathbf{F}^C_j(t)-\int \limits_{0}^{t} \Gamma_j(t-s) \mathbf{v}_j(s)~\text{d}s + \mathbf{F}^R_j(t) \\ \Gamma_j(t-s) = & \sum \limits_{k=1}^{N_k} \frac{c_k}{\tau_k} e^{-(t-s)/\tau_k} \\ - \langle{\bf F}^R_j(t),{\bf F}^R_j(s)\rangle = & \text{k$_\text{B}$T} ~\Gamma_j(t-s) + \langle\mathbf{F}^R_j(t),\mathbf{F}^R_j(s)\rangle = & \text{k$_\text{B}$T} ~\Gamma_j(t-s) Here, the first term is representative of all conservative (pairwise, bonded, etc) forces external to this fix, the second is the temporally diff --git a/doc/src/fix_lb_fluid.rst b/doc/src/fix_lb_fluid.rst index a461175f71..e49831986b 100644 --- a/doc/src/fix_lb_fluid.rst +++ b/doc/src/fix_lb_fluid.rst @@ -130,7 +130,7 @@ calculated as: .. math:: - {\bf F}_{j \alpha} = \gamma \left({\bf v}_n - {\bf u}_f \right) \zeta_{j\alpha} + \mathbf{F}_{j \alpha} = \gamma \left(\mathbf{v}_n - \mathbf{u}_f \right) \zeta_{j\alpha} where :math:`\mathbf{v}_n` is the velocity of the MD particle, :math:`\mathbf{u}_f` is the fluid velocity interpolated to the particle diff --git a/doc/src/fix_pimd.rst b/doc/src/fix_pimd.rst index f29124e9aa..3ee11014bf 100644 --- a/doc/src/fix_pimd.rst +++ b/doc/src/fix_pimd.rst @@ -101,7 +101,7 @@ by the following equations: .. math:: - Z = & \int d{\bf q} d{\bf p} \cdot \textrm{exp} [ -\beta H_{eff} ] \\ + Z = & \int d\mathbf{q} d\mathbf{p} \cdot \textrm{exp} [ -\beta H_{eff} ] \\ H_{eff} = & \bigg(\sum_{i=1}^P \frac{p_i^2}{2M_i}\bigg) + V_{eff} \\ V_{eff} = & \sum_{i=1}^P \bigg[ \frac{mP}{2\beta^2 \hbar^2} (q_i - q_{i+1})^2 + \frac{1}{P} V(q_i)\bigg] diff --git a/doc/src/fix_pimd_bosonic.rst b/doc/src/fix_pimd_bosonic.rst index 67dd60ed39..e54e87e8fb 100644 --- a/doc/src/fix_pimd_bosonic.rst +++ b/doc/src/fix_pimd_bosonic.rst @@ -97,7 +97,7 @@ inverse temperature :math:`\beta` is given by :ref:`(Tuckerman) .. math:: - Z \propto \int d{\bf q} \cdot \frac{1}{N!} \sum_\sigma \textrm{exp} [ -\beta \left( E^\sigma + V \right) ]. + Z \propto \int d\mathbf{q} \cdot \frac{1}{N!} \sum_\sigma \textrm{exp} [ -\beta \left( E^\sigma + V \right) ]. Here, :math:`V` is the potential between different particles at the same imaginary time slice, which is the same for bosons and distinguishable diff --git a/doc/src/pair_aip_water_2dm.rst b/doc/src/pair_aip_water_2dm.rst index 65f2e4d912..b7c33e9c86 100644 --- a/doc/src/pair_aip_water_2dm.rst +++ b/doc/src/pair_aip_water_2dm.rst @@ -57,8 +57,8 @@ materials as described in :ref:`(Feng1) ` and :ref:`(Feng2) `. \left [ \epsilon + f(\rho_{ij}) + f(\rho_{ji})\right ] - \frac{1}{1+e^{-d\left [ \left ( r_{ij}/\left (s_R \cdot r^{eff} \right ) \right )-1 \right ]}} \cdot \frac{C_6}{r^6_{ij}} \right \}\\ - \rho_{ij}^2 = & r_{ij}^2 - ({\bf r}_{ij} \cdot {\bf n}_i)^2 \\ - \rho_{ji}^2 = & r_{ij}^2 - ({\bf r}_{ij} \cdot {\bf n}_j)^2 \\ + \rho_{ij}^2 = & r_{ij}^2 - (\mathbf{r}_{ij} \cdot \mathbf{n}_i)^2 \\ + \rho_{ji}^2 = & r_{ij}^2 - (\mathbf{r}_{ij} \cdot \mathbf{n}_j)^2 \\ f(\rho) = & C e^{ -( \rho / \delta )^2 } \\ \mathrm{Tap}(r_{ij}) = & 20\left ( \frac{r_{ij}}{R_{cut}} \right )^7 - 70\left ( \frac{r_{ij}}{R_{cut}} \right )^6 + diff --git a/doc/src/pair_ilp_graphene_hbn.rst b/doc/src/pair_ilp_graphene_hbn.rst index 7fa7d6800f..e50509497f 100644 --- a/doc/src/pair_ilp_graphene_hbn.rst +++ b/doc/src/pair_ilp_graphene_hbn.rst @@ -48,8 +48,8 @@ in :ref:`(Kolmogorov) `. \left [ \epsilon + f(\rho_{ij}) + f(\rho_{ji})\right ] - \frac{1}{1+e^{-d\left [ \left ( r_{ij}/\left (s_R \cdot r^{eff} \right ) \right )-1 \right ]}} \cdot \frac{C_6}{r^6_{ij}} \right \}\\ - \rho_{ij}^2 = & r_{ij}^2 - ({\bf r}_{ij} \cdot {\bf n}_i)^2 \\ - \rho_{ji}^2 = & r_{ij}^2 - ({\bf r}_{ij} \cdot {\bf n}_j)^2 \\ + \rho_{ij}^2 = & r_{ij}^2 - (\mathbf{r}_{ij} \cdot \mathbf{n}_i)^2 \\ + \rho_{ji}^2 = & r_{ij}^2 - (\mathbf{r}_{ij} \cdot \mathbf{n}_j)^2 \\ f(\rho) = & C e^{ -( \rho / \delta )^2 } \\ \mathrm{Tap}(r_{ij}) = & 20\left ( \frac{r_{ij}}{R_{cut}} \right )^7 - 70\left ( \frac{r_{ij}}{R_{cut}} \right )^6 + diff --git a/doc/src/pair_ilp_tmd.rst b/doc/src/pair_ilp_tmd.rst index 133e5f9093..f486f73c69 100644 --- a/doc/src/pair_ilp_tmd.rst +++ b/doc/src/pair_ilp_tmd.rst @@ -45,8 +45,8 @@ as described in :ref:`(Ouyang7) ` and :ref:`(Jiang) `. \left [ \epsilon + f(\rho_{ij}) + f(\rho_{ji})\right ] - \frac{1}{1+e^{-d\left [ \left ( r_{ij}/\left (s_R \cdot r^{eff} \right ) \right )-1 \right ]}} \cdot \frac{C_6}{r^6_{ij}} \right \}\\ - \rho_{ij}^2 = & r_{ij}^2 - ({\bf r}_{ij} \cdot {\bf n}_i)^2 \\ - \rho_{ji}^2 = & r_{ij}^2 - ({\bf r}_{ij} \cdot {\bf n}_j)^2 \\ + \rho_{ij}^2 = & r_{ij}^2 - (\mathbf{r}_{ij} \cdot \mathbf{n}_i)^2 \\ + \rho_{ji}^2 = & r_{ij}^2 - (\mathbf{r}_{ij} \cdot \mathbf{n}_j)^2 \\ f(\rho) = & C e^{ -( \rho / \delta )^2 } \\ \mathrm{Tap}(r_{ij}) = & 20\left ( \frac{r_{ij}}{R_{cut}} \right )^7 - 70\left ( \frac{r_{ij}}{R_{cut}} \right )^6 + @@ -67,7 +67,7 @@ calculating the normals. normal vectors used for graphene and h-BN is no longer valid for TMDs. In :ref:`(Ouyang7) `, a new definition is proposed, where for each atom `i`, its six nearest neighboring atoms belonging to the same - sub-layer are chosen to define the normal vector `{\bf n}_i`. + sub-layer are chosen to define the normal vector `\mathbf{n}_i`. The parameter file (e.g. TMD.ILP), is intended for use with *metal* :doc:`units `, with energies in meV. Two additional parameters, diff --git a/doc/src/pair_kolmogorov_crespi_full.rst b/doc/src/pair_kolmogorov_crespi_full.rst index 1a4706dd6f..2af56cbf9b 100644 --- a/doc/src/pair_kolmogorov_crespi_full.rst +++ b/doc/src/pair_kolmogorov_crespi_full.rst @@ -37,8 +37,8 @@ No simplification is made, E = & \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\ V_{ij} = & e^{-\lambda (r_{ij} -z_0)} \left [ C + f(\rho_{ij}) + f(\rho_{ji}) \right ] - A \left ( \frac{r_{ij}}{z_0}\right )^{-6} \\ - \rho_{ij}^2 = & r_{ij}^2 - ({\bf r}_{ij}\cdot {\bf n}_{i})^2 \\ - \rho_{ji}^2 = & r_{ij}^2 - ({\bf r}_{ij}\cdot {\bf n}_{j})^2 \\ + \rho_{ij}^2 = & r_{ij}^2 - (\mathbf{r}_{ij}\cdot \mathbf{n}_{i})^2 \\ + \rho_{ji}^2 = & r_{ij}^2 - (\mathbf{r}_{ij}\cdot \mathbf{n}_{j})^2 \\ f(\rho) & = e^{-(\rho/\delta)^2} \sum_{n=0}^2 C_{2n} { (\rho/\delta) }^{2n} It is important to have a sufficiently large cutoff to ensure smooth diff --git a/doc/src/pair_mgpt.rst b/doc/src/pair_mgpt.rst index 13a4bcb079..e492e555ac 100644 --- a/doc/src/pair_mgpt.rst +++ b/doc/src/pair_mgpt.rst @@ -33,7 +33,7 @@ elemental bulk material in the form .. math:: - E_\mathrm{tot}({\bf R}_1 \ldots {\bf R}_N) = NE_\mathrm{vol}(\Omega ) + E_\mathrm{tot}(\mathbf{R}_1 \ldots \mathbf{R}_N) = NE_\mathrm{vol}(\Omega ) + \frac{1}{2} \sum _{i,j} \mbox{}^\prime \ v_2(ij;\Omega ) + \frac{1}{6} \sum _{i,j,k} \mbox{}^\prime \ v_3(ijk;\Omega ) + \frac{1}{24} \sum _{i,j,k,l} \mbox{}^\prime \ v_4(ijkl;\Omega ) diff --git a/doc/src/pair_saip_metal.rst b/doc/src/pair_saip_metal.rst index 098edff916..211e5e9359 100644 --- a/doc/src/pair_saip_metal.rst +++ b/doc/src/pair_saip_metal.rst @@ -45,8 +45,8 @@ potential (ILP) potential for hetero-junctions formed with hexagonal \left [ \epsilon + f(\rho_{ij}) + f(\rho_{ji})\right ] - \frac{1}{1+e^{-d\left [ \left ( r_{ij}/\left (s_R \cdot r^{eff} \right ) \right )-1 \right ]}} \cdot \frac{C_6}{r^6_{ij}} \right \}\\ - \rho_{ij}^2 = & r_{ij}^2 - ({\bf r}_{ij} \cdot {\bf n}_i)^2 \\ - \rho_{ji}^2 = & r_{ij}^2 - ({\bf r}_{ij} \cdot {\bf n}_j)^2 \\ + \rho_{ij}^2 = & r_{ij}^2 - (\mathbf{r}_{ij} \cdot \mathbf{n}_i)^2 \\ + \rho_{ji}^2 = & r_{ij}^2 - (\mathbf{r}_{ij} \cdot \mathbf{n}_j)^2 \\ f(\rho) = & C e^{ -( \rho / \delta )^2 } \\ \mathrm{Tap}(r_{ij}) = & 20\left ( \frac{r_{ij}}{R_{cut}} \right )^7 - 70\left ( \frac{r_{ij}}{R_{cut}} \right )^6 + @@ -63,8 +63,8 @@ calculating the normals. .. note:: To account for the isotropic nature of the isolated gold atom - electron cloud, their corresponding normal vectors (`{\bf n}_i`) are - assumed to lie along the interatomic vector `{\bf r}_ij`. Notably, this + electron cloud, their corresponding normal vectors (`\mathbf{n}_i`) are + assumed to lie along the interatomic vector `\mathbf{r}_ij`. Notably, this assumption is suitable for many bulk material surfaces, for example, for systems possessing s-type valence orbitals or metallic surfaces, whose valence electrons are mostly From e3de43f2b0ba2e1b21cce9a514c10eb3da5c093f Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 13 Mar 2025 22:25:14 -0400 Subject: [PATCH 102/113] modernize use of \it and \sf --- doc/src/compute_sna_atom.rst | 6 +++--- doc/src/minimize.rst | 12 ++++++------ 2 files changed, 9 insertions(+), 9 deletions(-) diff --git a/doc/src/compute_sna_atom.rst b/doc/src/compute_sna_atom.rst index d0c76dd4ca..2f8c4c4f5d 100644 --- a/doc/src/compute_sna_atom.rst +++ b/doc/src/compute_sna_atom.rst @@ -139,11 +139,11 @@ mapped on to a third polar angle :math:`\theta_0` defined by, .. math:: - \theta_0 = {\sf rfac0} \frac{r-r_{min0}}{R_{ii'}-r_{min0}} \pi + \theta_0 = \mathsf{rfac0} \frac{r-r_{min0}}{R_{ii'}-r_{min0}} \pi In this way, all possible neighbor positions are mapped on to a subset -of the 3-sphere. Points south of the latitude :math:`\theta_0` = -*rfac0* :math:`\pi` are excluded. +of the 3-sphere. Points south of the latitude +:math:`\theta_0 = \mathsf{rfac0} \pi` are excluded. The natural basis for functions on the 3-sphere is formed by the representatives of *SU(2)*, the matrices :math:`U^j_{m,m'}(\theta, \phi, diff --git a/doc/src/minimize.rst b/doc/src/minimize.rst index c201e53340..84ee4b99fc 100644 --- a/doc/src/minimize.rst +++ b/doc/src/minimize.rst @@ -108,12 +108,12 @@ potential energy of the system as a function of the N atom coordinates: .. math:: - E(r_1,r_2, \ldots ,r_N) = & \sum_{i,j} E_{\it pair}(r_i,r_j) + - \sum_{ij} E_{\it bond}(r_i,r_j) + - \sum_{ijk} E_{\it angle}(r_i,r_j,r_k) + \\ - & \sum_{ijkl} E_{\it dihedral}(r_i,r_j,r_k,r_l) + - \sum_{ijkl} E_{\it improper}(r_i,r_j,r_k,r_l) + - \sum_i E_{\it fix}(r_i) + E(r_1,r_2, \ldots ,r_N) = & \sum_{i,j} E_{pair}(r_i,r_j) + + \sum_{ij} E_{bond}(r_i,r_j) + + \sum_{ijk} E_{angle}(r_i,r_j,r_k) + \\ + & \sum_{ijkl} E_{dihedral}(r_i,r_j,r_k,r_l) + + \sum_{ijkl} E_{improper}(r_i,r_j,r_k,r_l) + + \sum_i E_{fix}(r_i) where the first term is the sum of all non-bonded :doc:`pairwise interactions ` including :doc:`long-range Coulombic From d784706a68b96fe8b8334a9547c677d9b90342a3 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 14 Mar 2025 02:47:14 -0400 Subject: [PATCH 103/113] small changes to appease coverity scan --- src/BPM/bond_bpm_spring_plastic.cpp | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/BPM/bond_bpm_spring_plastic.cpp b/src/BPM/bond_bpm_spring_plastic.cpp index 35fd8e4691..35df659992 100644 --- a/src/BPM/bond_bpm_spring_plastic.cpp +++ b/src/BPM/bond_bpm_spring_plastic.cpp @@ -430,7 +430,7 @@ double BondBPMSpringPlastic::single(int type, double rsq, int i, int j, double & { if (type <= 0) return 0.0; - double r0, ep; + double r0 = 0.0, ep = 0.0; for (int n = 0; n < atom->num_bond[i]; n++) { if (atom->bond_atom[i][n] == atom->tag[j]) { r0 = fix_bond_history->get_atom_value(i, n, 0); @@ -471,7 +471,7 @@ double BondBPMSpringPlastic::single(int type, double rsq, int i, int j, double & // set single_extra quantities svector[0] = r0; - svector[0] = (1.0 + ep) * r0; + svector[1] = (1.0 + ep) * r0; return 0.0; } From b11672a99ff4203d479152947cf8db4606db4f5f Mon Sep 17 00:00:00 2001 From: Evangelos Voyiatzis Date: Fri, 14 Mar 2025 09:16:57 +0100 Subject: [PATCH 104/113] define extract() in pair_yukawa.h --- src/pair_yukawa.h | 1 + 1 file changed, 1 insertion(+) diff --git a/src/pair_yukawa.h b/src/pair_yukawa.h index 5a2e282ef1..386e948997 100644 --- a/src/pair_yukawa.h +++ b/src/pair_yukawa.h @@ -39,6 +39,7 @@ class PairYukawa : public Pair { void write_data(FILE *) override; void write_data_all(FILE *) override; double single(int, int, int, int, double, double, double, double &) override; + void *extract(const char *, int &) override; protected: double cut_global; From 419b18bd164408fc0db7120c489c0823e59c8f7f Mon Sep 17 00:00:00 2001 From: Evangelos Voyiatzis Date: Fri, 14 Mar 2025 09:25:28 +0100 Subject: [PATCH 105/113] implement extract() in pair_yukawa.cpp --- src/pair_yukawa.cpp | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/src/pair_yukawa.cpp b/src/pair_yukawa.cpp index 55a686e5f0..28b63d3834 100644 --- a/src/pair_yukawa.cpp +++ b/src/pair_yukawa.cpp @@ -332,3 +332,12 @@ double PairYukawa::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq phi = a[itype][jtype] * screening * rinv - offset[itype][jtype]; return factor_lj * phi; } + +/* ---------------------------------------------------------------------- */ + +void *PairYukawa::extract(const char *str, int &dim) +{ + dim = 2; + if (strcmp(str, "alpha") == 0) return (void *) a; + return nullptr; +} From 7374d38b44aaf10953de57e25c66c333c9706fec Mon Sep 17 00:00:00 2001 From: Evangelos Voyiatzis Date: Fri, 14 Mar 2025 09:27:32 +0100 Subject: [PATCH 106/113] Update mol-pair-yukawa.yaml --- unittest/force-styles/tests/mol-pair-yukawa.yaml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/unittest/force-styles/tests/mol-pair-yukawa.yaml b/unittest/force-styles/tests/mol-pair-yukawa.yaml index 6268ed2d6d..b224143def 100644 --- a/unittest/force-styles/tests/mol-pair-yukawa.yaml +++ b/unittest/force-styles/tests/mol-pair-yukawa.yaml @@ -17,7 +17,8 @@ pair_coeff: ! | 3 3 350.0 4 4 250.0 5 5 250.0 -extract: ! "" +extract: ! | + alpha 2 natoms: 29 init_vdwl: 12.114009254533281 init_coul: 0 From 5ab442f10bc087481ff7d173fa05993ce0619661 Mon Sep 17 00:00:00 2001 From: Evangelos Voyiatzis Date: Fri, 14 Mar 2025 09:32:10 +0100 Subject: [PATCH 107/113] Include yukawa in the list of supported pair styles in fix_adapt.rst --- doc/src/fix_adapt.rst | 2 ++ 1 file changed, 2 insertions(+) diff --git a/doc/src/fix_adapt.rst b/doc/src/fix_adapt.rst index 93bd8da041..34e3e450f6 100644 --- a/doc/src/fix_adapt.rst +++ b/doc/src/fix_adapt.rst @@ -236,6 +236,8 @@ formulas for the meaning of these parameters: +------------------------------------------------------------------------------+--------------------------------------------------+-------------+ | :doc:`wf/cut ` | epsilon,sigma,nu,mu | type pairs | +------------------------------------------------------------------------------+--------------------------------------------------+-------------+ +| :doc:`yukawa ` | alpha | type pairs | ++------------------------------------------------------------------------------+--------------------------------------------------+-------------+ .. note:: From 29558a1141f20d75095053131023df63035f6a1a Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 14 Mar 2025 06:59:33 -0400 Subject: [PATCH 108/113] key word -> keyword --- doc/src/fix_neb.rst | 2 +- doc/src/fix_wall_piston.rst | 2 +- doc/src/timer.rst | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/doc/src/fix_neb.rst b/doc/src/fix_neb.rst index 51066675b8..0dbf4f5a18 100644 --- a/doc/src/fix_neb.rst +++ b/doc/src/fix_neb.rst @@ -180,7 +180,7 @@ force is added. By default, no additional forces act on the first and last replicas during the NEB relaxation, so these replicas simply relax toward their -respective local minima. By using the key word *end*, additional forces +respective local minima. By using the keyword *end*, additional forces can be applied to the first and/or last replicas, to enable them to relax toward a MEP while constraining their energy E to the target energy ETarget. diff --git a/doc/src/fix_wall_piston.rst b/doc/src/fix_wall_piston.rst index d60d8cb731..9102cc579e 100644 --- a/doc/src/fix_wall_piston.rst +++ b/doc/src/fix_wall_piston.rst @@ -33,7 +33,7 @@ Syntax *box* = the wall position is defined in simulation box units .. - FIXME: There are several "undocumented" key words for this fix: *rough*, + FIXME: There are several "undocumented" keywords for this fix: *rough*, *rampNL1*, *rampNL2*, *rampNL3*, *rampNL4*, and *rampNL5*. Examples diff --git a/doc/src/timer.rst b/doc/src/timer.rst index 13d5a92473..46a67c89b2 100644 --- a/doc/src/timer.rst +++ b/doc/src/timer.rst @@ -87,7 +87,7 @@ negative, if the timeout time is expired and positive if there is time remaining and in this case the value of the variable are the number of seconds remaining. -When the *timeout* key word is used a second time, the timer is +When the *timeout* keyword is used a second time, the timer is restarted with a new time limit. The timeout *elapse* value can be specified as *off* or *unlimited* to impose a no timeout condition (which is the default). The *elapse* setting can be specified as From e97807b92ec58a572b176ec97b6561b9f343db4a Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 14 Mar 2025 07:00:30 -0400 Subject: [PATCH 109/113] clarify. mention using timer command to re-enable regular runs --- doc/src/fix_halt.rst | 26 ++++++++++++++++++-------- 1 file changed, 18 insertions(+), 8 deletions(-) diff --git a/doc/src/fix_halt.rst b/doc/src/fix_halt.rst index f17cafc58c..1fb1a99da0 100644 --- a/doc/src/fix_halt.rst +++ b/doc/src/fix_halt.rst @@ -144,18 +144,28 @@ The optional *error* keyword determines how the current run is halted. If its value is *hard*, then LAMMPS will stop with an error message. If its value is *soft*, LAMMPS will exit the current run, but continue -to execute subsequent commands in the input script. However, -additional :doc:`run ` or :doc:`minimize ` commands will be -skipped. For example, this allows a script to output the current -state of the system, e.g. via a :doc:`write_dump ` or -:doc:`write_restart ` command. +to execute subsequent commands in the input script. However, additional +:doc:`run ` or :doc:`minimize ` commands will be skipped. +For example, this allows a script to output the current state of the +system, e.g. via a :doc:`write_dump ` or :doc:`write_restart +` command. To re-enable regular runs after *fix halt* +stopped a run, you need to issue a :doc:`timer timeout unlimited +` command. If its value is *continue*, the behavior is the same as for *soft*, except subsequent :doc:`run ` or :doc:`minimize ` commands are executed. This allows your script to remedy the condition that -triggered the halt, if necessary. Note that you may wish use the -:doc:`unfix ` command on the fix halt ID, so that the same -condition is not immediately triggered in a subsequent run. +triggered the halt, if necessary. This is the equivalent of stopping +with *error soft* and followed by :doc:`timer timeout unlimited +` command. This can have undesired consequences, when a +:doc:`run command ` uses the *every* keyword, so using *error soft* +and resetting the timer manually may be the preferred option. + +.. note:: + + You may wish use the :doc:`unfix ` command on the fix halt ID + before starting a subsequent run, so that the same condition is not + immediately triggered again. The optional *message* keyword determines whether a message is printed to the screen and logfile when the halt condition is triggered. If From fcb2eee6863455e8b63b9f690cc7ee8920b60382 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 14 Mar 2025 09:54:26 -0400 Subject: [PATCH 110/113] corrections for documentation of bosonic PIMD fix styles --- doc/src/Commands_fix.rst | 4 +- doc/src/fix.rst | 4 +- doc/src/fix_pimd.rst | 46 ++++--- doc/src/fix_pimd_bosonic.rst | 237 ----------------------------------- 4 files changed, 31 insertions(+), 260 deletions(-) delete mode 100644 doc/src/fix_pimd_bosonic.rst diff --git a/doc/src/Commands_fix.rst b/doc/src/Commands_fix.rst index c173216887..ed9bf6429b 100644 --- a/doc/src/Commands_fix.rst +++ b/doc/src/Commands_fix.rst @@ -162,8 +162,8 @@ OPT. * :doc:`phonon ` * :doc:`pimd/langevin ` * :doc:`pimd/nvt ` - * :doc:`pimd/langevin/bosonic ` - * :doc:`pimd/nvt/bosonic ` + * :doc:`pimd/langevin/bosonic ` + * :doc:`pimd/nvt/bosonic ` * :doc:`planeforce ` * :doc:`plumed ` * :doc:`poems ` diff --git a/doc/src/fix.rst b/doc/src/fix.rst index 1d508b4ed4..f024fc6974 100644 --- a/doc/src/fix.rst +++ b/doc/src/fix.rst @@ -341,8 +341,8 @@ accelerated styles exist. * :doc:`phonon ` - calculate dynamical matrix from MD simulations * :doc:`pimd/langevin ` - Feynman path-integral molecular dynamics with stochastic thermostat * :doc:`pimd/nvt ` - Feynman path-integral molecular dynamics with Nose-Hoover thermostat -* :doc:`pimd/langevin/bosonic ` - Bosonic Feynman path-integral molecular dynamics for with stochastic thermostat -* :doc:`pimd/nvt/bosonic ` - Bosonic Feynman path-integral molecular dynamics with Nose-Hoover thermostat +* :doc:`pimd/langevin/bosonic ` - Bosonic Feynman path-integral molecular dynamics for with stochastic thermostat +* :doc:`pimd/nvt/bosonic ` - Bosonic Feynman path-integral molecular dynamics with Nose-Hoover thermostat * :doc:`planeforce ` - constrain atoms to move in a plane * :doc:`plumed ` - wrapper on PLUMED free energy library * :doc:`poems ` - constrain clusters of atoms to move as coupled rigid bodies diff --git a/doc/src/fix_pimd.rst b/doc/src/fix_pimd.rst index 3ee11014bf..2ba0d384fd 100644 --- a/doc/src/fix_pimd.rst +++ b/doc/src/fix_pimd.rst @@ -9,11 +9,11 @@ fix pimd/langevin command fix pimd/nvt command ==================== -:doc:`fix pimd/langevin/bosonic ` command -=========================================================== +fix pimd/langevin/bosonic command +================================= -:doc:`fix pimd/nvt/bosonic ` command -====================================================== +fix pimd/nvt/bosonic command +============================ Syntax """""" @@ -23,7 +23,7 @@ Syntax fix ID group-ID style keyword value ... * ID, group-ID are documented in :doc:`fix ` command -* style = *pimd/langevin* or *pimd/nvt* = style name of this fix command +* style = *pimd/langevin* or *pimd/nvt* or *pimd/langevin/bosonic* or *pimd/nvt/bosonic* = style name of this fix command * zero or more keyword/value pairs may be appended * keywords for style *pimd/nvt* @@ -89,12 +89,13 @@ partition function for the original system to a classical partition function for a ring-polymer system is exploited, to efficiently sample configurations from the canonical ensemble :ref:`(Feynman) `. -.. versionadded:: 11Mar2025 +.. versionadded:: TBD Fix *pimd/langevin/bosonic* and *pimd/nvt/bosonic* were added. Fix *pimd/nvt* and fix *pimd/langevin* simulate *distinguishable* quantum particles. -Simulations of bosons, including exchange effects, are supported with the :doc:`fix pimd/langevin/bosonic ` and :doc:`fix pimd/nvt/bosonic ` commands. +Simulations of bosons, including exchange effects, are supported with the +fix *pimd/langevin/bosonic* and the *pimd/nvt/bosonic* commands. For distinguishable particles, the isomorphic classical partition function and its components are given by the following equations: @@ -173,15 +174,17 @@ normal-mode PIMD. A value of *cmd* is for centroid molecular dynamics Mode *pimd* added to fix pimd/langevin. -Fix pimd/langevin supports the *method* values *nmpimd* and *pimd*. The default value is *nmpimd*. -If *method* is *nmpimd*, the normal mode representation is used to integrate the equations of motion. -The exact solution of harmonic oscillator is used to propagate the free ring polymer part of the Hamiltonian. -If *method* is *pimd*, the Cartesian representation is used to integrate the equations of motion. -The harmonic force is added to the total force of the system, and the numerical integrator is used to propagate the Hamiltonian. +Fix pimd/langevin supports the *method* values *nmpimd* and *pimd*. The default +value is *nmpimd*. If *method* is *nmpimd*, the normal mode representation is +used to integrate the equations of motion. The exact solution of harmonic +oscillator is used to propagate the free ring polymer part of the Hamiltonian. +If *method* is *pimd*, the Cartesian representation is used to integrate the +equations of motion. The harmonic force is added to the total force of the +system, and the numerical integrator is used to propagate the Hamiltonian. -The keyword *integrator* specifies the Trotter splitting method used by *fix pimd/langevin*. -See :ref:`(Liu) ` for a discussion on the OBABO and BAOAB splitting schemes. Typically -either of the two should work fine. +The keyword *integrator* specifies the Trotter splitting method used by *fix +pimd/langevin*. See :ref:`(Liu) ` for a discussion on the OBABO and BAOAB +splitting schemes. Typically either of the two should work fine. The keyword *fmass* sets a further scaling factor for the fictitious masses of beads, which can be used for the Partial Adiabatic CMD @@ -231,8 +234,8 @@ a positive floating-point number. For pimd simulations, a temperature values should be specified even for nve ensemble. Temperature will make a difference for nve pimd, since the spring elastic frequency between the beads will be affected by the temperature. -The keyword *thermostat* reads *style* and *seed* of thermostat for fix style *pimd/langevin*. *style* can only -be *PILE_L* (path integral Langevin equation local thermostat, as described in :ref:`Ceriotti `), and *seed* should a positive integer number, which serves as the seed of the pseudo random number generator. +The keyword *thermostat* reads *style* and *seed* of thermostat for fix style *pimd/langevin*. +*style* can only be *PILE_L* (path integral Langevin equation local thermostat, as described in :ref:`Ceriotti `), and *seed* should a positive integer number, which serves as the seed of the pseudo random number generator. .. note:: @@ -418,7 +421,12 @@ LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Fix *pimd/nvt* cannot be used with :doc:`lj units `. -Fix *pimd/langevin* can be used with :doc:`lj units `. See the above part for how to use it. +Fix *pimd/langevin* can be used with :doc:`lj units `. +See the documentation above for how to use it. + +Only some combinations of fix styles and their options support +partitions with multiple processors. LAMMPS will stop with an +error if multi-processor partitions are not supported. A PIMD simulation can be initialized with a single data file read via the :doc:`read_data ` command. However, this means all @@ -435,7 +443,7 @@ variable, e.g. Related commands """""""""""""""" -:doc:`pimd/nvt/bosonic `, :doc:`pimd/langevin/bosonic ` +:doc:`fix ipi ` Default """"""" diff --git a/doc/src/fix_pimd_bosonic.rst b/doc/src/fix_pimd_bosonic.rst deleted file mode 100644 index e54e87e8fb..0000000000 --- a/doc/src/fix_pimd_bosonic.rst +++ /dev/null @@ -1,237 +0,0 @@ -.. index:: fix pimd/langevin/bosonic -.. index:: fix pimd/nvt/bosonic - -fix pimd/langevin/bosonic command -================================= - -fix pimd/nvt/bosonic command -============================ - -Syntax -"""""" - -.. code-block:: LAMMPS - - fix ID group-ID style keyword value ... - -* ID, group-ID are documented in :doc:`fix ` command -* style = *pimd/langevin/bosonic* or *pimd/nvt/bosonic* = style name of this fix command -* zero or more keyword/value pairs may be appended -* keywords for style *pimd/nvt/bosonic* - - .. parsed-literal:: - - *keywords* = *method* or *fmass* or *sp* or *temp* or *nhc* - *method* value = *pimd* or *nmpimd* - *fmass* value = scaling factor on mass - *sp* value = scaling factor on Planck constant - *temp* value = temperature (temperature units) - *nhc* value = Nc = number of chains in Nose-Hoover thermostat - -* keywords for style *pimd/langevin/bosonic* - - .. parsed-literal:: - - *keywords* = *integrator* or *ensemble* or *fmass* or *temp* or *thermostat* or *tau* or *fixcom* or *lj* or *esych* - *integrator* value = *obabo* or *baoab* - *ensemble* value = *nvt* or *nve* - *fmass* value = scaling factor on mass - *temp* value = temperature (temperature unit) - temperature = target temperature of the thermostat - *thermostat* values = style seed - style value = *PILE_L* - seed = random number generator seed - *tau* value = thermostat damping parameter (time unit) - *fixcom* value = *yes* or *no* - *lj* values = epsilon sigma mass planck mvv2e - epsilon = energy scale for reduced units (energy units) - sigma = length scale for reduced units (length units) - mass = mass scale for reduced units (mass units) - planck = Planck's constant for other unit style - mvv2e = mass * velocity^2 to energy conversion factor for other unit style - *esynch* value = *yes* or *no* - -Examples -"""""""" - -.. code-block:: LAMMPS - - fix 1 all pimd/nvt/bosonic method pimd fmass 1.0 sp 1.0 temp 2.0 nhc 4 - fix 1 all pimd/langevin/bosonic integrator obabo temp 113.15 thermostat PILE_L 1234 tau 1.0 - -Example input files are provided in the examples/PACKAGES/pimd_bosonic directory. - -Description -""""""""""" - -These fix commands are based on the fixes :doc:`pimd/nvt and -pimd/langevin ` for performing quantum molecular dynamics -simulations based on the Feynman path-integral formalism. The key -difference is that fix *pimd/nvt* and fix *pimd/langevin* simulate -*distinguishable* particles, while fix *pimd/nvt/bosonic* and fix -*pimd/langevin/bosonic* perform simulations of bosons, including exchange -effects. The *bosonic* commands share syntax with the equivalent commands for distinguishable particles. -The user is referred to the documentation of :doc:`these commands ` -for a detailed syntax description and additional, general capabilities -of the commands. The major differences from fix *pimd/nvt* and fix *pimd/langevin* in terms of -capabilities are: - -* Fix *pimd/nvt/bosonic* only supports the "pimd" and "nmpimd" methods. Fix - *pimd/langevin/bosonic* only supports the "pimd" method, which is the default - in this fix. These restrictions are related to the use of normal - modes, which change in bosons. For similar reasons, *fmmode* of - *pimd/langevin* should not be used, and would raise an error if set to - a value other than *physical*. -* Fix *pimd/langevin/bosonic* currently does not support *ensemble* other than - *nve*, *nvt*. The barostat related keywords *iso*, *aniso*, - *barostat*, *taup* are not supported. -* Fix *pimd/langevin/bosonic* also has a keyword not available in fix - *pimd/langevin*: *esynch*, with default *yes*. If set to *no*, some - time consuming synchronization of spring energies and the primitive - kinetic energy estimator between processors is avoided. - -The isomorphism between the partition function of :math:`N` bosonic -quantum particles and that of a system of classical ring polymers at -inverse temperature :math:`\beta` is given by :ref:`(Tuckerman) -`: - -.. math:: - - Z \propto \int d\mathbf{q} \cdot \frac{1}{N!} \sum_\sigma \textrm{exp} [ -\beta \left( E^\sigma + V \right) ]. - -Here, :math:`V` is the potential between different particles at the same -imaginary time slice, which is the same for bosons and distinguishable -particles. The sum is over all permutations :math:`\sigma`. Recall that -a permutation matches each element :math:`l` in :math:`1, ..., N` to an -element :math:`\sigma(l)` in :math:`1, ..., N` without repetitions. The -energies :math:`E^\sigma` correspond to the linking of ring polymers of -different particles according to the permutations: - -.. math:: - - E^\sigma = \frac{mP}{2\beta^2 \hbar^2} \sum_{\ell=1}^N \sum_{j=1}^P \left(\mathbf{q}_\ell^j - \mathbf{q}_\ell^{j+1}\right)^2, - -where :math:`P` is the number of beads and :math:`\mathbf{q}_\ell^{P+1}=\mathbf{q}_{\sigma(\ell)}^1.` - -Hirshberg et. al. showed that the ring polymer potential -:math:`-\frac{1}{\beta}\textrm{ln}\left[ \frac{1}{N!} \sum_\sigma e ^ { --\beta E^\sigma } \right]`, which scales exponentially with :math:`N`, -can be replaced by a potential :math:`V^{[1,N]}` defined through a -recurrence relation :ref:`(Hirshberg1) `: - -.. math:: - - e ^ { -\beta V^{[1,N]} } = \frac{1}{N} \sum_{k=1}^N e ^ { -\beta \left( V^{[1,N-k]} + E^{[N-K+1,N]} \right)}. - -Here, :math:`E^{[N-K+1,N]}` is the spring energy of the ring polymer -obtained by connecting the beads of particles :math:`N - k + 1, N - k + -2, ..., N` in a cycle. This potential does not include all :math:`N!` -permutations, but samples the same bosonic partition function. The -implemented algorithm in LAMMPS for calculating the potential is the one -developed by Feldman and Hirshberg, which scales like :math:`N^2+PN` -:ref:`(Feldman) `. The forces are calculated as weighted -averages over the representative permutations, through an algorithm that -scales the same as the one for the potential calculation, :math:`N^2+PN` -:ref:`(Feldman) `. The minimum-image convention is employed on -the springs to account for periodic boundary conditions; an elaborate -discussion of the validity of the approximation is available in -:ref:`(Higer) `. - -Restart, fix_modify, output, run start/stop, minimize info -""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" - -The use of :doc:`binary restart files ` and :doc:`fix_modify -` is the same as in :doc:`fix pimd `. - -Fix *pimd/nvt/bosonic* computes a global 4-vector, which can be accessed by -various :doc:`output commands `. The quantities in -the global vector are: - - #. the total spring energy of the quasi-beads, - #. the current temperature of the classical system of ring polymers, - #. the current value of the scalar virial estimator for the kinetic - energy of the quantum system :ref:`(Herman) ` (see the justification in the supporting information of :ref:`(Hirshberg2) `), - #. the current value of the scalar primitive estimator for the kinetic - energy of the quantum system :ref:`(Hirshberg1) `. - -The vector values calculated by fix *pimd/nvt/bosonic* are "extensive", except -for the temperature, which is "intensive". - -Fix *pimd/langevin/bosonic* computes a global 6-vector, which can be accessed -by various :doc:`output commands `. The quantities in the -global vector are: - - #. kinetic energy of the beads, - #. spring elastic energy of the beads, - #. potential energy of the bead, - #. total energy of all beads (conserved if *ensemble* is *nve*) if *esynch* is *yes* - #. primitive kinetic energy estimator :ref:`(Hirshberg1) ` - #. virial energy estimator :ref:`(Herman) ` (see the justification in the supporting information of :ref:`(Hirshberg2) `). - -The first three are different for different log files, and the others -are the same for different log files, except for the primitive kinetic -energy estimator when setting *esynch* to *no*. Then, the primitive -kinetic energy estimator is obtained by summing over all log files. -Also note that when *esynch* is set to *no*, the fourth output gives the -total energy of all beads excluding the spring elastic energy; the total -classical energy can then be obtained by adding the sum of second output -over all log files. All vector values calculated by fix -*pimd/langevin/bosonic* are "extensive". - -For both *pimd/nvt/bosonic* and *pimd/langevin/bosonic*, the contribution of the -exterior spring to the primitive estimator is printed to the first log -file. The contribution of the :math:`P-1` interior springs is printed -to the other :math:`P-1` log files. The contribution of the constant -:math:`\frac{PdN}{2 \beta}` (with :math:`d` being the dimensionality) is -equally divided over log files. - -Restrictions -"""""""""""" - -These fixes are part of the REPLICA package. They are only enabled if -LAMMPS was built with that package. See the :doc:`Build package -` page for more info. - -The restrictions of :doc:`fix pimd ` apply. - -Related commands -"""""""""""""""" - -:doc:`pimd/nvt `, :doc:`pimd/langevin ` - -Default -""""""" - -The keyword defaults for fix *pimd/nvt/bosonic* are method = pimd, fmass = 1.0, -sp = 1.0, temp = 300.0, and nhc = 2. - -The keyword defaults for fix *pimd/langevin/bosonic* are integrator = obabo, -method = pimd, ensemble = nvt, fmass = 1.0, temp = 298.15, thermostat = -PILE_L, tau = 1.0, fixcom = yes, esynch = yes, and lj = 1 for all its -arguments. - ----------- - -.. _book-Tuckerman: - -**(Tuckerman)** M. Tuckerman, Statistical Mechanics: Theory and Molecular Simulation (Oxford University Press, 2010) - -.. _Hirshberg: - -**(Hirshberg1)** B. Hirshberg, V. Rizzi, and M. Parrinello, "Path integral molecular dynamics for bosons," Proc. Natl. Acad. Sci. U. S. A. 116, 21445 (2019) - -.. _HirshbergInvernizzi: - -**(Hirshberg2)** B. Hirshberg, M. Invernizzi, and M. Parrinello, "Path integral molecular dynamics for fermions: Alleviating the sign problem with the Bogoliubov inequality," J Chem Phys, 152, 171102 (2020) - -.. _Feldman: - -**(Feldman)** Y. M. Y. Feldman and B. Hirshberg, "Quadratic scaling bosonic path integral molecular dynamics," J. Chem. Phys. 159, 154107 (2023) - -.. _HigerFeldman: - -**(Higer)** J. Higer, Y. M. Y. Feldman, and B. Hirshberg, "Periodic Boundary Conditions for Bosonic Path Integral Molecular Dynamics," arXiv:2501.17618 (2025) - -.. _HermanBB: - -**(Herman)** M. F. Herman, E. J. Bruskin, B. J. Berne, J Chem Phys, 76, 5150 (1982). From a0d1deea446497a90768a2ba751b4cd7fe3212a0 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 14 Mar 2025 09:54:55 -0400 Subject: [PATCH 111/113] small clarification. add version tag for universe keyword --- doc/src/fix_halt.rst | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/doc/src/fix_halt.rst b/doc/src/fix_halt.rst index 1fb1a99da0..e2f74eae77 100644 --- a/doc/src/fix_halt.rst +++ b/doc/src/fix_halt.rst @@ -161,20 +161,20 @@ with *error soft* and followed by :doc:`timer timeout unlimited :doc:`run command ` uses the *every* keyword, so using *error soft* and resetting the timer manually may be the preferred option. -.. note:: - - You may wish use the :doc:`unfix ` command on the fix halt ID - before starting a subsequent run, so that the same condition is not - immediately triggered again. +You may wish use the :doc:`unfix ` command on the *fix halt* ID +before starting a subsequent run, so that the same condition is not +immediately triggered again. The optional *message* keyword determines whether a message is printed to the screen and logfile when the halt condition is triggered. If *message* is set to yes, a one line message with the values that -triggered the halt is printed. If *message* is set to no, no message -is printed; the run simply exits. The latter may be desirable for +triggered the halt is printed. If *message* is set to no, no message is +printed; the run simply exits. The latter may be desirable for post-processing tools that extract thermodynamic information from log files. +.. versionadded:: TBD + The optional *universe* keyword determines whether the halt request should be synchronized across the partitions of a :doc:`multi-partition run `. If *universe* is set to yes, fix halt will check if From 4c3260a0dc4690b4c24ab0c22e434a372fa51ac8 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 14 Mar 2025 12:18:23 -0400 Subject: [PATCH 112/113] fix bug missing a read_int() when reading general triclinic rotation matrix --- src/read_restart.cpp | 1 + 1 file changed, 1 insertion(+) diff --git a/src/read_restart.cpp b/src/read_restart.cpp index 615dd4b4b0..8e8fc84cd8 100644 --- a/src/read_restart.cpp +++ b/src/read_restart.cpp @@ -788,6 +788,7 @@ void ReadRestart::header() } else if (flag == TRICLINIC_GENERAL) { domain->triclinic_general = read_int(); } else if (flag == ROTATE_G2R) { + read_int(); read_double_vec(9,&domain->rotate_g2r[0][0]); MathExtra::transpose3(domain->rotate_g2r,domain->rotate_r2g); From 4e0d37ecc2bb3e33a7a8901c4a0d92b0e411d21d Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 14 Mar 2025 12:19:00 -0400 Subject: [PATCH 113/113] ensure that df[] array is always initialized --- src/EXTRA-COMPUTE/compute_stress_mop.cpp | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/src/EXTRA-COMPUTE/compute_stress_mop.cpp b/src/EXTRA-COMPUTE/compute_stress_mop.cpp index 7c66c1fe50..4dcab3e322 100644 --- a/src/EXTRA-COMPUTE/compute_stress_mop.cpp +++ b/src/EXTRA-COMPUTE/compute_stress_mop.cpp @@ -1117,6 +1117,11 @@ void ComputeStressMop::compute_dihedrals() df[1] = sgn * (f1[1] + f3[1]); df[2] = sgn * (f1[2] + f3[2]); } + + // no if matches + else { + df[0] = df[1] = df[2] = 0.0; + } local_contribution[0] += df[0] / area * nktv2p; local_contribution[1] += df[1] / area * nktv2p; local_contribution[2] += df[2] / area * nktv2p;