Loading cmake/presets/all_off.cmake +3 −3 Original line number Diff line number Diff line Loading @@ -7,11 +7,11 @@ set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU SRD VORONOI USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO USER-H5MD USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESODPD USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK USER-YAFF) USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK USER-YAFF) foreach(PKG ${ALL_PACKAGES}) set(PKG_${PKG} OFF CACHE BOOL "" FORCE) Loading cmake/presets/all_on.cmake +3 −3 Original line number Diff line number Diff line Loading @@ -9,11 +9,11 @@ set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU SRD VORONOI USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO USER-H5MD USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESODPD USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK USER-YAFF) USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK USER-YAFF) foreach(PKG ${ALL_PACKAGES}) set(PKG_${PKG} ON CACHE BOOL "" FORCE) Loading cmake/presets/most.cmake +7 −7 Original line number Diff line number Diff line Loading @@ -2,13 +2,13 @@ # external libraries. Compared to all_on.cmake some more unusual packages # are removed. The resulting binary should be able to run most inputs. set(ALL_PACKAGES ASPHERE CLASS2 COLLOID CORESHELL DIPOLE GRANULAR KSPACE MANYBODY MC MISC MOLECULE OPT PERI PYTHON QEQ REPLICA RIGID SHOCK SNAP SRD VORONOI USER-CGDNA USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-FEP USER-MEAMC USER-MESO USER-MISC USER-MOFFF USER-OMP USER-PHONON USER-REAXC USER-SPH USER-SMD USER-UEF USER-YAFF) set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GRANULAR KSPACE MANYBODY MC MISC MOLECULE OPT PERI POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN SRD VORONOI USER-CGDNA USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-FEP USER-MEAMC USER-MESODPD USER-MISC USER-MOFFF USER-OMP USER-PHONON USER-REACTION USER-REAXC USER-SPH USER-SMD USER-UEF USER-YAFF) foreach(PKG ${ALL_PACKAGES}) set(PKG_${PKG} ON CACHE BOOL "" FORCE) Loading doc/src/pair_dpd.rst +7 −3 Original line number Diff line number Diff line Loading @@ -129,13 +129,17 @@ the work of :ref:`(Afshar) <Afshar>` and :ref:`(Phillips) <Phillips>`. .. note:: The virial calculation for pressure when using this pair style The virial calculation for pressure when using these pair styles includes all the components of force listed above, including the random force. random force. Since the random force depends on random numbers, everything that changes the order of atoms in the neighbor list (e.g. different number of MPI ranks or a different neighbor list skin distance) will also change the sequence in which the random numbers are applied and thus the individual forces and therefore also the virial/pressure. ---------- Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available Loading doc/src/pair_srp.rst +6 −6 Original line number Diff line number Diff line Loading @@ -34,7 +34,7 @@ Examples pair_coeff 1 2 none pair_coeff 2 2 srp 100.0 0.8 pair_style hybrid dpd 1.0 1.0 12345 srp 0.8 \* min exclude yes pair_style hybrid dpd 1.0 1.0 12345 srp 0.8 * min exclude yes pair_coeff 1 1 dpd 60.0 50 1.0 pair_coeff 1 2 none pair_coeff 2 2 srp 40.0 Loading @@ -60,7 +60,7 @@ bond-pairwise potential, such that the force on bond *i* due to bond .. math:: F^{SRP}_{ij} & = C(1-r/r_c)\hat{r}_{ij} \qquad r < r_c F^{\mathrm{SRP}}_{ij} = C(1-r/r_c)\hat{r}_{ij} \qquad r < r_c where *r* and :math:`\hat{r}_{ij}` are the distance and unit vector Loading @@ -74,8 +74,8 @@ lever rule, .. math:: F_{i1}^{SRP} & = F^{SRP}_{ij}(L) \\ F_{i2}^{SRP} & = F^{SRP}_{ij}(1-L) F_{i1}^{\mathrm{SRP}} & = F^{\mathrm{SRP}}_{ij}(L) \\ F_{i2}^{\mathrm{SRP}} & = F^{\mathrm{SRP}}_{ij}(1-L) where *L* is the normalized distance from the atom to the point of Loading Loading
cmake/presets/all_off.cmake +3 −3 Original line number Diff line number Diff line Loading @@ -7,11 +7,11 @@ set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU SRD VORONOI USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO USER-H5MD USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESODPD USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK USER-YAFF) USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK USER-YAFF) foreach(PKG ${ALL_PACKAGES}) set(PKG_${PKG} OFF CACHE BOOL "" FORCE) Loading
cmake/presets/all_on.cmake +3 −3 Original line number Diff line number Diff line Loading @@ -9,11 +9,11 @@ set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU SRD VORONOI USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO USER-H5MD USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESODPD USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK USER-YAFF) USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK USER-YAFF) foreach(PKG ${ALL_PACKAGES}) set(PKG_${PKG} ON CACHE BOOL "" FORCE) Loading
cmake/presets/most.cmake +7 −7 Original line number Diff line number Diff line Loading @@ -2,13 +2,13 @@ # external libraries. Compared to all_on.cmake some more unusual packages # are removed. The resulting binary should be able to run most inputs. set(ALL_PACKAGES ASPHERE CLASS2 COLLOID CORESHELL DIPOLE GRANULAR KSPACE MANYBODY MC MISC MOLECULE OPT PERI PYTHON QEQ REPLICA RIGID SHOCK SNAP SRD VORONOI USER-CGDNA USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-FEP USER-MEAMC USER-MESO USER-MISC USER-MOFFF USER-OMP USER-PHONON USER-REAXC USER-SPH USER-SMD USER-UEF USER-YAFF) set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GRANULAR KSPACE MANYBODY MC MISC MOLECULE OPT PERI POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN SRD VORONOI USER-CGDNA USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-FEP USER-MEAMC USER-MESODPD USER-MISC USER-MOFFF USER-OMP USER-PHONON USER-REACTION USER-REAXC USER-SPH USER-SMD USER-UEF USER-YAFF) foreach(PKG ${ALL_PACKAGES}) set(PKG_${PKG} ON CACHE BOOL "" FORCE) Loading
doc/src/pair_dpd.rst +7 −3 Original line number Diff line number Diff line Loading @@ -129,13 +129,17 @@ the work of :ref:`(Afshar) <Afshar>` and :ref:`(Phillips) <Phillips>`. .. note:: The virial calculation for pressure when using this pair style The virial calculation for pressure when using these pair styles includes all the components of force listed above, including the random force. random force. Since the random force depends on random numbers, everything that changes the order of atoms in the neighbor list (e.g. different number of MPI ranks or a different neighbor list skin distance) will also change the sequence in which the random numbers are applied and thus the individual forces and therefore also the virial/pressure. ---------- Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available Loading
doc/src/pair_srp.rst +6 −6 Original line number Diff line number Diff line Loading @@ -34,7 +34,7 @@ Examples pair_coeff 1 2 none pair_coeff 2 2 srp 100.0 0.8 pair_style hybrid dpd 1.0 1.0 12345 srp 0.8 \* min exclude yes pair_style hybrid dpd 1.0 1.0 12345 srp 0.8 * min exclude yes pair_coeff 1 1 dpd 60.0 50 1.0 pair_coeff 1 2 none pair_coeff 2 2 srp 40.0 Loading @@ -60,7 +60,7 @@ bond-pairwise potential, such that the force on bond *i* due to bond .. math:: F^{SRP}_{ij} & = C(1-r/r_c)\hat{r}_{ij} \qquad r < r_c F^{\mathrm{SRP}}_{ij} = C(1-r/r_c)\hat{r}_{ij} \qquad r < r_c where *r* and :math:`\hat{r}_{ij}` are the distance and unit vector Loading @@ -74,8 +74,8 @@ lever rule, .. math:: F_{i1}^{SRP} & = F^{SRP}_{ij}(L) \\ F_{i2}^{SRP} & = F^{SRP}_{ij}(1-L) F_{i1}^{\mathrm{SRP}} & = F^{\mathrm{SRP}}_{ij}(L) \\ F_{i2}^{\mathrm{SRP}} & = F^{\mathrm{SRP}}_{ij}(1-L) where *L* is the normalized distance from the atom to the point of Loading
