From 27bf4d797466a0c664b593ee6e2a76ac6b30f31e Mon Sep 17 00:00:00 2001 From: Jacob Gissinger Date: Thu, 15 Aug 2024 18:15:30 -0400 Subject: [PATCH 01/11] bond/react: change where to reset mol IDs needs to happen after topology changes communicated --- src/REACTION/fix_bond_react.cpp | 14 ++++++++++---- src/REACTION/fix_bond_react.h | 1 + 2 files changed, 11 insertions(+), 4 deletions(-) diff --git a/src/REACTION/fix_bond_react.cpp b/src/REACTION/fix_bond_react.cpp index 8c241355fd..f2968a2001 100644 --- a/src/REACTION/fix_bond_react.cpp +++ b/src/REACTION/fix_bond_react.cpp @@ -716,6 +716,7 @@ int FixBondReact::setmask() int mask = 0; mask |= POST_INTEGRATE; mask |= POST_INTEGRATE_RESPA; + mask |= POST_FORCE; return mask; } @@ -3620,10 +3621,6 @@ void FixBondReact::update_everything() atom->natoms -= ndel; // done deleting atoms - - // reset mol ids - if (reset_mol_ids_flag) reset_mol_ids->reset(); - // something to think about: this could done much more concisely if // all atom-level info (bond,angles, etc...) were kinda inherited from a common data struct --JG @@ -4071,6 +4068,8 @@ void FixBondReact::CreateAtoms(char *line, int myrxn) readline(line); rv = sscanf(line,"%d",&tmp); if (rv != 1) error->one(FLERR, "CreateIDs section is incorrectly formatted"); + if (tmp > twomol->natoms) + error->one(FLERR,"Fix bond/react: Invalid atom ID in CreateIDs section of map file"); create_atoms[tmp-1][myrxn] = 1; } if (twomol->xflag == 0) @@ -4331,6 +4330,13 @@ void FixBondReact::post_integrate_respa(int ilevel, int /*iloop*/) /* ---------------------------------------------------------------------- */ +void FixBondReact::post_force(int /*vflag*/) +{ + if (reset_mol_ids_flag) reset_mol_ids->reset(); +} + +/* ---------------------------------------------------------------------- */ + int FixBondReact::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int * /*pbc*/) { diff --git a/src/REACTION/fix_bond_react.h b/src/REACTION/fix_bond_react.h index 8c9fc9dce4..d79588c6dd 100644 --- a/src/REACTION/fix_bond_react.h +++ b/src/REACTION/fix_bond_react.h @@ -46,6 +46,7 @@ class FixBondReact : public Fix { void init_list(int, class NeighList *) override; void post_integrate() override; void post_integrate_respa(int, int) override; + void post_force(int) override; int pack_forward_comm(int, int *, double *, int, int *) override; void unpack_forward_comm(int, int, double *) override; From c68ea4fe1e8c409daf26d8b99c2359cea0e8dbfa Mon Sep 17 00:00:00 2001 From: Jacob Gissinger Date: Thu, 15 Aug 2024 19:09:16 -0400 Subject: [PATCH 02/11] better place for error check --- src/REACTION/fix_bond_react.cpp | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/src/REACTION/fix_bond_react.cpp b/src/REACTION/fix_bond_react.cpp index f2968a2001..ab9f734a8d 100644 --- a/src/REACTION/fix_bond_react.cpp +++ b/src/REACTION/fix_bond_react.cpp @@ -486,10 +486,6 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : get_molxspecials(); read_map_file(i); fclose(fp); - if (ncreate == 0 && onemol->natoms != twomol->natoms) - error->all(FLERR,"Fix bond/react: Reaction templates must contain the same number of atoms"); - else if (ncreate > 0 && onemol->natoms + ncreate != twomol->natoms) - error->all(FLERR,"Fix bond/react: Incorrect number of created atoms"); iatomtype[i] = onemol->type[ibonding[i]-1]; jatomtype[i] = onemol->type[jbonding[i]-1]; find_landlocked_atoms(i); @@ -3967,6 +3963,11 @@ void FixBondReact::read_map_file(int myrxn) } else break; } + if (ncreate == 0 && onemol->natoms != twomol->natoms) + error->all(FLERR,"Fix bond/react: Reaction templates must contain the same number of atoms"); + else if (ncreate > 0 && onemol->natoms + ncreate != twomol->natoms) + error->all(FLERR,"Fix bond/react: Incorrect number of created atoms"); + // grab keyword and skip next line parse_keyword(0,line,keyword); From 732be489a330d5872bde1c0f08edac09b17bdd7e Mon Sep 17 00:00:00 2001 From: Jacob Gissinger Date: Thu, 15 Aug 2024 19:48:17 -0400 Subject: [PATCH 03/11] another error check --- src/REACTION/fix_bond_react.cpp | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/src/REACTION/fix_bond_react.cpp b/src/REACTION/fix_bond_react.cpp index ab9f734a8d..bd8b3459e2 100644 --- a/src/REACTION/fix_bond_react.cpp +++ b/src/REACTION/fix_bond_react.cpp @@ -4010,6 +4010,13 @@ void FixBondReact::read_map_file(int myrxn) } + // error check + for (int i = 0; i < onemol->natoms; i++) { + int my_equiv = reverse_equiv[i][1][myrxn]; + if (create_atoms[my_equiv-1][myrxn] == 1) + error->all(FLERR,"Fix bond/react: Created atoms cannot also be listed in Equivalences section\n"); + } + // error check if (bondflag == 0 || equivflag == 0) error->all(FLERR,"Fix bond/react: Map file missing InitiatorIDs or Equivalences section\n"); From 7de2073e8ebd7d7c83fa54d558f5eb925f87b111 Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Wed, 21 Aug 2024 12:46:45 -0600 Subject: [PATCH 04/11] better explanations of vector outputs for compute temp commands --- doc/src/compute_temp.rst | 33 ++++++++------- doc/src/compute_temp_asphere.rst | 25 ++++++++--- doc/src/compute_temp_body.rst | 29 +++++++------ doc/src/compute_temp_chunk.rst | 28 +++++++------ doc/src/compute_temp_com.rst | 31 ++++++++------ doc/src/compute_temp_cs.rst | 51 ++++++++++++----------- doc/src/compute_temp_deform.rst | 30 ++++++++------ doc/src/compute_temp_deform_eff.rst | 33 ++++++++------- doc/src/compute_temp_partial.rst | 28 +++++++------ doc/src/compute_temp_profile.rst | 64 +++++++++++++++++------------ doc/src/compute_temp_ramp.rst | 36 +++++++++------- doc/src/compute_temp_region.rst | 44 +++++++++++--------- doc/src/compute_temp_region_eff.rst | 29 ++++++------- doc/src/compute_temp_rotate.rst | 30 ++++++++------ doc/src/compute_temp_sphere.rst | 24 ++++++++--- doc/src/compute_viscosity_cos.rst | 37 +++++++++-------- 16 files changed, 322 insertions(+), 230 deletions(-) diff --git a/doc/src/compute_temp.rst b/doc/src/compute_temp.rst index e081280496..4c7a46b822 100644 --- a/doc/src/compute_temp.rst +++ b/doc/src/compute_temp.rst @@ -48,14 +48,18 @@ the group, :math:`N_\mathrm{fix DOFs}` is the number of degrees of freedom removed by fix commands (see below), :math:`k_B` is the Boltzmann constant, and :math:`T` is the resulting computed temperature. -A kinetic energy tensor, stored as a six-element vector, is also -calculated by this compute for use in the computation of a pressure -tensor. The formula for the components of the tensor is the same as the -above expression for :math:`E_\mathrm{kin}`, except that :math:`v_i^2` is -replaced by :math:`v_{i,x} v_{i,y}` for the :math:`xy` component, and so on. -The six components of the vector are ordered :math:`xx`, :math:`yy`, -:math:`zz`, :math:`xy`, :math:`xz`, :math:`yz`. - +A symmetric tensor, stored as a six-element vector, is also calculated +by this compute for use in the computation of a pressure tensor by the +:doc:`compute pressue ` command. The formula for +the components of the tensor is the same as the above expression for +:math:`E_\mathrm{kin}`, except that the 1/2 factor is NOT included and +the :math:`v_i^2` is replaced by :math:`v_{i,x} v_{i,y}` for the +:math:`xy` component, and so on. Note that because it lacks the 1/2 +factor, these tensor components are twice those of the traditional +kinetic energy tensor. The six components of the vector are ordered +:math:`xx`, :math:`yy`, :math:`zz`, :math:`xy`, :math:`xz`, +:math:`yz`. + The number of atoms contributing to the temperature is assumed to be constant for the duration of the run; use the *dynamic* option of the :doc:`compute_modify ` command if this is not the case. @@ -94,16 +98,17 @@ Output info """"""""""" This compute calculates a global scalar (the temperature) and a global -vector of length six (KE tensor), which can be accessed by indices -1--6. These values can be used by any command that uses global scalar -or vector values from a compute as input. See the :doc:`Howto output -` page for an overview of LAMMPS output options. +vector of length six (symmetric tensor), which can be accessed by +indices 1--6. These values can be used by any command that uses +global scalar or vector values from a compute as input. See the +:doc:`Howto output ` page for an overview of LAMMPS +output options. The scalar value calculated by this compute is "intensive". The vector values are "extensive". -The scalar value will be in temperature :doc:`units `. The -vector values will be in energy :doc:`units `. +The scalar value is in temperature :doc:`units `. The vector +values are in energy :doc:`units `. Restrictions """""""""""" diff --git a/doc/src/compute_temp_asphere.rst b/doc/src/compute_temp_asphere.rst index 5741db76aa..c9b1e51532 100644 --- a/doc/src/compute_temp_asphere.rst +++ b/doc/src/compute_temp_asphere.rst @@ -90,6 +90,19 @@ for the :math:`xy` component, and the appropriate elements of the moment of inertia tensor are used. The six components of the vector are ordered :math:`xx`, :math:`yy`, :math:`zz`, :math:`xy`, :math:`xz`, :math:`yz`. +A symmetric tensor, stored as a six-element vector, is also calculated +by this compute for use in the computation of a pressure tensor by the +:doc:`compute pressue ` command. The formula for +the components of the tensor is the same as the above expression for +:math:`E_\mathrm{kin}`, except that the 1/2 factor is NOT included and +the :math:`v_i^2` and :math:`\omega^2` are replaced by :math:`v_x v_y` +and :math:`\omega_x \omega_y` for the :math:`xy` component, and so on. +And the appropriate elements of the moment of inertia tensor are used. +Note that because it lacks the 1/2 factor, these tensor components are +twice those of the traditional kinetic energy tensor. The six +components of the vector are ordered :math:`xx`, :math:`yy`, +:math:`zz`, :math:`xy`, :math:`xz`, :math:`yz`. + The number of atoms contributing to the temperature is assumed to be constant for the duration of the run; use the *dynamic/dof* option of the :doc:`compute_modify ` command if this is not the @@ -131,17 +144,17 @@ Output info """"""""""" This compute calculates a global scalar (the temperature) and a global -vector of length 6 (KE tensor), which can be accessed by indices 1--6. -These values can be used by any command that uses global scalar or -vector values from a compute as input. -See the :doc:`Howto output ` page for an overview of LAMMPS +vector of length 6 (symmertic tensor), which can be accessed by +indices 1--6. These values can be used by any command that uses +global scalar or vector values from a compute as input. See the +:doc:`Howto output ` page for an overview of LAMMPS output options. The scalar value calculated by this compute is "intensive". The vector values are "extensive". -The scalar value will be in temperature :doc:`units `. The -vector values will be in energy :doc:`units `. +The scalar value is in temperature :doc:`units `. The vector +values are in energy :doc:`units `. Restrictions """""""""""" diff --git a/doc/src/compute_temp_body.rst b/doc/src/compute_temp_body.rst index f29ca5c39b..ef536c1af7 100644 --- a/doc/src/compute_temp_body.rst +++ b/doc/src/compute_temp_body.rst @@ -62,12 +62,17 @@ kinetic energy is computed as :math:`\frac12 I \omega^2`, where :math:`I` is the moment of inertia tensor for the aspherical particle and :math:`\omega` is its angular velocity, which is computed from its angular momentum. -A kinetic energy tensor, stored as a 6-element vector, is also calculated by -this compute. The formula for the components of the tensor is the same as the -above formula, except that :math:`v^2` and :math:`\omega^2` are -replaced by :math:`v_x v_y` and :math:`\omega_x \omega_y` for the -math:`xy` component, and the appropriate elements of the inertia tensor are -used. The six components of the vector are ordered :math:`xx`, :math:`yy`, +A symmetric tensor, stored as a six-element vector, is also calculated +by this compute for use in the computation of a pressure tensor by the +:doc:`compute pressue ` command. The formula for +the components of the tensor is the same as the above expression for +:math:`E_\mathrm{kin}`, except that the 1/2 factor is NOT included and +the :math:`v_i^2` and :math:`\omega^2` are replaced by :math:`v_x v_y` +and :math:`\omega_x \omega_y` for the :math:`xy` component, and so on. +And the appropriate elements of the moment of inertia tensor are used. +Note that because it lacks the 1/2 factor, these tensor components are +twice those of the traditional kinetic energy tensor. The six +components of the vector are ordered :math:`xx`, :math:`yy`, :math:`zz`, :math:`xy`, :math:`xz`, :math:`yz`. The number of atoms contributing to the temperature is assumed to be @@ -111,17 +116,17 @@ Output info """"""""""" This compute calculates a global scalar (the temperature) and a global -vector of length 6 (KE tensor), which can be accessed by indices 1--6. -These values can be used by any command that uses global scalar or -vector values from a compute as input. -See the :doc:`Howto output ` page for an overview of LAMMPS +vector of length 6 (symmetric tensor), which can be accessed by +indices 1--6. These values can be used by any command that uses +global scalar or vector values from a compute as input. See the +:doc:`Howto output ` page for an overview of LAMMPS output options. The scalar value calculated by this compute is "intensive". The vector values are "extensive". -The scalar value will be in temperature :doc:`units `. -The vector values will be in energy :doc:`units `. +The scalar value is in temperature :doc:`units `. The vector +values are in energy :doc:`units `. Restrictions """""""""""" diff --git a/doc/src/compute_temp_chunk.rst b/doc/src/compute_temp_chunk.rst index c92b4e36e9..33eab04343 100644 --- a/doc/src/compute_temp_chunk.rst +++ b/doc/src/compute_temp_chunk.rst @@ -85,12 +85,14 @@ By default, *adof* = 2 or 3 = dimensionality of system, as set via the :doc:`dimension ` command, and *cdof* = 0.0. This gives the usual formula for temperature. -A kinetic energy tensor, stored as a six-element vector, is also -calculated by this compute for use in the computation of a pressure -tensor. The formula for the components of the tensor is the same as -the above formula, except that :math:`v^2` is replaced by -:math:`v_x v_y` for the :math:`xy` component, and so on. -The six components of the vector are ordered :math:`xx`, :math:`yy`, +A symmetric tensor, stored as a six-element vector, is also calculated +by this compute. The formula for the components of the tensor is the +same as the above expression for :math:`E_\mathrm{kin}`, except that +the 1/2 factor is NOT included and the :math:`v_i^2` is replaced by +:math:`v_{i,x} v_{i,y}` for the :math:`xy` component, and so on. Note +that because it lacks the 1/2 factor, these tensor components are +twice those of the traditional kinetic energy tensor. The six +components of the vector are ordered :math:`xx`, :math:`yy`, :math:`zz`, :math:`xy`, :math:`xz`, :math:`yz`. Note that the number of atoms contributing to the temperature is @@ -227,10 +229,10 @@ Output info """"""""""" This compute calculates a global scalar (the temperature) and a global -vector of length 6 (KE tensor), which can be accessed by indices 1--6. -These values can be used by any command that uses global scalar or -vector values from a compute as input. -See the :doc:`Howto output ` page for an overview of LAMMPS +vector of length 6 (symmetric tensor), which can be accessed by +indices 1--6. These values can be used by any command that uses +global scalar or vector values from a compute as input. See the +:doc:`Howto output ` page for an overview of LAMMPS output options. This compute also optionally calculates a global array, if one or more @@ -245,9 +247,9 @@ page for an overview of LAMMPS output options. The scalar value calculated by this compute is "intensive". The vector values are "extensive". The array values are "intensive". -The scalar value will be in temperature :doc:`units `. The -vector values will be in energy :doc:`units `. The array values -will be in temperature :doc:`units ` for the *temp* value, and in +The scalar value is in temperature :doc:`units `. The vector +values are in energy :doc:`units `. The array values will be +in temperature :doc:`units ` for the *temp* value, and in energy :doc:`units ` for the *kecom* and *internal* values. Restrictions diff --git a/doc/src/compute_temp_com.rst b/doc/src/compute_temp_com.rst index d54fa7dfa6..e94c911dfa 100644 --- a/doc/src/compute_temp_com.rst +++ b/doc/src/compute_temp_com.rst @@ -44,12 +44,17 @@ where KE is the total kinetic energy of the group of atoms (sum of simulation, :math:`N` is number of atoms in the group, :math:`k_B` is the Boltzmann constant, and :math:`T` is the absolute temperature. -A kinetic energy tensor, stored as a six-element vector, is also -calculated by this compute for use in the computation of a pressure -tensor. The formula for the components of the tensor is the same as -the above formula, except that :math:`v^2` is replaced by :math:`v_x v_y` -for the :math:`xy` component, and so on. The six components of the vector are -ordered :math:`xx`, :math:`yy`, :math:`zz`, :math:`xy`, :math:`xz`, :math:`yz`. +A symmetric tensor, stored as a six-element vector, is also calculated +by this compute for use in the computation of a pressure tensor by the +:doc:`compute pressue ` command. The formula for +the components of the tensor is the same as the above expression for +:math:`E_\mathrm{kin}`, except that the 1/2 factor is NOT included and +the :math:`v_i^2` is replaced by :math:`v_{i,x} v_{i,y}` for the +:math:`xy` component, and so on. Note that because it lacks the 1/2 +factor, these tensor components are twice those of the traditional +kinetic energy tensor. The six components of the vector are ordered +:math:`xx`, :math:`yy`, :math:`zz`, :math:`xy`, :math:`xz`, +:math:`yz`. The number of atoms contributing to the temperature is assumed to be constant for the duration of the run; use the *dynamic* option of the @@ -81,17 +86,17 @@ Output info """"""""""" This compute calculates a global scalar (the temperature) and a global -vector of length 6 (KE tensor), which can be accessed by indices 1--6. -These values can be used by any command that uses global scalar or -vector values from a compute as input. See the -:doc:`Howto output ` page for an overview of LAMMPS output -options. +vector of length 6 (symmetric tensor), which can be accessed by +indices 1--6. These values can be used by any command that uses +global scalar or vector values from a compute as input. See the +:doc:`Howto output ` page for an overview of LAMMPS +output options. The scalar value calculated by this compute is "intensive". The vector values are "extensive". -The scalar value will be in temperature :doc:`units `. -The vector values will be in energy :doc:`units `. +The scalar value is in temperature :doc:`units `. The vector +values is in energy :doc:`units `. Restrictions """""""""""" diff --git a/doc/src/compute_temp_cs.rst b/doc/src/compute_temp_cs.rst index a33fbf7ffb..0620fea9b7 100644 --- a/doc/src/compute_temp_cs.rst +++ b/doc/src/compute_temp_cs.rst @@ -67,26 +67,31 @@ the velocity of each core or shell atom used in the KE calculation is the velocity of the center-of-mass (COM) of the core/shell pair the atom is part of. -A kinetic energy tensor, stored as a six-element vector, is also calculated by -this compute for use in the computation of a pressure tensor. The formula for -the components of the tensor is the same as the above formula, except that -:math:`v^2` is replaced by :math:`v_x v_y` for the :math:`xy` component, and so -on. The six components of the vector are ordered :math:`xx`, :math:`yy`, -:math:`zz`, :math:`xy`, :math:`xz`, :math:`yz`. In contrast to the temperature, -the velocity of each core or shell atom is taken individually. +A symmetric tensor, stored as a six-element vector, is also calculated +by this compute for use in the computation of a pressure tensor by the +:doc:`compute pressue ` command. The formula for +the components of the tensor is the same as the above expression for +:math:`E_\mathrm{kin}`, except that the 1/2 factor is NOT included and +the :math:`v_i^2` is replaced by :math:`v_{i,x} v_{i,y}` for the +:math:`xy` component, and so on. Note that because it lacks the 1/2 +factor, these tensor components are twice those of the traditional +kinetic energy tensor. The six components of the vector are ordered +:math:`xx`, :math:`yy`, :math:`zz`, :math:`xy`, :math:`xz`, +:math:`yz`. The change this fix makes to core/shell atom velocities is essentially -computing the temperature after a "bias" has been removed from the velocity of -the atoms. This "bias" is the velocity of the atom relative to the -center-of-mass velocity of the core/shell pair. If this compute is used with a -fix command that performs thermostatting then this bias will be subtracted from -each atom, thermostatting of the remaining center-of-mass velocity will be -performed, and the bias will be added back in. This means the thermostatting -will effectively be performed on the core/shell pairs, instead of on the -individual core and shell atoms. Thermostatting fixes that work in this way -include :doc:`fix nvt `, :doc:`fix temp/rescale `, -:doc:`fix temp/berendsen `, and -:doc:`fix langevin `. +computing the temperature after a "bias" has been removed from the +velocity of the atoms. This "bias" is the velocity of the atom +relative to the center-of-mass velocity of the core/shell pair. If +this compute is used with a fix command that performs thermostatting +then this bias will be subtracted from each atom, thermostatting of +the remaining center-of-mass velocity will be performed, and the bias +will be added back in. This means the thermostatting will effectively +be performed on the core/shell pairs, instead of on the individual +core and shell atoms. Thermostatting fixes that work in this way +include :doc:`fix nvt `, :doc:`fix temp/rescale +`, :doc:`fix temp/berendsen `, +and :doc:`fix langevin `. The internal energy of core/shell pairs can be calculated by the :doc:`compute temp/chunk ` command, if chunks are defined @@ -97,15 +102,15 @@ Output info """"""""""" This compute calculates a global scalar (the temperature) and a global -vector of length 6 (KE tensor), which can be accessed by indices 1--6. -These values can be used by any command that uses global scalar or -vector values from a compute as input. +vector of length 6 (symmertric tensor), which can be accessed by +indices 1--6. These values can be used by any command that uses +global scalar or vector values from a compute as input. The scalar value calculated by this compute is "intensive". The vector values are "extensive". -The scalar value will be in temperature :doc:`units `. The -vector values will be in energy :doc:`units `. +The scalar value is in temperature :doc:`units `. The vector +values are in energy :doc:`units `. Restrictions """""""""""" diff --git a/doc/src/compute_temp_deform.rst b/doc/src/compute_temp_deform.rst index adf76564a8..1c8c2da096 100644 --- a/doc/src/compute_temp_deform.rst +++ b/doc/src/compute_temp_deform.rst @@ -73,12 +73,16 @@ simulation, :math:`N` is the number of atoms in the group, :math:`k_B` is the Boltzmann constant, and :math:`T` is the temperature. Note that :math:`v` in the kinetic energy formula is the atom's velocity. -A kinetic energy tensor, stored as a six-element vector, is also -calculated by this compute for use in the computation of a pressure -tensor. The formula for the components of the tensor is the same as -the above formula, except that :math:`v^2` is replaced by :math:`v_x v_y` for -the :math:`xy` component, and so on. The six components of the vector are -ordered :math:`xx`, :math:`yy`, :math:`zz`, :math:`xy`, :math:`xz`, +A symmetric tensor, stored as a six-element vector, is also calculated +by this compute for use in the computation of a pressure tensor by the +:doc:`compute pressue ` command. The formula for +the components of the tensor is the same as the above expression for +:math:`E_\mathrm{kin}`, except that the 1/2 factor is NOT included and +the :math:`v_i^2` is replaced by :math:`v_{i,x} v_{i,y}` for the +:math:`xy` component, and so on. Note that because it lacks the 1/2 +factor, these tensor components are twice those of the traditional +kinetic energy tensor. The six components of the vector are ordered +:math:`xx`, :math:`yy`, :math:`zz`, :math:`xy`, :math:`xz`, :math:`yz`. The number of atoms contributing to the temperature is assumed to be @@ -128,17 +132,17 @@ Output info """"""""""" This compute calculates a global scalar (the temperature) and a global -vector of length 6 (KE tensor), which can be accessed by indices 1--6. -These values can be used by any command that uses global scalar or -vector values from a compute as input. See the -:doc:`Howto output ` page for an overview of LAMMPS output -options. +vector of length 6 (symmetric tensor), which can be accessed by +indices 1--6. These values can be used by any command that uses +global scalar or vector values from a compute as input. See the +:doc:`Howto output ` page for an overview of LAMMPS +output options. The scalar value calculated by this compute is "intensive". The vector values are "extensive". -The scalar value will be in temperature :doc:`units `. -The vector values will be in energy :doc:`units `. +The scalar value is in temperature :doc:`units `. The vector +values are in energy :doc:`units `. Restrictions """""""""""" diff --git a/doc/src/compute_temp_deform_eff.rst b/doc/src/compute_temp_deform_eff.rst index 83535f4727..3c22ad8045 100644 --- a/doc/src/compute_temp_deform_eff.rst +++ b/doc/src/compute_temp_deform_eff.rst @@ -29,17 +29,20 @@ model, after subtracting out a streaming velocity induced by the simulation box changing size and/or shape, for example in a non-equilibrium MD (NEMD) simulation. The size/shape change is induced by use of the :doc:`fix deform ` command. A -compute of this style is created by the -:doc:`fix nvt/sllod/eff ` command to compute the thermal -temperature of atoms for thermostatting purposes. A compute of this -style can also be used by any command that computes a temperature -(e.g., :doc:`thermo_modify `, :doc:`fix npt/eff `). +compute of this style is created by the :doc:`fix nvt/sllod/eff +` command to compute the thermal temperature of +atoms for thermostatting purposes. A compute of this style can also +be used by any command that computes a temperature (e.g., +:doc:`thermo_modify `, :doc:`fix npt/eff +`). The calculation performed by this compute is exactly like that described by the :doc:`compute temp/deform ` -command, except that the formula for the temperature includes the -radial electron velocity contributions, as discussed by the :doc:`compute temp/eff ` command. Note that only the -translational degrees of freedom for each nuclei or electron are +command, except that the formulas for the temperature (scalar) and +diagonal components of the symmetric tensor (vector) include the +radial electron velocity contributions, as discussed by the +:doc:`compute temp/eff ` command. Note that only +the translational degrees of freedom for each nuclei or electron are affected by the streaming velocity adjustment. The radial velocity component of the electrons is not affected. @@ -47,17 +50,17 @@ Output info """"""""""" This compute calculates a global scalar (the temperature) and a global -vector of length 6 (KE tensor), which can be accessed by indices 1--6. -These values can be used by any command that uses global scalar or -vector values from a compute as input. See the -:doc:`Howto output ` page for an overview of LAMMPS output -options. +vector of length 6 (symmetric tensor), which can be accessed by +indices 1--6. These values can be used by any command that uses +global scalar or vector values from a compute as input. See the +:doc:`Howto output ` page for an overview of LAMMPS +output options. The scalar value calculated by this compute is "intensive". The vector values are "extensive". -The scalar value will be in temperature :doc:`units `. The -vector values will be in energy :doc:`units `. +The scalar value is in temperature :doc:`units `. The vector +values are in energy :doc:`units `. Restrictions """""""""""" diff --git a/doc/src/compute_temp_partial.rst b/doc/src/compute_temp_partial.rst index d5628e0d60..d98558c159 100644 --- a/doc/src/compute_temp_partial.rst +++ b/doc/src/compute_temp_partial.rst @@ -44,12 +44,16 @@ constant, and :math:`T` = temperature. The calculation of KE excludes the is 0. The dim parameter is adjusted to give the correct number of degrees of freedom. -A kinetic energy tensor, stored as a six-element vector, is also -calculated by this compute for use in the calculation of a pressure -tensor. The formula for the components of the tensor is the same as -the above formula, except that :math:`v^2` is replaced by :math:`v_x v_y` for -the :math:`xy` component, and so on. The six components of the vector are -ordered :math:`xx`, :math:`yy`, :math:`zz`, :math:`xy`, :math:`xz`, +A symmetric tensor, stored as a six-element vector, is also calculated +by this compute for use in the computation of a pressure tensor by the +:doc:`compute pressue ` command. The formula for +the components of the tensor is the same as the above expression for +:math:`E_\mathrm{kin}`, except that the 1/2 factor is NOT included and +the :math:`v_i^2` is replaced by :math:`v_{i,x} v_{i,y}` for the +:math:`xy` component, and so on. Note that because it lacks the 1/2 +factor, these tensor components are twice those of the traditional +kinetic energy tensor. The six components of the vector are ordered +:math:`xx`, :math:`yy`, :math:`zz`, :math:`xy`, :math:`xz`, :math:`yz`. The number of atoms contributing to the temperature is assumed to be @@ -88,17 +92,17 @@ Output info """"""""""" This compute calculates a global scalar (the temperature) and a global -vector of length 6 (KE tensor), which can be accessed by indices 1--6. -These values can be used by any command that uses global scalar or -vector values from a compute as input. -See the :doc:`Howto output ` page for an overview of LAMMPS +vector of length 6 (symmetric tensor), which can be accessed by +indices 1--6. These values can be used by any command that uses +global scalar or vector values from a compute as input. See the +:doc:`Howto output ` page for an overview of LAMMPS output options. The scalar value calculated by this compute is "intensive". The vector values are "extensive". -The scalar value will be in temperature :doc:`units `. The -vector values will be in energy :doc:`units `. +The scalar value is in temperature :doc:`units `. The vector +values are in energy :doc:`units `. Restrictions """""""""""" diff --git a/doc/src/compute_temp_profile.rst b/doc/src/compute_temp_profile.rst index 566d8cf3fc..47725cdcbc 100644 --- a/doc/src/compute_temp_profile.rst +++ b/doc/src/compute_temp_profile.rst @@ -97,21 +97,27 @@ center-of-mass velocity across the group in directions where streaming velocity is *not* subtracted. This can be altered using the *extra* option of the :doc:`compute_modify ` command. -If the *out* keyword is used with a *tensor* value, which is the default, -a kinetic energy tensor, stored as a six-element vector, is also calculated by -this compute for use in the computation of a pressure tensor. The formula for -the components of the tensor is the same as the above formula, except that -:math:`v^2` is replaced by :math:`v_x v_y` for the :math:`xy` component, and -so on. The six components of the vector are ordered :math:`xx`, :math:`yy`, +If the *out* keyword is used with a *tensor* value, which is the +default, then a symmetric tensor, stored as a six-element vector, is +also calculated by this compute for use in the computation of a +pressure tensor by the :doc:`compute pressue ` +command. The formula for the components of the tensor is the same as +the above expression for :math:`E_\mathrm{kin}`, except that the 1/2 +factor is NOT included and the :math:`v_i^2` is replaced by +:math:`v_{i,x} v_{i,y}` for the :math:`xy` component, and so on. Note +that because it lacks the 1/2 factor, these tensor components are +twice those of the traditional kinetic energy tensor. The six +components of the vector are ordered :math:`xx`, :math:`yy`, :math:`zz`, :math:`xy`, :math:`xz`, :math:`yz`. -If the *out* keyword is used with a *bin* value, the count of atoms and -computed temperature for each bin are stored for output, as an array of values, -as described below. The temperature of each bin is calculated as described -above, where the bias velocity is subtracted and only the remaining thermal -velocity of atoms in the bin contributes to the temperature. See the note -below for how the temperature is normalized by the degrees-of-freedom of atoms -in the bin. +If the *out* keyword is used with a *bin* value, the count of atoms +and computed temperature for each bin are stored for output, as an +array of values, as described below. The temperature of each bin is +calculated as described above, where the bias velocity is subtracted +and only the remaining thermal velocity of atoms in the bin +contributes to the temperature. See the note below for how the +temperature is normalized by the degrees-of-freedom of atoms in the +bin. The number of atoms contributing to the temperature is assumed to be constant for the duration of the run; use the *dynamic* option of the @@ -166,16 +172,17 @@ Output info This compute calculates a global scalar (the temperature). Depending on the setting of the *out* keyword, it also calculates a global vector or array. For *out* = *tensor*, it calculates a vector of -length 6 (KE tensor), which can be accessed by indices 1--6. For *out* -= *bin* it calculates a global array which has 2 columns and :math:`N` rows, -where :math:`N` is the number of bins. The first column contains the number -of atoms in that bin. The second contains the temperature of that -bin, calculated as described above. The ordering of rows in the array -is as follows. Bins in :math:`x` vary fastest, then :math:`y`, then -:math:`z`. Thus for a :math:`10\times 10\times 10` 3d array of bins, there -will be 1000 rows. The bin with indices :math:`(i_x,i_y,i_z) = (2,3,4)` would -map to row :math:`M = 10^2(i_z-1) + 10(i_y-1) + i_x = 322`, where the rows are -numbered from 1 to 1000 and the bin indices are numbered from 1 to 10 in each +length 6 (symmetric tensor), which can be accessed by indices 1--6. +For *out* = *bin* it calculates a global array which has 2 columns and +:math:`N` rows, where :math:`N` is the number of bins. The first +column contains the number of atoms in that bin. The second contains +the temperature of that bin, calculated as described above. The +ordering of rows in the array is as follows. Bins in :math:`x` vary +fastest, then :math:`y`, then :math:`z`. Thus for a :math:`10\times +10\times 10` 3d array of bins, there will be 1000 rows. The bin with +indices :math:`(i_x,i_y,i_z) = (2,3,4)` would map to row :math:`M = +10^2(i_z-1) + 10(i_y-1) + i_x = 322`, where the rows are numbered from +1 to 1000 and the bin indices are numbered from 1 to 10 in each dimension. These values can be used by any command that uses global scalar or @@ -186,9 +193,9 @@ options. The scalar value calculated by this compute is "intensive". The vector values are "extensive". The array values are "intensive". -The scalar value will be in temperature :doc:`units `. The -vector values will be in energy :doc:`units `. The first column -of array values are counts; the values in the second column will be in +The scalar value us in temperature :doc:`units `. The vector +values are in energy :doc:`units `. The first column of array +values are counts; the values in the second column will be in temperature :doc:`units `. Restrictions @@ -203,7 +210,10 @@ will be for most thermostats. Related commands """""""""""""""" -:doc:`compute temp `, :doc:`compute temp/ramp `, :doc:`compute temp/deform `, :doc:`compute pressure ` +:doc:`compute temp `, :doc:`compute temp/ramp + `, :doc:`compute temp/deform + `, :doc:`compute pressure + ` Default """"""" diff --git a/doc/src/compute_temp_ramp.rst b/doc/src/compute_temp_ramp.rst index 2e170316fb..d89a98fbea 100644 --- a/doc/src/compute_temp_ramp.rst +++ b/doc/src/compute_temp_ramp.rst @@ -63,12 +63,17 @@ command (e.g., :math:`\AA` for units = real or metal). A velocity in lattice spacings per unit time). The :doc:`lattice ` command must have been previously used to define the lattice spacing. -A kinetic energy tensor, stored as a six-element vector, is also calculated by -this compute for use in the computation of a pressure tensor. The formula for -the components of the tensor is the same as the above formula, except that -:math:`v^2` is replaced by :math:`v_x v_y` for the :math:`xy` component, and -so on. The six components of the vector are ordered :math:`xx`, :math:`yy`, -:math:`zz`, :math:`xy`, :math:`xz`, :math:`yz`. +A symmetric tensor, stored as a six-element vector, is also calculated +by this compute for use in the computation of a pressure tensor by the +:doc:`compute pressue ` command. The formula for +the components of the tensor is the same as the above expression for +:math:`E_\mathrm{kin}`, except that the 1/2 factor is NOT included and +the :math:`v_i^2` is replaced by :math:`v_{i,x} v_{i,y}` for the +:math:`xy` component, and so on. Note that because it lacks the 1/2 +factor, these tensor components are twice those of the traditional +kinetic energy tensor. The six components of the vector are ordered +:math:`xx`, :math:`yy`, :math:`zz`, :math:`xy`, :math:`xz`, +:math:`yz`. The number of atoms contributing to the temperature is assumed to be constant for the duration of the run; use the *dynamic* option of the @@ -100,17 +105,17 @@ Output info """"""""""" This compute calculates a global scalar (the temperature) and a global -vector of length 6 (KE tensor), which can be accessed by indices 1--6. -These values can be used by any command that uses global scalar or -vector values from a compute as input. See the -:doc:`Howto output ` page for an overview of LAMMPS output -options. +vector of length 6 (symmetric tensor), which can be accessed by +indices 1--6. These values can be used by any command that uses +global scalar or vector values from a compute as input. See the +:doc:`Howto output ` page for an overview of LAMMPS +output options. The scalar value calculated by this compute is "intensive". The vector values are "extensive". -The scalar value will be in temperature :doc:`units `. The -vector values will be in energy :doc:`units `. +The scalar value is in temperature :doc:`units `. The vector +values are in energy :doc:`units `. Restrictions """""""""""" @@ -119,7 +124,10 @@ Restrictions Related commands """""""""""""""" -:doc:`compute temp `, :doc:`compute temp/profie `, :doc:`compute temp/deform `, :doc:`compute pressure ` +:doc:`compute temp `, :doc:`compute temp/profie + `, :doc:`compute temp/deform + `, :doc:`compute pressure + ` Default """"""" diff --git a/doc/src/compute_temp_region.rst b/doc/src/compute_temp_region.rst index 77954e8898..d2fc8a1633 100644 --- a/doc/src/compute_temp_region.rst +++ b/doc/src/compute_temp_region.rst @@ -49,12 +49,17 @@ where KE = is the total kinetic energy of the group of atoms (sum of :math:`N` is the number of atoms in both the group and region, :math:`k_B` is the Boltzmann constant, and :math:`T` temperature. -A kinetic energy tensor, stored as a six-element vector, is also -calculated by this compute for use in the computation of a pressure -tensor. The formula for the components of the tensor is the same as -the above formula, except that :math:`v^2` is replaced by :math:`v_x v_y` -for the :math:`xy` component, and so on. The six components of the vector are -ordered :math:`xx`, :math:`yy`, :math:`zz`, :math:`xy`, :math:`xz`, :math:`yz`. +A symmetric tensor, stored as a six-element vector, is also calculated +by this compute for use in the computation of a pressure tensor by the +:doc:`compute pressue ` command. The formula for +the components of the tensor is the same as the above expression for +:math:`E_\mathrm{kin}`, except that the 1/2 factor is NOT included and +the :math:`v_i^2` is replaced by :math:`v_{i,x} v_{i,y}` for the +:math:`xy` component, and so on. Note that because it lacks the 1/2 +factor, these tensor components are twice those of the traditional +kinetic energy tensor. The six components of the vector are ordered +:math:`xx`, :math:`yy`, :math:`zz`, :math:`xy`, :math:`xz`, +:math:`yz`. The number of atoms contributing to the temperature is calculated each time the temperature is evaluated since it is assumed atoms can @@ -78,12 +83,13 @@ will operate only on atoms that are currently in the geometric region. Unlike other compute styles that calculate temperature, this compute does not subtract out degrees-of-freedom due to fixes that constrain -motion, such as :doc:`fix shake ` and :doc:`fix rigid `. This is because those degrees of freedom -(e.g., a constrained bond) could apply to sets of atoms that straddle -the region boundary, and hence the concept is somewhat ill-defined. -If needed the number of subtracted degrees of freedom can be set -explicitly using the *extra* option of the -:doc:`compute_modify ` command. +motion, such as :doc:`fix shake ` and :doc:`fix rigid +`. This is because those degrees of freedom (e.g., a +constrained bond) could apply to sets of atoms that straddle the +region boundary, and hence the concept is somewhat ill-defined. If +needed the number of subtracted degrees of freedom can be set +explicitly using the *extra* option of the :doc:`compute_modify +` command. See the :doc:`Howto thermostat ` page for a discussion of different ways to compute temperature and perform @@ -93,17 +99,17 @@ Output info """"""""""" This compute calculates a global scalar (the temperature) and a global -vector of length 6 (KE tensor), which can be accessed by indices 1--6. -These values can be used by any command that uses global scalar or -vector values from a compute as input. See the -:doc:`Howto output ` page for an overview of LAMMPS output -options. +vector of length 6 (symmetric tensor), which can be accessed by +indices 1--6. These values can be used by any command that uses +global scalar or vector values from a compute as input. See the +:doc:`Howto output ` page for an overview of LAMMPS +output options. The scalar value calculated by this compute is "intensive". The vector values are "extensive". -The scalar value will be in temperature :doc:`units `. -The vector values will be in energy :doc:`units `. +The scalar value is in temperature :doc:`units `. The vector +values are in energy :doc:`units `. Restrictions """""""""""" diff --git a/doc/src/compute_temp_region_eff.rst b/doc/src/compute_temp_region_eff.rst index b8cd73f4fd..12bc3f01a1 100644 --- a/doc/src/compute_temp_region_eff.rst +++ b/doc/src/compute_temp_region_eff.rst @@ -32,32 +32,33 @@ temperature (e.g., :doc:`thermo_modify `). The operation of this compute is exactly like that described by the :doc:`compute temp/region ` command, except that -the formula for the temperature itself includes the radial electron -velocity contributions, as discussed by the -:doc:`compute temp/eff ` command. +the formulas for the temperature (scalar) and diagonal components of +the symmetric tensor (vector) include the radial electron velocity +contributions, as discussed by the :doc:`compute temp/eff +` command. Output info -""""""""""" +"""""""""" This compute calculates a global scalar (the temperature) and a global -vector of length 6 (KE tensor), which can be accessed by indices 1--6. -These values can be used by any command that uses global scalar or -vector values from a compute as input. See the -:doc:`Howto output ` page for an overview of LAMMPS output -options. +vector of length 6 (symmetric tensor), which can be accessed by +indices 1--6. These values can be used by any command that uses +global scalar or vector values from a compute as input. See the +:doc:`Howto output ` page for an overview of LAMMPS +output options. The scalar value calculated by this compute is "intensive". The vector values are "extensive". -The scalar value will be in temperature :doc:`units `. The -vector values will be in energy :doc:`units `. +The scalar value is in temperature :doc:`units `. The vector +values are in energy :doc:`units `. Restrictions """""""""""" -This compute is part of the EFF package. It is only enabled if -LAMMPS was built with that package. -See the :doc:`Build package ` page for more info. +This compute is part of the EFF package. It is only enabled if LAMMPS +was built with that package. See the :doc:`Build package +` page for more info. Related commands """""""""""""""" diff --git a/doc/src/compute_temp_rotate.rst b/doc/src/compute_temp_rotate.rst index 7c445109a1..7fab9a1325 100644 --- a/doc/src/compute_temp_rotate.rst +++ b/doc/src/compute_temp_rotate.rst @@ -43,12 +43,17 @@ where KE is the total kinetic energy of the group of atoms (sum of :math:`N` is the number of atoms in the group, :math:`k_B` is the Boltzmann constant, and :math:`T` is the absolute temperature. -A kinetic energy tensor, stored as a six-element vector, is also calculated by -this compute for use in the computation of a pressure tensor. The formula for -the components of the tensor is the same as the above formula, except that -:math:`v^2` is replaced by :math:`v_x v_y` for the :math:`xy` component, and -so on. The six components of the vector are ordered :math:`xx`, :math:`yy`, -:math:`zz`, :math:`xy`, :math:`xz`, :math:`yz`. +A symmetric tensor, stored as a six-element vector, is also calculated +by this compute for use in the computation of a pressure tensor by the +:doc:`compute pressue ` command. The formula for +the components of the tensor is the same as the above expression for +:math:`E_\mathrm{kin}`, except that the 1/2 factor is NOT included and +the :math:`v_i^2` is replaced by :math:`v_{i,x} v_{i,y}` for the +:math:`xy` component, and so on. Note that because it lacks the 1/2 +factor, these tensor components are twice those of the traditional +kinetic energy tensor. The six components of the vector are ordered +:math:`xx`, :math:`yy`, :math:`zz`, :math:`xy`, :math:`xz`, +:math:`yz`. The number of atoms contributing to the temperature is assumed to be constant for the duration of the run; use the *dynamic* option of the @@ -80,17 +85,16 @@ Output info """"""""""" This compute calculates a global scalar (the temperature) and a global -vector of length 6 (KE tensor), which can be accessed by indices 1-6. -These values can be used by any command that uses global scalar or -vector values from a compute as input. See the -:doc:`Howto output ` page for an overview of LAMMPS output -options. +vector of length 6 (symmetric tensor), which can be accessed by +indices 1-6. These values can be used by any command that uses global +scalar or vector values from a compute as input. See the :doc:`Howto +output ` page for an overview of LAMMPS output options. The scalar value calculated by this compute is "intensive". The vector values are "extensive". -The scalar value will be in temperature :doc:`units `. The -vector values will be in energy :doc:`units `. +The scalar value is in temperature :doc:`units `. The vector +values are in energy :doc:`units `. Restrictions """""""""""" diff --git a/doc/src/compute_temp_sphere.rst b/doc/src/compute_temp_sphere.rst index d1891f64bf..5499b3aae9 100644 --- a/doc/src/compute_temp_sphere.rst +++ b/doc/src/compute_temp_sphere.rst @@ -77,6 +77,18 @@ tensor is the same as the above formulas, except that :math:`v^2` and vector are ordered :math:`xx`, :math:`yy`, :math:`zz`, :math:`xy`, :math:`xz`, :math:`yz`. +A symmetric tensor, stored as a six-element vector, is also calculated +by this compute for use in the computation of a pressure tensor by the +:doc:`compute pressue ` command. The formula for +the components of the tensor is the same as the above expression for +:math:`E_\mathrm{kin}`, except that the 1/2 factor is NOT included and +the :math:`v_i^2` and :math:`\omega^2` are replaced by :math:`v_x v_y` +and :math:`\omega_x \omega_y` for the :math:`xy` component, and so on. +Note that because it lacks the 1/2 factor, these tensor components are +twice those of the traditional kinetic energy tensor. The six +components of the vector are ordered :math:`xx`, :math:`yy`, +:math:`zz`, :math:`xy`, :math:`xz`, :math:`yz`. + The number of atoms contributing to the temperature is assumed to be constant for the duration of the run; use the *dynamic* option of the :doc:`compute_modify ` command if this is not the case. @@ -117,17 +129,17 @@ Output info """"""""""" This compute calculates a global scalar (the temperature) and a global -vector of length 6 (KE tensor), which can be accessed by indices 1--6. -These values can be used by any command that uses global scalar or -vector values from a compute as input. -See the :doc:`Howto output ` page for an overview of LAMMPS +vector of length 6 (symmetric tensor), which can be accessed by +indices 1--6. These values can be used by any command that uses +global scalar or vector values from a compute as input. See the +:doc:`Howto output ` page for an overview of LAMMPS output options. The scalar value calculated by this compute is "intensive". The vector values are "extensive". -The scalar value will be in temperature :doc:`units `. The -vector values will be in energy :doc:`units `. +The scalar value is in temperature :doc:`units `. The vector +values are in energy :doc:`units `. Restrictions """""""""""" diff --git a/doc/src/compute_viscosity_cos.rst b/doc/src/compute_viscosity_cos.rst index 87cfec56cf..bfc0c03d79 100644 --- a/doc/src/compute_viscosity_cos.rst +++ b/doc/src/compute_viscosity_cos.rst @@ -86,12 +86,17 @@ where KE is the total kinetic energy of the group of atoms (sum of :math:`N` is the number of atoms in the group, :math:`k_B` is the Boltzmann constant, and :math:`T` is the absolute temperature. -A kinetic energy tensor, stored as a six-element vector, is also -calculated by this compute for use in the computation of a pressure -tensor. The formula for the components of the tensor is the same as -the above formula, except that :math:`v^2` is replaced by :math:`v_x v_y` for -the :math:`xy` component, and so on. The six components of the vector are -ordered :math:`xx`, :math:`yy`, :math:`zz`, :math:`xy`, :math:`xz`, :math:`yz`. +A symmetric tensor, stored as a six-element vector, is also calculated +by this compute for use in the computation of a pressure tensor by the +:doc:`compute pressue ` command. The formula for +the components of the tensor is the same as the above expression for +:math:`E_\mathrm{kin}`, except that the 1/2 factor is NOT included and +the :math:`v_i^2` is replaced by :math:`v_{i,x} v_{i,y}` for the +:math:`xy` component, and so on. Note that because it lacks the 1/2 +factor, these tensor components are twice those of the traditional +kinetic energy tensor. The six components of the vector are ordered +:math:`xx`, :math:`yy`, :math:`zz`, :math:`xy`, :math:`xz`, +:math:`yz`. The number of atoms contributing to the temperature is assumed to be constant for the duration of the run; use the *dynamic* option of the @@ -126,21 +131,21 @@ Output info """"""""""" This compute calculates a global scalar (the temperature) and a global -vector of length 7, which can be accessed by indices 1--7. -The first six elements of the vector are the KE tensor, -and the seventh is the cosine-shaped velocity amplitude :math:`V`, -which can be used to calculate the reciprocal viscosity, as shown in the example. -These values can be used by any command that uses global scalar or -vector values from a compute as input. -See the :doc:`Howto output ` page for an overview of LAMMPS output options. +vector of length 7, which can be accessed by indices 1--7. The first +six elements of the vector are those of the symmetric tensor discussed +above. The seventh is the cosine-shaped velocity amplitude :math:`V`, +which can be used to calculate the reciprocal viscosity, as shown in +the example. These values can be used by any command that uses global +scalar or vector values from a compute as input. See the :doc:`Howto +output ` page for an overview of LAMMPS output options. The scalar value calculated by this compute is "intensive". The first six elements of vector values are "extensive", and the seventh element of vector values is "intensive". -The scalar value will be in temperature :doc:`units `. -The first six elements of vector values will be in energy :doc:`units `. -The seventh element of vector value will be in velocity :doc:`units `. +The scalar value is in temperature :doc:`units `. The first +six elements of vector values are in energy :doc:`units `. The +seventh element of vector value us in velocity :doc:`units `. Restrictions """""""""""" From 32a6db151f29d4f439313fba20dfa24712a83294 Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Wed, 21 Aug 2024 13:07:51 -0600 Subject: [PATCH 05/11] clarify compute pressure doc page as well --- doc/src/compute_pressure.rst | 32 +++++++++++++++++++------------- 1 file changed, 19 insertions(+), 13 deletions(-) diff --git a/doc/src/compute_pressure.rst b/doc/src/compute_pressure.rst index 03dfbb841b..2b75721890 100644 --- a/doc/src/compute_pressure.rst +++ b/doc/src/compute_pressure.rst @@ -59,11 +59,12 @@ may also contribute to the virial term. A symmetric pressure tensor, stored as a 6-element vector, is also calculated by this compute. The six components of the vector are -ordered :math:`xx,` :math:`yy,` :math:`zz,` :math:`xy,` :math:`xz,` :math:`yz.` -The equation for the :math:`(I,J)` components (where :math:`I` and :math:`J` -are :math:`x`, :math:`y`, or :math:`z`) is similar to the above formula, -except that the first term uses components of the kinetic energy tensor and the -second term uses components of the virial tensor: +ordered :math:`xx,` :math:`yy,` :math:`zz,` :math:`xy,` :math:`xz,` +:math:`yz.` The equation for the :math:`(I,J)` components (where +:math:`I` and :math:`J` are :math:`x`, :math:`y`, or :math:`z`) is +similar to the above formula, except that the first term uses +components derived from the kinetic energy tensor and the second term +uses components of the virial tensor: .. math:: @@ -86,9 +87,15 @@ system, including for many-body potentials and accounting for the effects of periodic boundary conditions are discussed in :ref:`(Thompson) `. -The temperature and kinetic energy tensor is not calculated by this +The temperature and kinetic energy tensor are not calculated by this compute, but rather by the temperature compute specified with the -command. If the kinetic energy is not included in the pressure, than +command. See the doc pages for individual compute temp variants for +an explation of how they calculate temperature and a symmetric tensor +(6-element vector) whose components are twice that of the traditional +KE tensor. That tensor is what appears in the pressure tensor formula +above. + +If the kinetic energy is not included in the pressure, than the temperature compute is not used and can be specified as NULL. Normally the temperature compute used by compute pressure should calculate the temperature of all atoms for consistency with the virial @@ -98,14 +105,13 @@ term, but any compute style that calculates temperature can be used Note that if desired the specified temperature compute can be one that subtracts off a bias to calculate a temperature using only the thermal velocity of the atoms (e.g., by subtracting a background streaming -velocity). -See the doc pages for individual :doc:`compute commands ` to determine -which ones include a bias. +velocity). See the doc pages for individual :doc:`compute commands +` to determine which ones include a bias. Also note that the :math:`N` in the first formula above is really -degrees-of-freedom divided by :math:`d` = dimensionality, where the DOF value -is calculated by the temperature compute. -See the various :doc:`compute temperature ` styles for details. +degrees-of-freedom divided by :math:`d` = dimensionality, where the +DOF value is calculated by the temperature compute. See the various +:doc:`compute temperature ` styles for details. A compute of this style with the ID of thermo_press is created when LAMMPS starts up, as if this command were in the input script: From 7eb105adbe4f43a214e4b260d5fa8ff35a70564f Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Wed, 21 Aug 2024 13:09:00 -0600 Subject: [PATCH 06/11] tweak --- doc/src/compute_pressure.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/src/compute_pressure.rst b/doc/src/compute_pressure.rst index 2b75721890..980a8f6481 100644 --- a/doc/src/compute_pressure.rst +++ b/doc/src/compute_pressure.rst @@ -63,7 +63,7 @@ ordered :math:`xx,` :math:`yy,` :math:`zz,` :math:`xy,` :math:`xz,` :math:`yz.` The equation for the :math:`(I,J)` components (where :math:`I` and :math:`J` are :math:`x`, :math:`y`, or :math:`z`) is similar to the above formula, except that the first term uses -components derived from the kinetic energy tensor and the second term +components related to the kinetic energy tensor and the second term uses components of the virial tensor: .. math:: From 827bc6361b3e71b155d32da703bf01f708220552 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 21 Aug 2024 20:18:28 -0400 Subject: [PATCH 07/11] fix spelling and formatting issues --- doc/src/compute_pressure.rst | 29 +++++---- doc/src/compute_temp_asphere.rst | 54 ++++++++--------- doc/src/compute_temp_cs.rst | 93 ++++++++++++++--------------- doc/src/compute_temp_profile.rst | 8 +-- doc/src/compute_temp_ramp.rst | 8 +-- doc/src/compute_temp_region_eff.rst | 2 +- 6 files changed, 96 insertions(+), 98 deletions(-) diff --git a/doc/src/compute_pressure.rst b/doc/src/compute_pressure.rst index 980a8f6481..439f701bd4 100644 --- a/doc/src/compute_pressure.rst +++ b/doc/src/compute_pressure.rst @@ -76,8 +76,8 @@ calculated. This includes a kinetic energy (temperature) term and the virial as the sum of pair, bond, angle, dihedral, improper, kspace (long-range), and fix contributions to the force on each atom. If any extra keywords are listed, then only those components are summed to -compute temperature or ke and/or the virial. The *virial* keyword -means include all terms except the kinetic energy *ke*\ . +compute temperature or ke and/or the virial. The *virial* keyword means +include all terms except the kinetic energy *ke*\ . The *pair/hybrid* keyword means to only include contribution from a sub-style in a *hybrid* or *hybrid/overlay* pair style. @@ -89,18 +89,18 @@ effects of periodic boundary conditions are discussed in The temperature and kinetic energy tensor are not calculated by this compute, but rather by the temperature compute specified with the -command. See the doc pages for individual compute temp variants for -an explation of how they calculate temperature and a symmetric tensor -(6-element vector) whose components are twice that of the traditional -KE tensor. That tensor is what appears in the pressure tensor formula +command. See the doc pages for individual compute temp variants for an +explanation of how they calculate temperature and a symmetric tensor +(6-element vector) whose components are twice that of the traditional KE +tensor. That tensor is what appears in the pressure tensor formula above. -If the kinetic energy is not included in the pressure, than -the temperature compute is not used and can be specified as NULL. -Normally the temperature compute used by compute pressure should -calculate the temperature of all atoms for consistency with the virial -term, but any compute style that calculates temperature can be used -(e.g., one that excludes frozen atoms or other degrees of freedom). +If the kinetic energy is not included in the pressure, than the +temperature compute is not used and can be specified as NULL. Normally +the temperature compute used by compute pressure should calculate the +temperature of all atoms for consistency with the virial term, but any +compute style that calculates temperature can be used (e.g., one that +excludes frozen atoms or other degrees of freedom). Note that if desired the specified temperature compute can be one that subtracts off a bias to calculate a temperature using only the thermal @@ -142,9 +142,8 @@ The ordering of values in the symmetric pressure tensor is as follows: :math:`p_{xx},` :math:`p_{yy},` :math:`p_{zz},` :math:`p_{xy},` :math:`p_{xz},` :math:`p_{yz}.` -The scalar and vector values calculated by this compute are -"intensive". The scalar and vector values will be in pressure -:doc:`units `. +The scalar and vector values calculated by this compute are "intensive". +The scalar and vector values will be in pressure :doc:`units `. Restrictions """""""""""" diff --git a/doc/src/compute_temp_asphere.rst b/doc/src/compute_temp_asphere.rst index c9b1e51532..d2af4278ad 100644 --- a/doc/src/compute_temp_asphere.rst +++ b/doc/src/compute_temp_asphere.rst @@ -41,8 +41,8 @@ translational and rotational kinetic energy. This differs from the usual :doc:`compute temp ` command, which assumes point particles with only translational kinetic energy. -Only finite-size particles (aspherical or spherical) can be included -in the group. For 3d finite-size particles, each has six degrees of +Only finite-size particles (aspherical or spherical) can be included in +the group. For 3d finite-size particles, each has six degrees of freedom (three translational, three rotational). For 2d finite-size particles, each has three degrees of freedom (two translational, one rotational). @@ -70,38 +70,39 @@ axis. It will also be the case for biaxial ellipsoids when exactly two of the semiaxes have the same length and the corresponding relative well depths are equal. -The translational kinetic energy is computed the same as is described -by the :doc:`compute temp ` command. The rotational -kinetic energy is computed as :math:`\frac12 I \omega^2`, where :math:`I` is -the inertia tensor for the aspherical particle and :math:`\omega` is its +The translational kinetic energy is computed the same as is described by +the :doc:`compute temp ` command. The rotational kinetic +energy is computed as :math:`\frac12 I \omega^2`, where :math:`I` is the +inertia tensor for the aspherical particle and :math:`\omega` is its angular velocity, which is computed from its angular momentum. .. note:: For :doc:`2d models `, particles are treated as - ellipsoids, not ellipses, meaning their moments of inertia will be the - same as in 3d. + ellipsoids, not ellipses, meaning their moments of inertia will be + the same as in 3d. A kinetic energy tensor, stored as a six-element vector, is also calculated by this compute. The formula for the components of the tensor is the same as the above formula, except that :math:`v^2` and -:math:`\omega^2` are replaced by :math:`v_x v_y` and :math:`\omega_x \omega_y` -for the :math:`xy` component, and the appropriate elements of the moment of -inertia tensor are used. The six components of the vector are ordered -:math:`xx`, :math:`yy`, :math:`zz`, :math:`xy`, :math:`xz`, :math:`yz`. +:math:`\omega^2` are replaced by :math:`v_x v_y` and :math:`\omega_x +\omega_y` for the :math:`xy` component, and the appropriate elements of +the moment of inertia tensor are used. The six components of the vector +are ordered :math:`xx`, :math:`yy`, :math:`zz`, :math:`xy`, :math:`xz`, +:math:`yz`. A symmetric tensor, stored as a six-element vector, is also calculated by this compute for use in the computation of a pressure tensor by the -:doc:`compute pressue ` command. The formula for -the components of the tensor is the same as the above expression for +:doc:`compute pressue ` command. The formula for the +components of the tensor is the same as the above expression for :math:`E_\mathrm{kin}`, except that the 1/2 factor is NOT included and the :math:`v_i^2` and :math:`\omega^2` are replaced by :math:`v_x v_y` and :math:`\omega_x \omega_y` for the :math:`xy` component, and so on. And the appropriate elements of the moment of inertia tensor are used. Note that because it lacks the 1/2 factor, these tensor components are twice those of the traditional kinetic energy tensor. The six -components of the vector are ordered :math:`xx`, :math:`yy`, -:math:`zz`, :math:`xy`, :math:`xz`, :math:`yz`. +components of the vector are ordered :math:`xx`, :math:`yy`, :math:`zz`, +:math:`xy`, :math:`xz`, :math:`yz`. The number of atoms contributing to the temperature is assumed to be constant for the duration of the run; use the *dynamic/dof* option of @@ -144,14 +145,13 @@ Output info """"""""""" This compute calculates a global scalar (the temperature) and a global -vector of length 6 (symmertic tensor), which can be accessed by -indices 1--6. These values can be used by any command that uses -global scalar or vector values from a compute as input. See the -:doc:`Howto output ` page for an overview of LAMMPS -output options. +vector of length 6 (symmetric tensor), which can be accessed by indices +1--6. These values can be used by any command that uses global scalar +or vector values from a compute as input. See the :doc:`Howto output +` page for an overview of LAMMPS output options. -The scalar value calculated by this compute is "intensive". The -vector values are "extensive". +The scalar value calculated by this compute is "intensive". The vector +values are "extensive". The scalar value is in temperature :doc:`units `. The vector values are in energy :doc:`units `. @@ -160,11 +160,11 @@ Restrictions """""""""""" This compute is part of the ASPHERE package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` page for more info. +LAMMPS was built with that package. See the :doc:`Build package +` page for more info. -This compute requires that atoms store angular momentum and a -quaternion as defined by the :doc:`atom_style ellipsoid ` -command. +This compute requires that atoms store angular momentum and a quaternion +as defined by the :doc:`atom_style ellipsoid ` command. All particles in the group must be finite-size. They cannot be point particles, but they can be aspherical or spherical as defined by their diff --git a/doc/src/compute_temp_cs.rst b/doc/src/compute_temp_cs.rst index 0620fea9b7..4908b12797 100644 --- a/doc/src/compute_temp_cs.rst +++ b/doc/src/compute_temp_cs.rst @@ -31,27 +31,27 @@ on the center-of-mass velocity of atom pairs that are bonded to each other. This compute is designed to be used with the adiabatic core/shell model of :ref:`(Mitchell and Fincham) `. See the :doc:`Howto coreshell ` page for an overview of -the model as implemented in LAMMPS. Specifically, this compute -enables correct temperature calculation and thermostatting of -core/shell pairs where it is desirable for the internal degrees of -freedom of the core/shell pairs to not be influenced by a thermostat. -A compute of this style can be used by any command that computes a -temperature via :doc:`fix_modify ` -(e.g., :doc:`fix temp/rescale `, :doc:`fix npt `). +the model as implemented in LAMMPS. Specifically, this compute enables +correct temperature calculation and thermostatting of core/shell pairs +where it is desirable for the internal degrees of freedom of the +core/shell pairs to not be influenced by a thermostat. A compute of +this style can be used by any command that computes a temperature via +:doc:`fix_modify ` (e.g., :doc:`fix temp/rescale +`, :doc:`fix npt `). -Note that this compute does not require all ions to be polarized, -hence defined as core/shell pairs. One can mix core/shell pairs and -ions without a satellite particle if desired. The compute will -consider the non-polarized ions according to the physical system. +Note that this compute does not require all ions to be polarized, hence +defined as core/shell pairs. One can mix core/shell pairs and ions +without a satellite particle if desired. The compute will consider the +non-polarized ions according to the physical system. For this compute, core and shell particles are specified by two -respective group IDs, which can be defined using the -:doc:`group ` command. The number of atoms in the two groups -must be the same and there should be one bond defined between a pair -of atoms in the two groups. Non-polarized ions which might also be -included in the treated system should not be included into either of -these groups, they are taken into account by the *group-ID* (second -argument) of the compute. +respective group IDs, which can be defined using the :doc:`group +` command. The number of atoms in the two groups must be the +same and there should be one bond defined between a pair of atoms in the +two groups. Non-polarized ions which might also be included in the +treated system should not be included into either of these groups, they +are taken into account by the *group-ID* (second argument) of the +compute. The temperature is calculated by the formula @@ -60,54 +60,53 @@ The temperature is calculated by the formula \text{KE} = \frac{\text{dim}}{2} N k_B T, where KE is the total kinetic energy of the group of atoms (sum of -:math:`\frac12 m v^2`), dim = 2 or 3 is the dimensionality of the simulation, -:math:`N` is the number of atoms in the group, :math:`k_B` is the Boltzmann -constant, and :math:`T` is the absolute temperature. Note that -the velocity of each core or shell atom used in the KE calculation is -the velocity of the center-of-mass (COM) of the core/shell pair the -atom is part of. +:math:`\frac12 m v^2`), dim = 2 or 3 is the dimensionality of the +simulation, :math:`N` is the number of atoms in the group, :math:`k_B` +is the Boltzmann constant, and :math:`T` is the absolute temperature. +Note that the velocity of each core or shell atom used in the KE +calculation is the velocity of the center-of-mass (COM) of the +core/shell pair the atom is part of. A symmetric tensor, stored as a six-element vector, is also calculated by this compute for use in the computation of a pressure tensor by the -:doc:`compute pressue ` command. The formula for -the components of the tensor is the same as the above expression for +:doc:`compute pressue ` command. The formula for the +components of the tensor is the same as the above expression for :math:`E_\mathrm{kin}`, except that the 1/2 factor is NOT included and the :math:`v_i^2` is replaced by :math:`v_{i,x} v_{i,y}` for the :math:`xy` component, and so on. Note that because it lacks the 1/2 factor, these tensor components are twice those of the traditional kinetic energy tensor. The six components of the vector are ordered -:math:`xx`, :math:`yy`, :math:`zz`, :math:`xy`, :math:`xz`, -:math:`yz`. +:math:`xx`, :math:`yy`, :math:`zz`, :math:`xy`, :math:`xz`, :math:`yz`. The change this fix makes to core/shell atom velocities is essentially computing the temperature after a "bias" has been removed from the -velocity of the atoms. This "bias" is the velocity of the atom -relative to the center-of-mass velocity of the core/shell pair. If -this compute is used with a fix command that performs thermostatting -then this bias will be subtracted from each atom, thermostatting of -the remaining center-of-mass velocity will be performed, and the bias -will be added back in. This means the thermostatting will effectively -be performed on the core/shell pairs, instead of on the individual -core and shell atoms. Thermostatting fixes that work in this way -include :doc:`fix nvt `, :doc:`fix temp/rescale -`, :doc:`fix temp/berendsen `, -and :doc:`fix langevin `. +velocity of the atoms. This "bias" is the velocity of the atom relative +to the center-of-mass velocity of the core/shell pair. If this compute +is used with a fix command that performs thermostatting then this bias +will be subtracted from each atom, thermostatting of the remaining +center-of-mass velocity will be performed, and the bias will be added +back in. This means the thermostatting will effectively be performed on +the core/shell pairs, instead of on the individual core and shell atoms. +Thermostatting fixes that work in this way include :doc:`fix nvt +`, :doc:`fix temp/rescale `, :doc:`fix +temp/berendsen `, and :doc:`fix langevin +`. The internal energy of core/shell pairs can be calculated by the -:doc:`compute temp/chunk ` command, if chunks are defined -as core/shell pairs. See the :doc:`Howto coreshell ` doc -page for more discussion on how to do this. +:doc:`compute temp/chunk ` command, if chunks are +defined as core/shell pairs. See the :doc:`Howto coreshell +` doc page for more discussion on how to do this. Output info """"""""""" This compute calculates a global scalar (the temperature) and a global -vector of length 6 (symmertric tensor), which can be accessed by -indices 1--6. These values can be used by any command that uses -global scalar or vector values from a compute as input. +vector of length 6 (symmetric tensor), which can be accessed by indices +1--6. These values can be used by any command that uses global scalar +or vector values from a compute as input. -The scalar value calculated by this compute is "intensive". The -vector values are "extensive". +The scalar value calculated by this compute is "intensive". The vector +values are "extensive". The scalar value is in temperature :doc:`units `. The vector values are in energy :doc:`units `. diff --git a/doc/src/compute_temp_profile.rst b/doc/src/compute_temp_profile.rst index 47725cdcbc..9f6bbfc89c 100644 --- a/doc/src/compute_temp_profile.rst +++ b/doc/src/compute_temp_profile.rst @@ -210,10 +210,10 @@ will be for most thermostats. Related commands """""""""""""""" -:doc:`compute temp `, :doc:`compute temp/ramp - `, :doc:`compute temp/deform - `, :doc:`compute pressure - ` +:doc:`compute temp `, +:doc:`compute temp/ramp `, +:doc:`compute temp/deform `, +:doc:`compute pressure ` Default """"""" diff --git a/doc/src/compute_temp_ramp.rst b/doc/src/compute_temp_ramp.rst index d89a98fbea..643ca9d1dd 100644 --- a/doc/src/compute_temp_ramp.rst +++ b/doc/src/compute_temp_ramp.rst @@ -124,10 +124,10 @@ Restrictions Related commands """""""""""""""" -:doc:`compute temp `, :doc:`compute temp/profie - `, :doc:`compute temp/deform - `, :doc:`compute pressure - ` +:doc:`compute temp `, +:doc:`compute temp/profile `, +:doc:`compute temp/deform `, +:doc:`compute pressure ` Default """"""" diff --git a/doc/src/compute_temp_region_eff.rst b/doc/src/compute_temp_region_eff.rst index 12bc3f01a1..4193a0a7ec 100644 --- a/doc/src/compute_temp_region_eff.rst +++ b/doc/src/compute_temp_region_eff.rst @@ -38,7 +38,7 @@ contributions, as discussed by the :doc:`compute temp/eff ` command. Output info -"""""""""" +""""""""""" This compute calculates a global scalar (the temperature) and a global vector of length 6 (symmetric tensor), which can be accessed by From 6514dbb4b60824701e4f2365fd7cf70772bcac66 Mon Sep 17 00:00:00 2001 From: Jacob Gissinger Date: Sun, 25 Aug 2024 13:42:51 -0400 Subject: [PATCH 08/11] refactor how to insert atoms --- src/REACTION/fix_bond_react.cpp | 118 +++++++++++++++++++------------- src/REACTION/fix_bond_react.h | 11 ++- 2 files changed, 79 insertions(+), 50 deletions(-) diff --git a/src/REACTION/fix_bond_react.cpp b/src/REACTION/fix_bond_react.cpp index bd8b3459e2..63781bfcdd 100644 --- a/src/REACTION/fix_bond_react.cpp +++ b/src/REACTION/fix_bond_react.cpp @@ -2962,6 +2962,8 @@ void FixBondReact::update_everything() int *type = atom->type; int **nspecial = atom->nspecial; tagint **special = atom->special; + tagint *tag = atom->tag; + AtomVec *avec = atom->avec; int **bond_type = atom->bond_type; tagint **bond_atom = atom->bond_atom; @@ -2974,13 +2976,16 @@ void FixBondReact::update_everything() memory->create(mark,nmark,"bond/react:mark"); for (int i = 0; i < nmark; i++) mark[i] = 0; + // used when creating atoms + addatomtag = 0; + for (int i = 0; i < nlocal; i++) addatomtag = MAX(addatomtag,tag[i]); + MPI_Allreduce(MPI_IN_PLACE,&addatomtag,1,MPI_LMP_TAGINT,MPI_MAX,world); + addatoms.clear(); + // flag used to delete special interactions int *delflag; memory->create(delflag,atom->maxspecial,"bond/react:delflag"); - tagint *tag = atom->tag; - AtomVec *avec = atom->avec; - // used when creating atoms int inserted_atoms_flag = 0; @@ -3029,6 +3034,7 @@ void FixBondReact::update_everything() for (int i = 0; i < local_num_mega; i++) { rxnID = (int) local_mega_glove[0][i]; // reactions already shuffled from dedup procedure, so can skip first N + // wait, this check needs to be after add atoms, because they can also be 'skipped' due to overlap if (iskip[rxnID]++ < nlocalskips[rxnID]) continue; // this will be overwritten if reaction skipped by create_atoms below @@ -3040,7 +3046,7 @@ void FixBondReact::update_everything() if (create_atoms_flag[rxnID] == 1) { onemol = atom->molecules[unreacted_mol[rxnID]]; twomol = atom->molecules[reacted_mol[rxnID]]; - if (insert_atoms(update_mega_glove,update_num_mega)) { + if (insert_atoms_setup(update_mega_glove,update_num_mega)) { inserted_atoms_flag = 1; } else { // create aborted reaction_count_total[rxnID]--; @@ -3068,7 +3074,7 @@ void FixBondReact::update_everything() if (create_atoms_flag[rxnID] == 1) { onemol = atom->molecules[unreacted_mol[rxnID]]; twomol = atom->molecules[reacted_mol[rxnID]]; - if (insert_atoms(update_mega_glove,update_num_mega)) { + if (insert_atoms_setup(update_mega_glove,update_num_mega)) { inserted_atoms_flag = 1; } else { // create aborted reaction_count_total[rxnID]--; @@ -3084,13 +3090,31 @@ void FixBondReact::update_everything() if (update_num_mega == 0) continue; - // if inserted atoms and global map exists, reset map now instead - // of waiting for comm since other pre-exchange fixes may use it - // invoke map_init() b/c atom count has grown - // do this once after all atom insertions - if (inserted_atoms_flag == 1 && atom->map_style != Atom::MAP_NONE) { - atom->map_init(); - atom->map_set(); + // insert all atoms for all rxns here + if (inserted_atoms_flag == 1) { + // clear to-be-overwritten ghost info + atom->nghost = 0; + atom->avec->clear_bonus(); + + for (auto & myaddatom : addatoms) { + atom->avec->create_atom(myaddatom.type,myaddatom.x); + int n = atom->nlocal - 1; + atom->tag[n] = myaddatom.tag; + atom->molecule[n] = myaddatom.molecule; + atom->mask[n] = myaddatom.mask; + atom->image[n] = myaddatom.image; + atom->v[n][0] = myaddatom.v[0]; + atom->v[n][1] = myaddatom.v[1]; + atom->v[n][2] = myaddatom.v[2]; + if (atom->rmass) atom->rmass[n]= myaddatom.rmass; + modify->create_attribute(n); + } + + // reset atom->map + if (atom->map_style != Atom::MAP_NONE) { + atom->map_init(); + atom->map_set(); + } } // mark to-delete atoms @@ -3644,10 +3668,11 @@ void FixBondReact::update_everything() } /* ---------------------------------------------------------------------- -insert created atoms +setup for inserting created atoms +atoms for all rxns are actually created all at once in update_everything ------------------------------------------------------------------------- */ -int FixBondReact::insert_atoms(tagint **my_update_mega_glove, int iupdate) +int FixBondReact::insert_atoms_setup(tagint **my_update_mega_glove, int iupdate) { // inserting atoms based off fix_deposit->pre_exchange int flag; @@ -3675,14 +3700,9 @@ int FixBondReact::insert_atoms(tagint **my_update_mega_glove, int iupdate) tagint *molecule = atom->molecule; int nlocal = atom->nlocal; - tagint maxtag_all,maxmol_all; - tagint max = 0; - for (int i = 0; i < nlocal; i++) max = MAX(max,tag[i]); - MPI_Allreduce(&max,&maxtag_all,1,MPI_LMP_TAGINT,MPI_MAX,world); - - max = 0; - for (int i = 0; i < nlocal; i++) max = MAX(max,molecule[i]); - MPI_Allreduce(&max,&maxmol_all,1,MPI_LMP_TAGINT,MPI_MAX,world); + tagint maxmol_all; + for (int i = 0; i < nlocal; i++) maxmol_all = MAX(maxmol_all,molecule[i]); + MPI_Allreduce(MPI_IN_PLACE,&maxmol_all,1,MPI_LMP_TAGINT,MPI_MAX,world); int dimension = domain->dimension; @@ -3776,6 +3796,7 @@ int FixBondReact::insert_atoms(tagint **my_update_mega_glove, int iupdate) break; } } + // !! need to add check against soon-to-added atoms if (abortflag) break; } } @@ -3787,12 +3808,6 @@ int FixBondReact::insert_atoms(tagint **my_update_mega_glove, int iupdate) } } - // clear ghost count and any ghost bonus data internal to AtomVec - // same logic as beginning of Comm::exchange() - // do it now b/c inserting atoms will overwrite ghost atoms - atom->nghost = 0; - atom->avec->clear_bonus(); - // check if new atoms are in my sub-box or above it if I am highest proc // if so, add atom to my list via create_atom() // initialize additional info about the atoms @@ -3835,40 +3850,46 @@ int FixBondReact::insert_atoms(tagint **my_update_mega_glove, int iupdate) } int root = 0; + addatomtag++; if (flag) { + struct AddAtom myaddatom; root = comm->me; - atom->avec->create_atom(twomol->type[m],coords[m]); - int n = atom->nlocal - 1; - atom->tag[n] = maxtag_all + add_count; + myaddatom.type = twomol->type[m]; + myaddatom.x[0] = coords[m][0]; + myaddatom.x[1] = coords[m][1]; + myaddatom.x[2] = coords[m][2]; + myaddatom.tag = addatomtag; // locally update mega_glove - my_update_mega_glove[preID][iupdate] = atom->tag[n]; + my_update_mega_glove[preID][iupdate] = myaddatom.tag; + // could do better job choosing mol ID for added atoms if (atom->molecule_flag) { if (twomol->moleculeflag) { - atom->molecule[n] = maxmol_all + twomol->molecule[m]; + myaddatom.molecule = maxmol_all + twomol->molecule[m]; } else { - atom->molecule[n] = maxmol_all + 1; + myaddatom.molecule = maxmol_all + 1; } } - atom->mask[n] = 1 | groupbit; - atom->image[n] = imageflags[m]; + myaddatom.mask = 1 | groupbit; + myaddatom.image = imageflags[m]; // guess a somewhat reasonable initial velocity based on reaction site // further control is possible using bond_react_MASTER_group // compute |velocity| corresponding to a given temperature t, using specific atom's mass - double mymass = atom->rmass ? atom->rmass[n] : atom->mass[twomol->type[m]]; - double vtnorm = sqrt(t / (force->mvv2e / (dimension * force->boltz)) / mymass); - v[n][0] = random[rxnID]->uniform(); - v[n][1] = random[rxnID]->uniform(); - v[n][2] = random[rxnID]->uniform(); - double vnorm = sqrt(v[n][0]*v[n][0] + v[n][1]*v[n][1] + v[n][2]*v[n][2]); - v[n][0] = v[n][0]/vnorm*vtnorm; - v[n][1] = v[n][1]/vnorm*vtnorm; - v[n][2] = v[n][2]/vnorm*vtnorm; - modify->create_attribute(n); + myaddatom.rmass = atom->rmass ? twomol->rmass[m] : atom->mass[twomol->type[m]]; + double vtnorm = sqrt(t / (force->mvv2e / (dimension * force->boltz)) / myaddatom.rmass); + double myv[3]; + myv[0] = random[rxnID]->uniform(); + myv[1] = random[rxnID]->uniform(); + myv[2] = random[rxnID]->uniform(); + double vnorm = sqrt(myv[0]*myv[0] + myv[1]*myv[1] + myv[2]*myv[2]); + myaddatom.v[0] = myv[0]/vnorm*vtnorm; + myaddatom.v[1] = myv[1]/vnorm*vtnorm; + myaddatom.v[2] = myv[2]/vnorm*vtnorm; + addatoms.push_back(myaddatom); } // globally update mega_glove and equivalences MPI_Allreduce(MPI_IN_PLACE,&root,1,MPI_INT,MPI_SUM,world); @@ -3881,12 +3902,11 @@ int FixBondReact::insert_atoms(tagint **my_update_mega_glove, int iupdate) } // reset global natoms here - // reset atom map elsewhere, after all calls to 'insert_atoms' + // reset atom map elsewhere, after all calls to 'insert_atoms_setup' atom->natoms += add_count; if (atom->natoms < 0) error->all(FLERR,"Too many total atoms"); - maxtag_all += add_count; - if (maxtag_all >= MAXTAGINT) + if (addatomtag >= MAXTAGINT) error->all(FLERR,"New atom IDs exceed maximum allowed ID"); // atom creation successful memory->destroy(coords); diff --git a/src/REACTION/fix_bond_react.h b/src/REACTION/fix_bond_react.h index d79588c6dd..6267d20076 100644 --- a/src/REACTION/fix_bond_react.h +++ b/src/REACTION/fix_bond_react.h @@ -216,7 +216,7 @@ class FixBondReact : public Fix { void glove_ghostcheck(); void ghost_glovecast(); void update_everything(); - int insert_atoms(tagint **, int); + int insert_atoms_setup(tagint **, int); void unlimit_bond(); // removes atoms from stabilization, and other post-reaction every-step operations void dedup_mega_gloves(int); //dedup global mega_glove void write_restart(FILE *) override; @@ -246,6 +246,15 @@ class FixBondReact : public Fix { std::map, int> atoms2bond; // maps atom pair to index of local bond array std::vector> constraints; + tagint addatomtag; + struct AddAtom { + tagint tag, molecule; + int type, mask; + imageint image; + double rmass, x[3], v[3]; + }; + std::vector addatoms; + // DEBUG void print_bb(); From e94d32e7d3e1d854e76c10159e90e5e95f2f61e1 Mon Sep 17 00:00:00 2001 From: Jacob Gissinger Date: Sun, 25 Aug 2024 14:19:17 -0400 Subject: [PATCH 09/11] clean up tiny_nylon example --- .../tiny_nylon/in.tiny_nylon.stabilized | 1 + ...tiny_nylon.stabilized_variable_probability | 2 +- .../tiny_nylon/in.tiny_nylon.unstabilized | 2 +- .../rxn1_stp1_reacted.molecule_template | 21 - .../rxn1_stp2_reacted.molecule_template | 30 +- .../reaction/tiny_nylon/tiny_nylon.data | 1263 ++++++++--------- 6 files changed, 605 insertions(+), 714 deletions(-) diff --git a/examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.stabilized b/examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.stabilized index 60d33aa351..4998ea7d9d 100644 --- a/examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.stabilized +++ b/examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.stabilized @@ -44,6 +44,7 @@ thermo 50 fix myrxns all bond/react stabilization yes statted_grp .03 & react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map & react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map + react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map rescale_charges yes fix 1 statted_grp_REACT nvt temp 300 300 100 diff --git a/examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.stabilized_variable_probability b/examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.stabilized_variable_probability index 770f4fc3b1..4b268cf0d9 100644 --- a/examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.stabilized_variable_probability +++ b/examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.stabilized_variable_probability @@ -47,7 +47,7 @@ thermo 50 fix myrxns all bond/react stabilization yes statted_grp .03 & react rxn1 all 1 0.0 5.0 mol1 mol2 rxn1_stp1_map prob v_prob1 1234 & - react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map prob v_prob2 1234 + react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map prob v_prob2 1234 rescale_charges yes fix 1 statted_grp_REACT nvt temp 300 300 100 diff --git a/examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.unstabilized b/examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.unstabilized index 4ade3f8b99..3ecf552174 100644 --- a/examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.unstabilized +++ b/examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.unstabilized @@ -44,7 +44,7 @@ thermo 50 fix myrxns all bond/react stabilization no & react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map & - react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map + react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map rescale_charges yes fix 1 all nve/limit .03 diff --git a/examples/PACKAGES/reaction/tiny_nylon/rxn1_stp1_reacted.molecule_template b/examples/PACKAGES/reaction/tiny_nylon/rxn1_stp1_reacted.molecule_template index 40f3aa8276..594775b39c 100644 --- a/examples/PACKAGES/reaction/tiny_nylon/rxn1_stp1_reacted.molecule_template +++ b/examples/PACKAGES/reaction/tiny_nylon/rxn1_stp1_reacted.molecule_template @@ -48,27 +48,6 @@ Types 17 hc 18 hc -Charges - - 1 -0.300000 - 2 0.000000 - 3 0.000000 - 4 0.000000 - 5 0.000000 - 6 0.000000 - 7 0.000000 - 8 0.000000 - 9 0.000000 - 10 0.300000 - 11 0.000000 - 12 0.000000 - 13 0.000000 - 14 0.000000 - 15 0.000000 - 16 0.000000 - 17 0.000000 - 18 0.000000 - Molecules 1 1 diff --git a/examples/PACKAGES/reaction/tiny_nylon/rxn1_stp2_reacted.molecule_template b/examples/PACKAGES/reaction/tiny_nylon/rxn1_stp2_reacted.molecule_template index 2e91261468..7e1a350d16 100644 --- a/examples/PACKAGES/reaction/tiny_nylon/rxn1_stp2_reacted.molecule_template +++ b/examples/PACKAGES/reaction/tiny_nylon/rxn1_stp2_reacted.molecule_template @@ -44,21 +44,21 @@ Types Charges - 1 -0.300000 - 2 0.000000 - 3 0.000000 - 4 0.410000 - 5 0.000000 - 6 0.000000 - 7 0.000000 - 8 0.000000 - 9 0.000000 - 10 0.300000 - 11 0.000000 - 12 -0.820000 - 13 0.000000 - 14 0.000000 - 15 0.410000 + 1 -0.60533 + 2 -0.01149 + 3 -0.76306 + 4 0.38 + 5 0.29346 + 6 0.18360 + 7 0.15396 + 8 -0.72636 + 9 -0.27437 + 10 0.40603 + 11 -0.65530 + 12 -0.76 + 13 0.21423 + 14 0.18949 + 15 0.38 Molecules diff --git a/examples/PACKAGES/reaction/tiny_nylon/tiny_nylon.data b/examples/PACKAGES/reaction/tiny_nylon/tiny_nylon.data index ee8e397956..73c776c430 100644 --- a/examples/PACKAGES/reaction/tiny_nylon/tiny_nylon.data +++ b/examples/PACKAGES/reaction/tiny_nylon/tiny_nylon.data @@ -1,15 +1,15 @@ -this is LAMMPS data file containing two nylon monomers +LAMMPS data file via write_data, version 27 Jun 2024, timestep = 0, units = real 44 atoms 11 atom types 42 bonds -15 bond types +13 bond types 74 angles -29 angle types +26 angle types 100 dihedrals -36 dihedral types -44 impropers -13 improper types +33 dihedral types +16 impropers +5 improper types -25 25 xlo xhi -25 25 ylo yhi @@ -17,15 +17,15 @@ this is LAMMPS data file containing two nylon monomers Atom Type Labels -1 c2 -2 c_1 -3 o -4 hc -5 ho -6 o_1 -7 na -8 hn -9 n +1 c2 +2 c_1 +3 o +4 hc +5 ho +6 o_1 +7 na +8 hn +9 n 10 hw 11 o* @@ -37,102 +37,86 @@ Bond Type Labels 4 c2-c_1 5 c_1-o_1 6 o-ho -7 c2-c2-repeat -8 c2-hc-repeat -9 na-c2 -10 na-hn -11 n-c2 -12 n-hn -13 n-c_1 -14 c2-na -15 hw-o* +7 na-c2 +8 na-hn +9 n-c2 +10 n-hn +11 n-c_1 +12 c2-na +13 hw-o* Angle Type Labels -1 hc-c2-hc -2 c2-c2-hc -3 c2-c2-c2 -4 c2-c_1-o_1 -5 o-c_1-o_1 -6 c2-c_1-o -7 c_1-o-ho -8 c2-c2-c_1 -9 c_1-c2-hc -10 c2-c2-hc-repeat -11 c2-c2-c2-repeat -12 hc-c2-hc-repeat -13 c2-c2-na -14 na-c2-hc -15 c2-na-hn -16 hn-na-hn -17 c2-n-hn -18 c2-n-c_1 -19 hn-n-hn -20 hn-n-c_1 -21 n-c2-c2 -22 n-c2-hc -23 hc-c2-c_1 -24 n-c_1-c2 -25 o_1-c_1-o -26 n-c_1-o_1 -27 n-c_1-o -28 na-c2-c2 -29 hw-o*-hw +1 hc-c2-hc +2 c2-c2-hc +3 c2-c2-c2 +4 c2-c_1-o_1 +5 o-c_1-o_1 +6 c2-c_1-o +7 c_1-o-ho +8 c2-c2-c_1 +9 c_1-c2-hc +10 c2-c2-na +11 na-c2-hc +12 c2-na-hn +13 hn-na-hn +14 c2-n-hn +15 c2-n-c_1 +16 hn-n-hn +17 hn-n-c_1 +18 n-c2-c2 +19 n-c2-hc +20 hc-c2-c_1 +21 n-c_1-c2 +22 o_1-c_1-o +23 n-c_1-o_1 +24 n-c_1-o +25 na-c2-c2 +26 hw-o*-hw Dihedral Type Labels -1 c_1-c2-c2-hc -2 hc-c2-c2-hc -3 c2-c2-c2-c_1 -4 c2-c2-c2-hc -5 c2-c2-c2-c2 -6 c2-c_1-o-ho -7 o_1-c_1-o-ho -8 c2-c2-c_1-o -9 hc-c2-c_1-o +1 c_1-c2-c2-hc +2 hc-c2-c2-hc +3 c2-c2-c2-c_1 +4 c2-c2-c2-hc +5 c2-c2-c2-c2 +6 c2-c_1-o-ho +7 o_1-c_1-o-ho +8 c2-c2-c_1-o +9 hc-c2-c_1-o 10 c2-c2-c_1-o_1 11 hc-c2-c_1-o_1 12 na-c2-c2-hc -13 hc-c2-c2-hc-repeat -14 c2-c2-c2-na -15 c2-c2-c2-hc-repeat -16 c2-c2-c2-c2-repeat -17 c2-c2-na-hn -18 hn-na-c2-hc -19 hn-n-c2-c2 -20 hn-n-c2-hc -21 c_1-n-c2-c2 -22 c_1-n-c2-hc -23 c2-n-c_1-c2 -24 c2-n-c_1-o_1 -25 c2-n-c_1-o -26 hn-n-c_1-c2 -27 hn-n-c_1-o_1 -28 hn-n-c_1-o -29 n-c2-c2-c2 -30 n-c2-c2-hc -31 c2-c2-c_1-n -32 hc-c2-c_1-n -33 n-c_1-o-ho -34 hn-na-c2-c2 -35 hc-c2-na-hn -36 na-c2-c2-c2 +13 c2-c2-c2-na +14 c2-c2-na-hn +15 hn-na-c2-hc +16 hn-n-c2-c2 +17 hn-n-c2-hc +18 c_1-n-c2-c2 +19 c_1-n-c2-hc +20 c2-n-c_1-c2 +21 c2-n-c_1-o_1 +22 c2-n-c_1-o +23 hn-n-c_1-c2 +24 hn-n-c_1-o_1 +25 hn-n-c_1-o +26 n-c2-c2-c2 +27 n-c2-c2-hc +28 c2-c2-c_1-n +29 hc-c2-c_1-n +30 n-c_1-o-ho +31 hn-na-c2-c2 +32 hc-c2-na-hn +33 na-c2-c2-c2 Improper Type Labels -1 c2-c_1-o-o_1 -2 c2-na-hn-hn -3 c2-c_1-o_1-o -4 c2-n-hn-c_1 -5 zero5 -6 zero6 -7 zero7 -8 zero8 -9 zero9 -10 zero10 -11 zero11 -12 zero12 -13 n-c_1-c2-o_1 +1 c2-c_1-o-o_1 +2 c2-na-hn-hn +3 c2-c_1-o_1-o +4 c2-n-hn-c_1 +5 n-c_1-c2-o_1 Masses @@ -148,7 +132,7 @@ Masses 10 1.00797 11 15.9994 -Pair Coeffs # lj/class2/coul/cut +Pair Coeffs # lj/class2/coul/long 1 0.054 4.01 2 0.12 3.81 @@ -170,15 +154,13 @@ Bond Coeffs # class2 4 1.5202 253.707 -423.037 396.9 5 1.202 851.14 -1918.49 2160.77 6 0.965 532.506 -1282.9 2004.77 -7 1.53 299.67 -501.77 679.81 -8 1.101 345 -691.89 844.6 -9 1.457 365.805 -699.637 998.484 -10 1.006 466.74 -1073.6 1251.11 -11 1.452 327.166 -547.899 526.5 -12 1.01 462.75 -1053.63 1545.76 -13 1.416 359.159 -558.473 1146.38 -14 1.457 365.805 -699.637 998.484 -15 0.97 563.28 -1428.22 1902.12 +7 1.457 365.805 -699.637 998.484 +8 1.006 466.74 -1073.6 1251.11 +9 1.452 327.166 -547.899 526.5 +10 1.01 462.75 -1053.63 1545.76 +11 1.416 359.159 -558.473 1146.38 +12 1.457 365.805 -699.637 998.484 +13 0.97 563.28 -1428.22 1902.12 Angle Coeffs # class2 @@ -191,26 +173,23 @@ Angle Coeffs # class2 7 111.254 53.5303 -11.8454 -11.5405 8 108.53 51.9747 -9.4851 -10.9985 9 107.734 40.6099 -28.8121 0 -10 110.77 41.453 -10.604 5.129 -11 112.67 39.516 -7.443 -9.5583 -12 107.66 39.641 -12.921 -2.4318 -13 111.91 60.7147 -13.3366 -13.0785 -14 110.62 51.3137 -6.7198 -2.6003 -15 110.954 50.8652 -4.4522 -10.0298 -16 107.067 45.252 -7.5558 -9.512 -17 113.868 45.9271 -20.0824 0 -18 111.037 31.8958 -6.6942 -6.837 -19 116.94 37.5749 -8.6676 0 -20 117.961 37.4964 -8.1837 0 -21 114.302 42.6589 -10.5464 -9.3243 -22 108.937 57.401 2.9374 0 -23 107.734 40.6099 -28.8121 0 -24 116.926 39.4193 -10.9945 -8.7733 -25 118.986 98.6813 -22.2485 10.3673 -26 125.542 92.572 -34.48 -11.1871 -27 125.542 92.572 -34.48 -11.1871 -28 111.91 60.7147 -13.3366 -13.0785 -29 103.7 49.84 -11.6 -8 +10 111.91 60.7147 -13.3366 -13.0785 +11 110.62 51.3137 -6.7198 -2.6003 +12 110.954 50.8652 -4.4522 -10.0298 +13 107.067 45.252 -7.5558 -9.512 +14 113.868 45.9271 -20.0824 0 +15 111.037 31.8958 -6.6942 -6.837 +16 116.94 37.5749 -8.6676 0 +17 117.961 37.4964 -8.1837 0 +18 114.302 42.6589 -10.5464 -9.3243 +19 108.937 57.401 2.9374 0 +20 107.734 40.6099 -28.8121 0 +21 116.926 39.4193 -10.9945 -8.7733 +22 118.986 98.6813 -22.2485 10.3673 +23 125.542 92.572 -34.48 -11.1871 +24 125.542 92.572 -34.48 -11.1871 +25 111.91 60.7147 -13.3366 -13.0785 +26 103.7 49.84 -11.6 -8 BondBond Coeffs @@ -223,26 +202,23 @@ BondBond Coeffs 7 0 1.3649 0.965 8 5.4199 1.53 1.5202 9 0.7115 1.5202 1.101 -10 3.3872 1.53 1.101 -11 0 1.53 1.53 -12 5.3316 1.101 1.101 -13 4.6217 1.53 1.457 -14 12.426 1.457 1.101 -15 -6.4168 1.457 1.006 -16 -1.8749 1.006 1.006 -17 -3.471 1.452 1.01 -18 12.1186 1.452 1.416 -19 -0.5655 1.01 1.01 -20 -4.3126 1.01 1.416 -21 3.5446 1.452 1.53 -22 15.2994 1.452 1.101 -23 0.7115 1.101 1.5202 -24 0 1.416 1.5202 -25 0 1.202 1.3649 -26 138.495 1.416 1.202 -27 0 1.416 1.3649 -28 4.6217 1.457 1.53 -29 -9.5 0.97 0.97 +10 4.6217 1.53 1.457 +11 12.426 1.457 1.101 +12 -6.4168 1.457 1.006 +13 -1.8749 1.006 1.006 +14 -3.471 1.452 1.01 +15 12.1186 1.452 1.416 +16 -0.5655 1.01 1.01 +17 -4.3126 1.01 1.416 +18 3.5446 1.452 1.53 +19 15.2994 1.452 1.101 +20 0.7115 1.101 1.5202 +21 0 1.416 1.5202 +22 0 1.202 1.3649 +23 138.495 1.416 1.202 +24 0 1.416 1.3649 +25 4.6217 1.457 1.53 +26 -9.5 0.97 0.97 BondAngle Coeffs @@ -255,26 +231,23 @@ BondAngle Coeffs 7 0 0 1.3649 0.965 8 18.1678 15.8758 1.53 1.5202 9 12.4632 9.1765 1.5202 1.101 -10 20.754 11.421 1.53 1.101 -11 8.016 8.016 1.53 1.53 -12 18.103 18.103 1.101 1.101 -13 6.0876 16.5702 1.53 1.457 -14 42.4332 13.4582 1.457 1.101 -15 31.8096 20.5799 1.457 1.006 -16 28.0322 28.0322 1.006 1.006 -17 11.8828 5.9339 1.452 1.01 -18 3.7812 14.8633 1.452 1.416 -19 19.8125 19.8125 1.01 1.01 -20 10.8422 29.5743 1.01 1.416 -21 4.6031 -5.479 1.452 1.53 -22 34.8907 10.6917 1.452 1.101 -23 9.1765 12.4632 1.101 1.5202 -24 0 0 1.416 1.5202 -25 0 0 1.202 1.3649 -26 62.7124 52.4045 1.416 1.202 -27 0 0 1.416 1.3649 -28 16.5702 6.0876 1.457 1.53 -29 22.35 22.35 0.97 0.97 +10 6.0876 16.5702 1.53 1.457 +11 42.4332 13.4582 1.457 1.101 +12 31.8096 20.5799 1.457 1.006 +13 28.0322 28.0322 1.006 1.006 +14 11.8828 5.9339 1.452 1.01 +15 3.7812 14.8633 1.452 1.416 +16 19.8125 19.8125 1.01 1.01 +17 10.8422 29.5743 1.01 1.416 +18 4.6031 -5.479 1.452 1.53 +19 34.8907 10.6917 1.452 1.101 +20 9.1765 12.4632 1.101 1.5202 +21 0 0 1.416 1.5202 +22 0 0 1.202 1.3649 +23 62.7124 52.4045 1.416 1.202 +24 0 0 1.416 1.3649 +25 16.5702 6.0876 1.457 1.53 +26 22.35 22.35 0.97 0.97 Dihedral Coeffs # class2 @@ -290,30 +263,27 @@ Dihedral Coeffs # class2 10 0.0442 0 0.0292 0 0.0562 0 11 -0.1804 0 0.0012 0 0.0371 0 12 -0.2428 0 0.4065 0 -0.3079 0 -13 -0.1432 0 0.0617 0 -0.1083 0 -14 0.1764 0 0.1766 0 -0.5206 0 -15 0 0 0.0316 0 -0.1681 0 -16 0 0 0.0514 0 -0.143 0 -17 -1.1506 0 -0.6344 0 -0.1845 0 -18 -0.5187 0 -0.4837 0 -0.1692 0 -19 -0.0483 0 -0.0077 0 -0.0014 0 -20 -0.0148 0 -0.0791 0 -0.0148 0 -21 0.0143 0 -0.0132 0 0.0091 0 -22 0.0219 0 -0.026 0 0.0714 0 -23 -0.7532 0 2.7392 0 0.0907 0 -24 0.8297 0 3.7234 0 -0.0495 0 +13 0.1764 0 0.1766 0 -0.5206 0 +14 -1.1506 0 -0.6344 0 -0.1845 0 +15 -0.5187 0 -0.4837 0 -0.1692 0 +16 -0.0483 0 -0.0077 0 -0.0014 0 +17 -0.0148 0 -0.0791 0 -0.0148 0 +18 0.0143 0 -0.0132 0 0.0091 0 +19 0.0219 0 -0.026 0 0.0714 0 +20 -0.7532 0 2.7392 0 0.0907 0 +21 0.8297 0 3.7234 0 -0.0495 0 +22 0 0 0 0 0 0 +23 0 0 0 0 0 0 +24 -1.6938 0 2.7386 0 -0.336 0 25 0 0 0 0 0 0 -26 0 0 0 0 0 0 -27 -1.6938 0 2.7386 0 -0.336 0 -28 0 0 0 0 0 0 -29 0.0972 0 0.0722 0 -0.2581 0 -30 -0.0228 0 0.028 0 -0.1863 0 -31 0.1693 0 -0.009 0 -0.0687 0 -32 0.1693 0 -0.009 0 -0.0687 0 -33 0 0 0 0 0 0 -34 -1.1506 0 -0.6344 0 -0.1845 0 -35 -0.5187 0 -0.4837 0 -0.1692 0 -36 0.1764 0 0.1766 0 -0.5206 0 +26 0.0972 0 0.0722 0 -0.2581 0 +27 -0.0228 0 0.028 0 -0.1863 0 +28 0.1693 0 -0.009 0 -0.0687 0 +29 0.1693 0 -0.009 0 -0.0687 0 +30 0 0 0 0 0 0 +31 -1.1506 0 -0.6344 0 -0.1845 0 +32 -0.5187 0 -0.4837 0 -0.1692 0 +33 0.1764 0 0.1766 0 -0.5206 0 AngleAngleTorsion Coeffs @@ -329,30 +299,27 @@ AngleAngleTorsion Coeffs 10 -8.019 108.53 123.145 11 -15.3496 107.734 123.145 12 -15.7572 111.91 110.77 -13 -12.564 110.77 110.77 -14 -27.3953 112.67 111.91 -15 -16.164 112.67 110.77 -16 -22.045 112.67 112.67 -17 -7.5499 111.91 110.954 -18 -10.4258 110.62 110.954 -19 -4.6337 113.868 114.302 -20 -6.659 113.868 108.937 -21 -7.4314 111.037 114.302 -22 -8.1335 111.037 108.937 -23 -6.5335 111.037 116.926 -24 -15.5547 111.037 125.542 -25 0 111.037 0 -26 -1.3234 117.961 116.926 -27 -7.3186 117.961 125.542 -28 0 117.961 0 -29 -1.0631 114.302 112.67 -30 -12.7974 114.302 110.77 -31 -5.4514 108.53 116.926 -32 -12.2417 107.734 116.926 -33 0 0 111.254 -34 -7.5499 110.954 111.91 -35 -10.4258 110.954 110.62 -36 -27.3953 111.91 112.67 +13 -27.3953 112.67 111.91 +14 -7.5499 111.91 110.954 +15 -10.4258 110.62 110.954 +16 -4.6337 113.868 114.302 +17 -6.659 113.868 108.937 +18 -7.4314 111.037 114.302 +19 -8.1335 111.037 108.937 +20 -6.5335 111.037 116.926 +21 -15.5547 111.037 125.542 +22 0 111.037 0 +23 -1.3234 117.961 116.926 +24 -7.3186 117.961 125.542 +25 0 117.961 0 +26 -1.0631 114.302 112.67 +27 -12.7974 114.302 110.77 +28 -5.4514 108.53 116.926 +29 -12.2417 107.734 116.926 +30 0 0 111.254 +31 -7.5499 110.954 111.91 +32 -10.4258 110.954 110.62 +33 -27.3953 111.91 112.67 EndBondTorsion Coeffs @@ -368,30 +335,27 @@ EndBondTorsion Coeffs 10 0.2654 0.0503 0.1046 -0.281 0.0816 -0.1522 1.53 1.202 11 1.2143 0.2831 0.3916 -0.2298 0.0354 0.3853 1.101 1.202 12 0.1022 0.209 0.6433 0.196 0.7056 0.112 1.457 1.101 -13 0.213 0.312 0.0777 0.213 0.312 0.0777 1.101 1.101 -14 0.1032 0.5896 -0.4836 0.0579 -0.0043 -0.1906 1.53 1.457 -15 0.2486 0.2422 -0.0925 0.0814 0.0591 0.2219 1.53 1.101 -16 -0.0732 0 0 -0.0732 0 0 1.53 1.53 -17 -0.9466 0.9356 -0.5542 0.057 0.0625 0.4112 1.53 1.006 -18 -1.1685 0.9266 -0.0993 0.085 0.3061 0.2104 1.101 1.006 -19 -0.0992 -0.0727 -0.4139 0.132 0.0015 0.1324 1.01 1.53 -20 -0.4894 0.1644 0.3105 -0.8983 0.2826 0.0881 1.01 1.101 -21 -0.1245 -0.9369 0.7781 -0.2033 0.0035 0.056 1.416 1.53 -22 0.2292 1.1732 -0.058 -0.3667 0.8197 0.1335 1.416 1.101 -23 0.2299 -0.1141 -0.1424 0.0933 -0.4631 0.2883 1.452 1.5202 -24 0.1598 0.7253 -0.1007 0.1226 -2.1326 0.5581 1.452 1.202 -25 0 0 0 0 0 0 1.452 1.3649 -26 0.6413 0.1676 0.144 -0.6979 0.5619 0.4212 1.01 1.5202 -27 0.1214 0.1936 0.0816 -0.7604 -2.6431 1.2467 1.01 1.202 -28 0 0 0 0 0 0 1.01 1.3649 -29 -0.0797 -0.0406 0.0255 0.0742 0.0105 0.0518 1.452 1.53 -30 0.3022 0.2513 0.4641 -0.0601 -0.3763 -0.1876 1.452 1.101 -31 -0.2631 -0.0076 -0.1145 -0.2751 -0.3058 -0.1767 1.53 1.416 -32 -0.0268 0.7836 0.0035 0.3552 -0.2685 0.5834 1.101 1.416 -33 0 0 0 0 0 0 1.416 0.965 -34 0.057 0.0625 0.4112 -0.9466 0.9356 -0.5542 1.006 1.53 -35 0.085 0.3061 0.2104 -1.1685 0.9266 -0.0993 1.006 1.101 -36 0.0579 -0.0043 -0.1906 0.1032 0.5896 -0.4836 1.457 1.53 +13 0.1032 0.5896 -0.4836 0.0579 -0.0043 -0.1906 1.53 1.457 +14 -0.9466 0.9356 -0.5542 0.057 0.0625 0.4112 1.53 1.006 +15 -1.1685 0.9266 -0.0993 0.085 0.3061 0.2104 1.101 1.006 +16 -0.0992 -0.0727 -0.4139 0.132 0.0015 0.1324 1.01 1.53 +17 -0.4894 0.1644 0.3105 -0.8983 0.2826 0.0881 1.01 1.101 +18 -0.1245 -0.9369 0.7781 -0.2033 0.0035 0.056 1.416 1.53 +19 0.2292 1.1732 -0.058 -0.3667 0.8197 0.1335 1.416 1.101 +20 0.2299 -0.1141 -0.1424 0.0933 -0.4631 0.2883 1.452 1.5202 +21 0.1598 0.7253 -0.1007 0.1226 -2.1326 0.5581 1.452 1.202 +22 0 0 0 0 0 0 1.452 1.3649 +23 0.6413 0.1676 0.144 -0.6979 0.5619 0.4212 1.01 1.5202 +24 0.1214 0.1936 0.0816 -0.7604 -2.6431 1.2467 1.01 1.202 +25 0 0 0 0 0 0 1.01 1.3649 +26 -0.0797 -0.0406 0.0255 0.0742 0.0105 0.0518 1.452 1.53 +27 0.3022 0.2513 0.4641 -0.0601 -0.3763 -0.1876 1.452 1.101 +28 -0.2631 -0.0076 -0.1145 -0.2751 -0.3058 -0.1767 1.53 1.416 +29 -0.0268 0.7836 0.0035 0.3552 -0.2685 0.5834 1.101 1.416 +30 0 0 0 0 0 0 1.416 0.965 +31 0.057 0.0625 0.4112 -0.9466 0.9356 -0.5542 1.006 1.53 +32 0.085 0.3061 0.2104 -1.1685 0.9266 -0.0993 1.006 1.101 +33 0.0579 -0.0043 -0.1906 0.1032 0.5896 -0.4836 1.457 1.53 MiddleBondTorsion Coeffs @@ -407,30 +371,27 @@ MiddleBondTorsion Coeffs 10 0.3388 -0.1096 0.1219 1.5202 11 0.2359 0.9139 0.9594 1.5202 12 -10.4959 -0.7647 -0.0545 1.53 -13 -14.261 -0.5322 -0.4864 1.53 -14 -15.4174 -7.3055 -1.0749 1.53 -15 -14.879 -3.6581 -0.3138 1.53 -16 -17.787 -7.1877 0 1.53 -17 -2.2208 0.5479 -0.3527 1.457 -18 -3.4611 1.6996 -0.6007 1.457 -19 -3.5406 -3.3866 0.0352 1.452 -20 -1.1752 2.8058 0.8083 1.452 -21 -3.9501 -0.4002 -0.6798 1.452 -22 -0.6899 -2.2646 1.1579 1.452 +13 -15.4174 -7.3055 -1.0749 1.53 +14 -2.2208 0.5479 -0.3527 1.457 +15 -3.4611 1.6996 -0.6007 1.457 +16 -3.5406 -3.3866 0.0352 1.452 +17 -1.1752 2.8058 0.8083 1.452 +18 -3.9501 -0.4002 -0.6798 1.452 +19 -0.6899 -2.2646 1.1579 1.452 +20 0 0 0 1.416 +21 -8.8301 14.3079 -1.7716 1.416 +22 0 0 0 1.416 23 0 0 0 1.416 -24 -8.8301 14.3079 -1.7716 1.416 +24 -0.9084 6.1447 -0.4852 1.416 25 0 0 0 1.416 -26 0 0 0 1.416 -27 -0.9084 6.1447 -0.4852 1.416 -28 0 0 0 1.416 -29 -4.2324 -3.3023 -1.3244 1.53 -30 -4.1028 -0.5941 -0.047 1.53 -31 0 0 0 1.5202 -32 0 0 0 1.5202 -33 0 0 0 1.3649 -34 -2.2208 0.5479 -0.3527 1.457 -35 -3.4611 1.6996 -0.6007 1.457 -36 -15.4174 -7.3055 -1.0749 1.53 +26 -4.2324 -3.3023 -1.3244 1.53 +27 -4.1028 -0.5941 -0.047 1.53 +28 0 0 0 1.5202 +29 0 0 0 1.5202 +30 0 0 0 1.3649 +31 -2.2208 0.5479 -0.3527 1.457 +32 -3.4611 1.6996 -0.6007 1.457 +33 -15.4174 -7.3055 -1.0749 1.53 BondBond13 Coeffs @@ -446,30 +407,27 @@ BondBond13 Coeffs 10 0 1.53 1.202 11 0 1.101 1.202 12 0 1.457 1.101 -13 0 1.101 1.101 -14 0 1.53 1.457 -15 0 1.53 1.101 -16 0 1.53 1.53 -17 0 1.53 1.006 -18 0 1.101 1.006 -19 0 1.01 1.53 -20 0 1.01 1.101 -21 0 1.416 1.53 -22 0 1.416 1.101 -23 0 1.452 1.5202 -24 0 1.452 1.202 -25 0 1.452 1.3649 -26 0 1.01 1.5202 -27 0 1.01 1.202 -28 0 1.01 1.3649 -29 0 1.452 1.53 -30 0 1.452 1.101 -31 0 1.53 1.416 -32 0 1.101 1.416 -33 0 1.416 0.965 -34 0 1.006 1.53 -35 0 1.006 1.101 -36 0 1.457 1.53 +13 0 1.53 1.457 +14 0 1.53 1.006 +15 0 1.101 1.006 +16 0 1.01 1.53 +17 0 1.01 1.101 +18 0 1.416 1.53 +19 0 1.416 1.101 +20 0 1.452 1.5202 +21 0 1.452 1.202 +22 0 1.452 1.3649 +23 0 1.01 1.5202 +24 0 1.01 1.202 +25 0 1.01 1.3649 +26 0 1.452 1.53 +27 0 1.452 1.101 +28 0 1.53 1.416 +29 0 1.101 1.416 +30 0 1.416 0.965 +31 0 1.006 1.53 +32 0 1.006 1.101 +33 0 1.457 1.53 AngleTorsion Coeffs @@ -485,30 +443,27 @@ AngleTorsion Coeffs 10 0.0885 -1.3703 -0.5452 0.675 0.5965 0.6725 108.53 123.145 11 9.1299 -0.4847 0.3582 -1.4946 0.7308 -0.2083 107.734 123.145 12 -1.1075 0.282 0.8318 0.5111 1.6328 -1.0155 111.91 110.77 -13 -0.8085 0.5569 -0.2466 -0.8085 0.5569 -0.2466 110.77 110.77 -14 -1.9225 -1.345 0.221 2.0125 0.944 -2.7612 112.67 111.91 -15 -0.2454 0 -0.1136 0.3113 0.4516 -0.1988 112.67 110.77 -16 0.3886 -0.3139 0.1389 0.3886 -0.3139 0.1389 112.67 112.67 -17 -3.343 4.4558 -0.0346 0.2873 -0.8072 -0.096 111.91 110.954 -18 -3.9582 2.0063 0.3213 -0.4294 -0.4442 -0.6141 110.62 110.954 -19 -0.5807 0.2041 -0.1384 -2.8967 2.7084 -0.0375 113.868 114.302 -20 -0.3868 0.2041 0.0445 -3.7022 1.3876 0.2393 113.868 108.937 -21 -1.523 1.1296 0.7167 -0.7555 0.0564 1.2177 111.037 114.302 -22 0.0372 -0.3418 -0.0775 -1.5157 2.0781 0.5364 111.037 108.937 -23 5.916 1.7856 0.4052 4.2133 2.9302 3.2903 111.037 116.926 -24 7.4427 2.1505 -0.2206 4.4466 4.0317 1.7129 111.037 125.542 -25 0 0 0 0 0 0 111.037 0 -26 1.9306 0.2105 0.0557 -2.2134 1.2909 0.9726 117.961 116.926 -27 2.3848 0.703 0.1399 -2.6238 0.3606 0.5474 117.961 125.542 -28 0 0 0 0 0 0 117.961 0 -29 0.2039 0.1602 -0.7946 -0.5501 -1.6982 0.2485 114.302 112.67 -30 -1.982 0.2325 -0.3928 -1.2469 1.6933 -1.2081 114.302 110.77 -31 2.1802 -0.0335 -1.3816 2.1221 0.5032 -0.0767 108.53 116.926 -32 7.095 0.0075 0.691 2.0013 0.5068 0.8406 107.734 116.926 -33 0 0 0 0 0 0 0 111.254 -34 0.2873 -0.8072 -0.096 -3.343 4.4558 -0.0346 110.954 111.91 -35 -0.4294 -0.4442 -0.6141 -3.9582 2.0063 0.3213 110.954 110.62 -36 2.0125 0.944 -2.7612 -1.9225 -1.345 0.221 111.91 112.67 +13 -1.9225 -1.345 0.221 2.0125 0.944 -2.7612 112.67 111.91 +14 -3.343 4.4558 -0.0346 0.2873 -0.8072 -0.096 111.91 110.954 +15 -3.9582 2.0063 0.3213 -0.4294 -0.4442 -0.6141 110.62 110.954 +16 -0.5807 0.2041 -0.1384 -2.8967 2.7084 -0.0375 113.868 114.302 +17 -0.3868 0.2041 0.0445 -3.7022 1.3876 0.2393 113.868 108.937 +18 -1.523 1.1296 0.7167 -0.7555 0.0564 1.2177 111.037 114.302 +19 0.0372 -0.3418 -0.0775 -1.5157 2.0781 0.5364 111.037 108.937 +20 5.916 1.7856 0.4052 4.2133 2.9302 3.2903 111.037 116.926 +21 7.4427 2.1505 -0.2206 4.4466 4.0317 1.7129 111.037 125.542 +22 0 0 0 0 0 0 111.037 0 +23 1.9306 0.2105 0.0557 -2.2134 1.2909 0.9726 117.961 116.926 +24 2.3848 0.703 0.1399 -2.6238 0.3606 0.5474 117.961 125.542 +25 0 0 0 0 0 0 117.961 0 +26 0.2039 0.1602 -0.7946 -0.5501 -1.6982 0.2485 114.302 112.67 +27 -1.982 0.2325 -0.3928 -1.2469 1.6933 -1.2081 114.302 110.77 +28 2.1802 -0.0335 -1.3816 2.1221 0.5032 -0.0767 108.53 116.926 +29 7.095 0.0075 0.691 2.0013 0.5068 0.8406 107.734 116.926 +30 0 0 0 0 0 0 0 111.254 +31 0.2873 -0.8072 -0.096 -3.343 4.4558 -0.0346 110.954 111.91 +32 -0.4294 -0.4442 -0.6141 -3.9582 2.0063 0.3213 110.954 110.62 +33 2.0125 0.944 -2.7612 -1.9225 -1.345 0.221 111.91 112.67 Improper Coeffs # class2 @@ -516,15 +471,7 @@ Improper Coeffs # class2 2 0 0 3 0 0 4 0 0 -5 0 0 -6 0 0 -7 0 0 -8 0 0 -9 0 0 -10 0 0 -11 0 0 -12 0 0 -13 24.3329 0 +5 24.3329 0 AngleAngle Coeffs @@ -532,378 +479,342 @@ AngleAngle Coeffs 2 0.2738 -0.4825 0.2738 110.77 107.66 110.77 3 -1.3199 -1.3199 0.1184 112.67 110.77 110.77 4 2.0403 -1.8202 1.0827 108.53 107.734 110.77 -5 -3.3867 -3.4976 -3.3867 107.734 107.66 107.734 -6 0 0 0 110.954 107.067 110.954 -7 0.2738 -0.4825 0.2738 110.77 107.66 110.77 -8 -1.3199 -1.3199 0.1184 112.67 110.77 110.77 -9 -2.5301 0.5381 2.4286 111.91 110.62 110.77 -10 2.4321 -3.5496 2.4321 110.62 107.66 110.62 -11 0 0 0 123.145 118.985 0 -12 0 0 0 113.868 117.961 111.037 -13 0 0 0 116.926 123.145 125.542 +5 0 0 0 116.926 123.145 125.542 Atoms # full -1 1 1 0.0000000000000000e+00 12.288168 0.738732 4.374280 0 0 0 -2 1 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22 21 27 +34 c2-c2-hc 22 21 28 +35 c2-c2-c2 22 21 39 +36 hc-c2-hc 27 21 28 +37 c2-c2-hc 39 21 27 +38 c2-c2-hc 39 21 28 +39 c2-c2-na 21 22 23 +40 c2-c2-hc 21 22 29 +41 c2-c2-hc 21 22 30 +42 na-c2-hc 23 22 29 +43 na-c2-hc 23 22 30 +44 hc-c2-hc 29 22 30 +45 c2-na-hn 22 23 31 +46 c2-na-hn 22 23 32 +47 hn-na-hn 31 23 32 +48 c2-na-hn 25 24 33 +49 c2-na-hn 25 24 34 +50 hn-na-hn 33 24 34 +51 c2-c2-na 26 25 24 +52 na-c2-hc 24 25 35 +53 na-c2-hc 24 25 36 +54 c2-c2-hc 26 25 35 +55 c2-c2-hc 26 25 36 +56 hc-c2-hc 35 25 36 +57 c2-c2-hc 25 26 37 +58 c2-c2-hc 25 26 38 +59 c2-c2-c2 25 26 42 +60 hc-c2-hc 37 26 38 +61 c2-c2-hc 42 26 37 +62 c2-c2-hc 42 26 38 +63 c2-c2-hc 21 39 40 +64 c2-c2-hc 21 39 41 +65 c2-c2-c2 21 39 42 +66 hc-c2-hc 40 39 41 +67 c2-c2-hc 42 39 40 +68 c2-c2-hc 42 39 41 +69 c2-c2-c2 26 42 39 +70 c2-c2-hc 26 42 43 +71 c2-c2-hc 26 42 44 +72 c2-c2-hc 39 42 43 +73 c2-c2-hc 39 42 44 +74 hc-c2-hc 43 42 44 Dihedrals -1 2 5 1 7 14 -2 2 5 1 7 15 -3 2 4 1 7 14 -4 2 4 1 7 15 -5 3 8 1 7 2 -6 4 8 1 7 14 -7 4 8 1 7 15 -8 2 5 1 8 16 -9 2 5 1 8 17 -10 2 4 1 8 16 -11 2 4 1 8 17 -12 5 7 1 8 9 -13 4 7 1 8 16 -14 4 7 1 8 17 -15 6 7 2 3 6 -16 7 11 2 3 6 -17 1 2 7 1 5 -18 1 2 7 1 4 -19 8 1 7 2 3 -20 9 14 7 2 3 -21 9 15 7 2 3 -22 10 1 7 2 11 -23 11 14 7 2 11 -24 11 15 7 2 11 -25 4 9 8 1 5 -26 4 9 8 1 4 -27 3 1 8 9 10 -28 4 1 8 9 18 -29 4 1 8 9 19 -30 2 16 8 9 18 -31 2 16 8 9 19 -32 2 17 8 9 18 -33 2 17 8 9 19 -34 1 10 9 8 16 -35 1 10 9 8 17 -36 10 8 9 10 12 -37 8 8 9 10 13 -38 11 18 9 10 12 -39 9 18 9 10 13 -40 11 19 9 10 12 -41 9 19 9 10 13 -42 6 9 10 13 20 -43 7 12 10 13 20 -44 13 27 21 22 29 -45 13 27 21 22 30 -46 13 28 21 22 29 -47 13 28 21 22 30 -48 14 39 21 22 23 -49 15 39 21 22 29 -50 15 39 21 22 30 -51 15 22 21 39 40 -52 15 22 21 39 41 -53 16 22 21 39 42 -54 13 27 21 39 40 -55 13 27 21 39 41 -56 13 28 21 39 40 -57 13 28 21 39 41 -58 12 23 22 21 27 -59 12 23 22 21 28 -60 17 21 22 23 31 -61 17 21 22 23 32 -62 18 29 22 23 31 -63 18 29 22 23 32 -64 18 30 22 23 31 -65 18 30 22 23 32 -66 17 26 25 24 33 -67 18 35 25 24 33 -68 18 36 25 24 33 -69 17 26 25 24 34 -70 18 35 25 24 34 -71 18 36 25 24 34 -72 12 24 25 26 37 -73 12 24 25 26 38 -74 13 35 25 26 37 -75 13 35 25 26 38 -76 13 36 25 26 37 -77 13 36 25 26 38 -78 14 42 26 25 24 -79 15 42 26 25 35 -80 15 42 26 25 36 -81 16 25 26 42 39 -82 15 25 26 42 43 -83 15 25 26 42 44 -84 13 37 26 42 43 -85 13 37 26 42 44 -86 13 38 26 42 43 -87 13 38 26 42 44 -88 15 42 39 21 27 -89 15 42 39 21 28 -90 16 21 39 42 26 -91 15 21 39 42 43 -92 15 21 39 42 44 -93 13 40 39 42 43 -94 13 40 39 42 44 -95 13 41 39 42 43 -96 13 41 39 42 44 -97 15 39 42 26 37 -98 15 39 42 26 38 -99 15 26 42 39 40 -100 15 26 42 39 41 +1 hc-c2-c2-hc 5 1 7 14 +2 hc-c2-c2-hc 5 1 7 15 +3 hc-c2-c2-hc 4 1 7 14 +4 hc-c2-c2-hc 4 1 7 15 +5 c2-c2-c2-c_1 8 1 7 2 +6 c2-c2-c2-hc 8 1 7 14 +7 c2-c2-c2-hc 8 1 7 15 +8 hc-c2-c2-hc 5 1 8 16 +9 hc-c2-c2-hc 5 1 8 17 +10 hc-c2-c2-hc 4 1 8 16 +11 hc-c2-c2-hc 4 1 8 17 +12 c2-c2-c2-c2 7 1 8 9 +13 c2-c2-c2-hc 7 1 8 16 +14 c2-c2-c2-hc 7 1 8 17 +15 c2-c_1-o-ho 7 2 3 6 +16 o_1-c_1-o-ho 11 2 3 6 +17 c_1-c2-c2-hc 2 7 1 5 +18 c_1-c2-c2-hc 2 7 1 4 +19 c2-c2-c_1-o 1 7 2 3 +20 hc-c2-c_1-o 14 7 2 3 +21 hc-c2-c_1-o 15 7 2 3 +22 c2-c2-c_1-o_1 1 7 2 11 +23 hc-c2-c_1-o_1 14 7 2 11 +24 hc-c2-c_1-o_1 15 7 2 11 +25 c2-c2-c2-hc 9 8 1 5 +26 c2-c2-c2-hc 9 8 1 4 +27 c2-c2-c2-c_1 1 8 9 10 +28 c2-c2-c2-hc 1 8 9 18 +29 c2-c2-c2-hc 1 8 9 19 +30 hc-c2-c2-hc 16 8 9 18 +31 hc-c2-c2-hc 16 8 9 19 +32 hc-c2-c2-hc 17 8 9 18 +33 hc-c2-c2-hc 17 8 9 19 +34 c_1-c2-c2-hc 10 9 8 16 +35 c_1-c2-c2-hc 10 9 8 17 +36 c2-c2-c_1-o_1 8 9 10 12 +37 c2-c2-c_1-o 8 9 10 13 +38 hc-c2-c_1-o_1 18 9 10 12 +39 hc-c2-c_1-o 18 9 10 13 +40 hc-c2-c_1-o_1 19 9 10 12 +41 hc-c2-c_1-o 19 9 10 13 +42 c2-c_1-o-ho 9 10 13 20 +43 o_1-c_1-o-ho 12 10 13 20 +44 hc-c2-c2-hc 27 21 22 29 +45 hc-c2-c2-hc 27 21 22 30 +46 hc-c2-c2-hc 28 21 22 29 +47 hc-c2-c2-hc 28 21 22 30 +48 c2-c2-c2-na 39 21 22 23 +49 c2-c2-c2-hc 39 21 22 29 +50 c2-c2-c2-hc 39 21 22 30 +51 c2-c2-c2-hc 22 21 39 40 +52 c2-c2-c2-hc 22 21 39 41 +53 c2-c2-c2-c2 22 21 39 42 +54 hc-c2-c2-hc 27 21 39 40 +55 hc-c2-c2-hc 27 21 39 41 +56 hc-c2-c2-hc 28 21 39 40 +57 hc-c2-c2-hc 28 21 39 41 +58 na-c2-c2-hc 23 22 21 27 +59 na-c2-c2-hc 23 22 21 28 +60 c2-c2-na-hn 21 22 23 31 +61 c2-c2-na-hn 21 22 23 32 +62 hn-na-c2-hc 29 22 23 31 +63 hn-na-c2-hc 29 22 23 32 +64 hn-na-c2-hc 30 22 23 31 +65 hn-na-c2-hc 30 22 23 32 +66 c2-c2-na-hn 26 25 24 33 +67 hn-na-c2-hc 35 25 24 33 +68 hn-na-c2-hc 36 25 24 33 +69 c2-c2-na-hn 26 25 24 34 +70 hn-na-c2-hc 35 25 24 34 +71 hn-na-c2-hc 36 25 24 34 +72 na-c2-c2-hc 24 25 26 37 +73 na-c2-c2-hc 24 25 26 38 +74 hc-c2-c2-hc 35 25 26 37 +75 hc-c2-c2-hc 35 25 26 38 +76 hc-c2-c2-hc 36 25 26 37 +77 hc-c2-c2-hc 36 25 26 38 +78 c2-c2-c2-na 42 26 25 24 +79 c2-c2-c2-hc 42 26 25 35 +80 c2-c2-c2-hc 42 26 25 36 +81 c2-c2-c2-c2 25 26 42 39 +82 c2-c2-c2-hc 25 26 42 43 +83 c2-c2-c2-hc 25 26 42 44 +84 hc-c2-c2-hc 37 26 42 43 +85 hc-c2-c2-hc 37 26 42 44 +86 hc-c2-c2-hc 38 26 42 43 +87 hc-c2-c2-hc 38 26 42 44 +88 c2-c2-c2-hc 42 39 21 27 +89 c2-c2-c2-hc 42 39 21 28 +90 c2-c2-c2-c2 21 39 42 26 +91 c2-c2-c2-hc 21 39 42 43 +92 c2-c2-c2-hc 21 39 42 44 +93 hc-c2-c2-hc 40 39 42 43 +94 hc-c2-c2-hc 40 39 42 44 +95 hc-c2-c2-hc 41 39 42 43 +96 hc-c2-c2-hc 41 39 42 44 +97 c2-c2-c2-hc 39 42 26 37 +98 c2-c2-c2-hc 39 42 26 38 +99 c2-c2-c2-hc 26 42 39 40 +100 c2-c2-c2-hc 26 42 39 41 Impropers -1 2 7 1 4 5 -2 2 8 1 4 5 -3 3 7 1 8 5 -4 3 7 1 8 4 -5 1 7 2 3 11 -6 4 1 7 2 14 -7 4 1 7 2 15 -8 2 1 7 14 15 -9 5 2 7 14 15 -10 3 1 8 9 16 -11 3 1 8 9 17 -12 2 1 8 16 17 -13 2 9 8 16 17 -14 4 8 9 10 18 -15 4 8 9 10 19 -16 2 8 9 18 19 -17 5 10 9 18 19 -18 1 9 10 13 12 -19 7 22 21 27 28 -20 8 22 21 39 27 -21 8 22 21 39 28 -22 7 39 21 28 27 -23 9 21 22 23 29 -24 9 21 22 23 30 -25 7 21 22 29 30 -26 10 23 22 29 30 -27 6 22 23 31 32 -28 6 25 24 33 34 -29 9 26 25 24 35 -30 9 26 25 24 36 -31 10 24 25 35 36 -32 7 26 25 35 36 -33 7 25 26 37 38 -34 8 25 26 42 37 -35 8 25 26 42 38 -36 7 42 26 38 37 -37 7 21 39 40 41 -38 8 21 39 42 40 -39 8 21 39 42 41 -40 7 42 39 41 40 -41 8 26 42 39 43 -42 8 26 42 39 44 -43 7 26 42 43 44 -44 7 39 42 43 44 +1 c2-na-hn-hn 7 1 4 5 +2 c2-na-hn-hn 8 1 4 5 +3 c2-c_1-o_1-o 7 1 8 5 +4 c2-c_1-o_1-o 7 1 8 4 +5 c2-c_1-o-o_1 7 2 3 11 +6 c2-n-hn-c_1 1 7 2 14 +7 c2-n-hn-c_1 1 7 2 15 +8 c2-na-hn-hn 1 7 14 15 +9 c2-c_1-o_1-o 1 8 9 16 +10 c2-c_1-o_1-o 1 8 9 17 +11 c2-na-hn-hn 1 8 16 17 +12 c2-na-hn-hn 9 8 16 17 +13 c2-n-hn-c_1 8 9 10 18 +14 c2-n-hn-c_1 8 9 10 19 +15 c2-na-hn-hn 8 9 18 19 +16 c2-c_1-o-o_1 9 10 13 12 From a1a72f741a0436cd7b45a7645faa3dc5318825e4 Mon Sep 17 00:00:00 2001 From: Jacob Gissinger Date: Sun, 25 Aug 2024 14:54:51 -0400 Subject: [PATCH 10/11] update docs with recent paper --- doc/src/fix_bond_react.rst | 4 ++++ src/REACTION/fix_bond_react.cpp | 10 +++++++++- 2 files changed, 13 insertions(+), 1 deletion(-) diff --git a/doc/src/fix_bond_react.rst b/doc/src/fix_bond_react.rst index af3ee0fd48..08c2f5fb9d 100644 --- a/doc/src/fix_bond_react.rst +++ b/doc/src/fix_bond_react.rst @@ -785,3 +785,7 @@ reset_mol_ids = yes, custom_charges = no, molecule = off, modify_create = *fit a .. _Gissinger2020: **(Gissinger2020)** Gissinger, Jensen and Wise, Macromolecules, 53, 22, 9953-9961 (2020). + +.. _Gissinger2024: + +**(Gissinger2024)** Gissinger, Jensen and Wise, Computer Physics Communications, 304, 109287 (2024). diff --git a/src/REACTION/fix_bond_react.cpp b/src/REACTION/fix_bond_react.cpp index 63781bfcdd..5a4f6bea7d 100644 --- a/src/REACTION/fix_bond_react.cpp +++ b/src/REACTION/fix_bond_react.cpp @@ -58,7 +58,7 @@ using namespace MathConst; static const char cite_fix_bond_react[] = "fix bond/react: reacter.org doi:10.1016/j.polymer.2017.09.038, " - "doi:10.1021/acs.macromol.0c02012\n\n" + "doi:10.1021/acs.macromol.0c02012, doi:10.1016/j.cpc.2024.109287\n\n" "@Article{Gissinger17,\n" " author = {J. R. Gissinger and B. D. Jensen and K. E. Wise},\n" " title = {Modeling Chemical Reactions in Classical Molecular Dynamics Simulations},\n" @@ -75,6 +75,14 @@ static const char cite_fix_bond_react[] = " volume = 53,\n" " number = 22,\n" " pages = {9953--9961}\n" + "}\n\n" + "@Article{Gissinger24,\n" + " author = {J. R. Gissinger, B. D. Jensen, K. E. Wise},\n" + " title = {Molecular Modeling of Reactive Systems with REACTER},\n" + " journal = {Computer Physics Communications},\n" + " year = 2024,\n" + " volume = 304,\n" + " number = 109287\n" "}\n\n"; static constexpr double BIG = 1.0e20; From 99153f20becaa00df9b9cf6e21c53e6761e64a4d Mon Sep 17 00:00:00 2001 From: Jacob Gissinger Date: Sun, 25 Aug 2024 21:55:19 -0400 Subject: [PATCH 11/11] refactor how reactions are skipped better treatment of allowing all possible reactions when using 'overlap' keyword of 'create_atoms' feature --- src/REACTION/fix_bond_react.cpp | 85 +++++++++++++++++++++------------ src/REACTION/fix_bond_react.h | 2 +- 2 files changed, 56 insertions(+), 31 deletions(-) diff --git a/src/REACTION/fix_bond_react.cpp b/src/REACTION/fix_bond_react.cpp index 5a4f6bea7d..b80231cf44 100644 --- a/src/REACTION/fix_bond_react.cpp +++ b/src/REACTION/fix_bond_react.cpp @@ -233,8 +233,8 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : memory->create(reacted_mol,nreacts,"bond/react:reacted_mol"); memory->create(fraction,nreacts,"bond/react:fraction"); memory->create(max_rxn,nreacts,"bond/react:max_rxn"); - memory->create(nlocalskips,nreacts,"bond/react:nlocalskips"); - memory->create(nghostlyskips,nreacts,"bond/react:nghostlyskips"); + memory->create(nlocalkeep,nreacts,"bond/react:nlocalkeep"); + memory->create(nghostlykeep,nreacts,"bond/react:nghostlykeep"); memory->create(seed,nreacts,"bond/react:seed"); memory->create(limit_duration,nreacts,"bond/react:limit_duration"); memory->create(rate_limit,3,nreacts,"bond/react:rate_limit"); @@ -648,8 +648,8 @@ FixBondReact::~FixBondReact() memory->destroy(fraction); memory->destroy(seed); memory->destroy(max_rxn); - memory->destroy(nlocalskips); - memory->destroy(nghostlyskips); + memory->destroy(nlocalkeep); + memory->destroy(nghostlykeep); memory->destroy(limit_duration); memory->destroy(var_flag); memory->destroy(var_id); @@ -877,8 +877,8 @@ void FixBondReact::post_integrate() reaction_count[i] = 0; local_rxn_count[i] = 0; ghostly_rxn_count[i] = 0; - nlocalskips[i] = 0; - nghostlyskips[i] = 0; + nlocalkeep[i] = INT_MAX; + nghostlykeep[i] = INT_MAX; // update reaction probability if (var_flag[PROB][i]) fraction[i] = input->variable->compute_equal(var_id[PROB][i]); @@ -1429,10 +1429,13 @@ void FixBondReact::superimpose_algorithm() MPI_Allreduce(&local_rxn_count[0],&reaction_count[0],nreacts,MPI_INT,MPI_SUM,world); int rxnflag = 0; + int *delta_rxn; + memory->create(delta_rxn,nreacts,"bond/react:delta_rxn"); if (comm->me == 0) for (int i = 0; i < nreacts; i++) { - reaction_count_total[i] += reaction_count[i] + ghostly_rxn_count[i]; - rxnflag += reaction_count[i] + ghostly_rxn_count[i]; + delta_rxn[i] = reaction_count[i] + ghostly_rxn_count[i]; + reaction_count_total[i] += delta_rxn[i]; + rxnflag += delta_rxn[i]; } MPI_Bcast(&reaction_count_total[0], nreacts, MPI_INT, 0, world); @@ -1465,42 +1468,43 @@ void FixBondReact::superimpose_algorithm() if (overstep > 0) { // let's randomly choose rxns to skip, unbiasedly from local and ghostly int *local_rxncounts; - int *all_localskips; + int *all_localkeep; memory->create(local_rxncounts,nprocs,"bond/react:local_rxncounts"); - memory->create(all_localskips,nprocs,"bond/react:all_localskips"); + memory->create(all_localkeep,nprocs,"bond/react:all_localkeep"); MPI_Gather(&local_rxn_count[i],1,MPI_INT,local_rxncounts,1,MPI_INT,0,world); if (comm->me == 0) { - int delta_rxn = reaction_count[i] + ghostly_rxn_count[i]; // when using variable input for rate_limit, rate_limit_overstep could be > delta_rxn (below) // we need to limit overstep to the number of reactions on this timestep // essentially skipping all reactions, would be more efficient to use a skip_all flag - if (overstep > delta_rxn) overstep = delta_rxn; + if (overstep > delta_rxn[i]) overstep = delta_rxn[i]; + int nkeep = delta_rxn[i] - overstep; int *rxn_by_proc; - memory->create(rxn_by_proc,delta_rxn,"bond/react:rxn_by_proc"); - for (int j = 0; j < delta_rxn; j++) + memory->create(rxn_by_proc,delta_rxn[i],"bond/react:rxn_by_proc"); + for (int j = 0; j < delta_rxn[i]; j++) rxn_by_proc[j] = -1; // corresponds to ghostly int itemp = 0; for (int j = 0; j < nprocs; j++) for (int k = 0; k < local_rxncounts[j]; k++) rxn_by_proc[itemp++] = j; - std::shuffle(&rxn_by_proc[0],&rxn_by_proc[delta_rxn], park_rng); + std::shuffle(&rxn_by_proc[0],&rxn_by_proc[delta_rxn[i]], park_rng); for (int j = 0; j < nprocs; j++) - all_localskips[j] = 0; - nghostlyskips[i] = 0; - for (int j = 0; j < overstep; j++) { - if (rxn_by_proc[j] == -1) nghostlyskips[i]++; - else all_localskips[rxn_by_proc[j]]++; + all_localkeep[j] = 0; + nghostlykeep[i] = 0; + for (int j = 0; j < nkeep; j++) { + if (rxn_by_proc[j] == -1) nghostlykeep[i]++; + else all_localkeep[rxn_by_proc[j]]++; } memory->destroy(rxn_by_proc); reaction_count_total[i] -= overstep; } - MPI_Scatter(&all_localskips[0],1,MPI_INT,&nlocalskips[i],1,MPI_INT,0,world); - MPI_Bcast(&nghostlyskips[i],1,MPI_INT,0,world); + MPI_Scatter(&all_localkeep[0],1,MPI_INT,&nlocalkeep[i],1,MPI_INT,0,world); + MPI_Bcast(&nghostlykeep[i],1,MPI_INT,0,world); memory->destroy(local_rxncounts); - memory->destroy(all_localskips); + memory->destroy(all_localkeep); } } MPI_Bcast(&reaction_count_total[0], nreacts, MPI_INT, 0, world); + memory->destroy(delta_rxn); // this updates topology next step next_reneighbor = update->ntimestep; @@ -3036,14 +3040,14 @@ void FixBondReact::update_everything() for (int pass = 0; pass < 2; pass++) { update_num_mega = 0; - int *iskip = new int[nreacts]; - for (int i = 0; i < nreacts; i++) iskip[i] = 0; + int *noccur = new int[nreacts]; + for (int i = 0; i < nreacts; i++) noccur[i] = 0; if (pass == 0) { for (int i = 0; i < local_num_mega; i++) { rxnID = (int) local_mega_glove[0][i]; // reactions already shuffled from dedup procedure, so can skip first N // wait, this check needs to be after add atoms, because they can also be 'skipped' due to overlap - if (iskip[rxnID]++ < nlocalskips[rxnID]) continue; + if (noccur[rxnID] >= nlocalkeep[rxnID]) continue; // this will be overwritten if reaction skipped by create_atoms below update_mega_glove[0][update_num_mega] = (tagint) local_mega_glove[0][i]; @@ -3061,6 +3065,7 @@ void FixBondReact::update_everything() continue; } } + noccur[rxnID]++; if (rescale_charges_flag[rxnID]) sim_total_charges[update_num_mega] = local_mega_glove[1][i]; update_num_mega++; @@ -3069,7 +3074,7 @@ void FixBondReact::update_everything() for (int i = 0; i < global_megasize; i++) { rxnID = (int) global_mega_glove[0][i]; // reactions already shuffled from dedup procedure, so can skip first N - if (iskip[rxnID]++ < nghostlyskips[rxnID]) continue; + if (noccur[rxnID] >= nghostlykeep[rxnID]) continue; // this will be overwritten if reaction skipped by create_atoms below update_mega_glove[0][update_num_mega] = (tagint) global_mega_glove[0][i]; @@ -3089,12 +3094,13 @@ void FixBondReact::update_everything() continue; } } + noccur[rxnID]++; if (rescale_charges_flag[rxnID]) sim_total_charges[update_num_mega] = global_mega_glove[1][i]; update_num_mega++; } } - delete [] iskip; + delete [] noccur; if (update_num_mega == 0) continue; @@ -3804,10 +3810,29 @@ int FixBondReact::insert_atoms_setup(tagint **my_update_mega_glove, int iupdate) break; } } - // !! need to add check against soon-to-added atoms if (abortflag) break; } } + // also check against previous to-be-added atoms + if (!abortflag) { + for (auto & myaddatom : addatoms) { + for (int m = 0; m < twomol->natoms; m++) { + if (create_atoms[m][rxnID] == 1) { + delx = coords[m][0] - myaddatom.x[0]; + dely = coords[m][1] - myaddatom.x[1]; + delz = coords[m][2] - myaddatom.x[2]; + domain->minimum_image(delx,dely,delz); + rsq = delx*delx + dely*dely + delz*delz; + if (rsq < overlapsq[rxnID]) { + abortflag = 1; + break; + } + } + } + if (abortflag) break; + } + } + MPI_Allreduce(MPI_IN_PLACE,&abortflag,1,MPI_INT,MPI_MAX,world); if (abortflag) { memory->destroy(coords); @@ -3872,7 +3897,7 @@ int FixBondReact::insert_atoms_setup(tagint **my_update_mega_glove, int iupdate) // locally update mega_glove my_update_mega_glove[preID][iupdate] = myaddatom.tag; - // could do better job choosing mol ID for added atoms + // !! could do better job choosing mol ID for added atoms if (atom->molecule_flag) { if (twomol->moleculeflag) { myaddatom.molecule = maxmol_all + twomol->molecule[m]; diff --git a/src/REACTION/fix_bond_react.h b/src/REACTION/fix_bond_react.h index 6267d20076..c3a92d91a0 100644 --- a/src/REACTION/fix_bond_react.h +++ b/src/REACTION/fix_bond_react.h @@ -63,7 +63,7 @@ class FixBondReact : public Fix { int *iatomtype, *jatomtype; int *seed; double **cutsq, *fraction; - int *max_rxn, *nlocalskips, *nghostlyskips; + int *max_rxn, *nlocalkeep, *nghostlykeep; tagint lastcheck; int stabilization_flag; int reset_mol_ids_flag;