Loading doc/src/Manual.txt +2 −2 Original line number Diff line number Diff line <!-- HTML_ONLY --> <HEAD> <TITLE>LAMMPS Users Manual</TITLE> <META NAME="docnumber" CONTENT="13 Feb 2017 version"> <META NAME="docnumber" CONTENT="21 Feb 2017 version"> <META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories"> <META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License."> </HEAD> Loading @@ -21,7 +21,7 @@ <H1></H1> LAMMPS Documentation :c,h3 13 Feb 2017 version :c,h4 21 Feb 2017 version :c,h4 Version info: :h4 Loading doc/src/Section_commands.txt +4 −4 Original line number Diff line number Diff line Loading @@ -1076,7 +1076,7 @@ KOKKOS, o = USER-OMP, t = OPT. "none"_bond_none.html, "zero"_bond_zero.html, "hybrid"_bond_hybrid.html, "class2 (o)"_bond_class2.html, "class2 (ko)"_bond_class2.html, "fene (iko)"_bond_fene.html, "fene/expand (o)"_bond_fene_expand.html, "harmonic (ko)"_bond_harmonic.html, Loading Loading @@ -1109,7 +1109,7 @@ USER-OMP, t = OPT. "zero"_angle_zero.html, "hybrid"_angle_hybrid.html, "charmm (ko)"_angle_charmm.html, "class2 (o)"_angle_class2.html, "class2 (ko)"_angle_class2.html, "cosine (o)"_angle_cosine.html, "cosine/delta (o)"_angle_cosine_delta.html, "cosine/periodic (o)"_angle_cosine_periodic.html, Loading Loading @@ -1145,7 +1145,7 @@ USER-OMP, t = OPT. "zero"_dihedral_zero.html, "hybrid"_dihedral_hybrid.html, "charmm (ko)"_dihedral_charmm.html, "class2 (o)"_dihedral_class2.html, "class2 (ko)"_dihedral_class2.html, "harmonic (io)"_dihedral_harmonic.html, "helix (o)"_dihedral_helix.html, "multi/harmonic (o)"_dihedral_multi_harmonic.html, Loading Loading @@ -1177,7 +1177,7 @@ USER-OMP, t = OPT. "none"_improper_none.html, "zero"_improper_zero.html, "hybrid"_improper_hybrid.html, "class2 (o)"_improper_class2.html, "class2 (ko)"_improper_class2.html, "cvff (io)"_improper_cvff.html, "harmonic (ko)"_improper_harmonic.html, "umbrella (o)"_improper_umbrella.html :tb(c=4,ea=c) Loading doc/src/Section_howto.txt +52 −29 Original line number Diff line number Diff line Loading @@ -2573,7 +2573,7 @@ well. 6.26 Adiabatic core/shell model :link(howto_26),h4 The adiabatic core-shell model by "Mitchell and Finchham"_#MitchellFinchham is a simple method for adding Fincham"_#MitchellFincham is a simple method for adding polarizability to a system. In order to mimic the electron shell of an ion, a satellite particle is attached to it. This way the ions are split into a core and a shell where the latter is meant to react to Loading Loading @@ -2667,13 +2667,16 @@ bond_coeff 1 63.014 0.0 bond_coeff 2 25.724 0.0 :pre When running dynamics with the adiabatic core/shell model, the following issues should be considered. Since the relative motion of the core and shell particles corresponds to the polarization, typical thermostats can alter the polarization behaviour, meaning the shell will not react freely to its electrostatic environment. This is critical during the equilibration of the system. Therefore it's typically desirable to decouple the relative motion of the core/shell pair, which is an imaginary degree of freedom, from the following issues should be considered. The relative motion of the core and shell particles corresponds to the polarization, hereby an instantaneous relaxation of the shells is approximated and a fast core/shell spring frequency ensures a nearly constant internal kinetic energy during the simulation. Thermostats can alter this polarization behaviour, by scaling the internal kinetic energy, meaning the shell will not react freely to its electrostatic environment. Therefore it is typically desirable to decouple the relative motion of the core/shell pair, which is an imaginary degree of freedom, from the real physical system. To do that, the "compute temp/cs"_compute_temp_cs.html command can be used, in conjunction with any of the thermostat fixes, such as "fix nvt"_fix_nh.html or "fix Loading Loading @@ -2704,6 +2707,22 @@ fix thermostatequ all nve # integrator as needed f fix_modify thermoberendsen temp CSequ thermo_modify temp CSequ # output of center-of-mass derived temperature :pre The pressure for the core/shell system is computed via the regular LAMMPS convention by "treating the cores and shells as individual particles"_#MitchellFincham2. For the thermo output of the pressure as well as for the application of a barostat, it is necessary to use an additional "pressure"_compute_pressure compute based on the default "temperature"_compute_temp and specifying it as a second argument in "fix modify"_fix_modify.html and "thermo_modify"_thermo_modify.html resulting in: (...) compute CSequ all temp/cs cores shells compute thermo_press_lmp all pressure thermo_temp # pressure for individual particles thermo_modify temp CSequ press thermo_press_lmp # modify thermo to regular pressure fix press_bar all npt temp 300 300 0.04 iso 0 0 0.4 fix_modify press_bar temp CSequ press thermo_press_lmp # pressure modification for correct kinetic scalar :pre If "compute temp/cs"_compute_temp_cs.html is used, the decoupled relative motion of the core and the shell should in theory be stable. However numerical fluctuation can introduce a small Loading @@ -2724,24 +2743,18 @@ temp/cs"_compute_temp_cs.html command to the {temp} keyword of the velocity all create 1427 134 bias yes temp CSequ velocity all scale 1427 temp CSequ :pre It is important to note that the polarizability of the core/shell pairs is based on their relative motion. Therefore the choice of spring force and mass ratio need to ensure much faster relative motion of the 2 atoms within the core/shell pair than their center-of-mass velocity. This allow the shells to effectively react instantaneously to the electrostatic environment. This fast movement also limits the timestep size that can be used. To maintain the correct polarizability of the core/shell pairs, the kinetic energy of the internal motion shall remain nearly constant. Therefore the choice of spring force and mass ratio need to ensure much faster relative motion of the 2 atoms within the core/shell pair than their center-of-mass velocity. This allows the shells to effectively react instantaneously to the electrostatic environment and limits energy transfer to or from the core/shell oscillators. This fast movement also dictates the timestep that can be used. The primary literature of the adiabatic core/shell model suggests that the fast relative motion of the core/shell pairs only allows negligible energy transfer to the environment. Therefore it is not intended to decouple the core/shell degree of freedom from the physical system during production runs. In other words, the "compute temp/cs"_compute_temp_cs.html command should not be used during production runs and is only required during equilibration. This way one is consistent with literature (based on the code packages DL_POLY or GULP for instance). energy transfer to the environment. The mentioned energy transfer will typically lead to a small drift in total energy over time. This internal energy can be monitored using the "compute chunk/atom"_compute_chunk_atom.html and "compute Loading @@ -2761,15 +2774,21 @@ command, to use as input to the "compute chunk/atom"_compute_chunk_atom.html command to define the core/shell pairs as chunks. For example, For example if core/shell pairs are the only molecules: fix csinfo all property/atom i_CSID # property/atom command read_data NaCl_CS_x0.1_prop.data fix csinfo NULL CS-Info # atom property added in the data-file compute prop all property/atom i_CSID read_data NaCl_CS_x0.1_prop.data compute prop all property/atom molecule compute cs_chunk all chunk/atom c_prop compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0 # note the chosen degrees of freedom for the core/shell pairs fix ave_chunk all ave/time 10 1 10 c_cstherm file chunk.dump mode vector :pre For example if core/shell pairs and other molecules are present: fix csinfo all property/atom i_CSID # property/atom command read_data NaCl_CS_x0.1_prop.data fix csinfo NULL CS-Info # atom property added in the data-file compute prop all property/atom i_CSID (...) :pre The additional section in the date file would be formatted like this: CS-Info # header of additional section :pre Loading Loading @@ -2890,9 +2909,13 @@ Phys, 79, 926 (1983). :link(Shinoda) [(Shinoda)] Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004). :link(MitchellFinchham) [(Mitchell and Finchham)] Mitchell, Finchham, J Phys Condensed Matter, :link(MitchellFincham) [(Mitchell and Fincham)] Mitchell, Fincham, J Phys Condensed Matter, 5, 1031-1038 (1993). :link(MitchellFincham2) [(Fincham)] Fincham, Mackrodt and Mitchell, J Phys Condensed Matter, 6, 393-404 (1994). :link(howto-Lamoureux) [(Lamoureux and Roux)] G. Lamoureux, B. Roux, J. Chem. Phys 119, 3025 (2003) doc/src/angle_class2.txt +1 −0 Original line number Diff line number Diff line Loading @@ -8,6 +8,7 @@ angle_style class2 command :h3 angle_style class2/omp command :h3 angle_style class2/kk command :h3 [Syntax:] Loading doc/src/bond_class2.txt +1 −0 Original line number Diff line number Diff line Loading @@ -8,6 +8,7 @@ bond_style class2 command :h3 bond_style class2/omp command :h3 bond_style class2/kk command :h3 [Syntax:] Loading Loading
doc/src/Manual.txt +2 −2 Original line number Diff line number Diff line <!-- HTML_ONLY --> <HEAD> <TITLE>LAMMPS Users Manual</TITLE> <META NAME="docnumber" CONTENT="13 Feb 2017 version"> <META NAME="docnumber" CONTENT="21 Feb 2017 version"> <META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories"> <META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License."> </HEAD> Loading @@ -21,7 +21,7 @@ <H1></H1> LAMMPS Documentation :c,h3 13 Feb 2017 version :c,h4 21 Feb 2017 version :c,h4 Version info: :h4 Loading
doc/src/Section_commands.txt +4 −4 Original line number Diff line number Diff line Loading @@ -1076,7 +1076,7 @@ KOKKOS, o = USER-OMP, t = OPT. "none"_bond_none.html, "zero"_bond_zero.html, "hybrid"_bond_hybrid.html, "class2 (o)"_bond_class2.html, "class2 (ko)"_bond_class2.html, "fene (iko)"_bond_fene.html, "fene/expand (o)"_bond_fene_expand.html, "harmonic (ko)"_bond_harmonic.html, Loading Loading @@ -1109,7 +1109,7 @@ USER-OMP, t = OPT. "zero"_angle_zero.html, "hybrid"_angle_hybrid.html, "charmm (ko)"_angle_charmm.html, "class2 (o)"_angle_class2.html, "class2 (ko)"_angle_class2.html, "cosine (o)"_angle_cosine.html, "cosine/delta (o)"_angle_cosine_delta.html, "cosine/periodic (o)"_angle_cosine_periodic.html, Loading Loading @@ -1145,7 +1145,7 @@ USER-OMP, t = OPT. "zero"_dihedral_zero.html, "hybrid"_dihedral_hybrid.html, "charmm (ko)"_dihedral_charmm.html, "class2 (o)"_dihedral_class2.html, "class2 (ko)"_dihedral_class2.html, "harmonic (io)"_dihedral_harmonic.html, "helix (o)"_dihedral_helix.html, "multi/harmonic (o)"_dihedral_multi_harmonic.html, Loading Loading @@ -1177,7 +1177,7 @@ USER-OMP, t = OPT. "none"_improper_none.html, "zero"_improper_zero.html, "hybrid"_improper_hybrid.html, "class2 (o)"_improper_class2.html, "class2 (ko)"_improper_class2.html, "cvff (io)"_improper_cvff.html, "harmonic (ko)"_improper_harmonic.html, "umbrella (o)"_improper_umbrella.html :tb(c=4,ea=c) Loading
doc/src/Section_howto.txt +52 −29 Original line number Diff line number Diff line Loading @@ -2573,7 +2573,7 @@ well. 6.26 Adiabatic core/shell model :link(howto_26),h4 The adiabatic core-shell model by "Mitchell and Finchham"_#MitchellFinchham is a simple method for adding Fincham"_#MitchellFincham is a simple method for adding polarizability to a system. In order to mimic the electron shell of an ion, a satellite particle is attached to it. This way the ions are split into a core and a shell where the latter is meant to react to Loading Loading @@ -2667,13 +2667,16 @@ bond_coeff 1 63.014 0.0 bond_coeff 2 25.724 0.0 :pre When running dynamics with the adiabatic core/shell model, the following issues should be considered. Since the relative motion of the core and shell particles corresponds to the polarization, typical thermostats can alter the polarization behaviour, meaning the shell will not react freely to its electrostatic environment. This is critical during the equilibration of the system. Therefore it's typically desirable to decouple the relative motion of the core/shell pair, which is an imaginary degree of freedom, from the following issues should be considered. The relative motion of the core and shell particles corresponds to the polarization, hereby an instantaneous relaxation of the shells is approximated and a fast core/shell spring frequency ensures a nearly constant internal kinetic energy during the simulation. Thermostats can alter this polarization behaviour, by scaling the internal kinetic energy, meaning the shell will not react freely to its electrostatic environment. Therefore it is typically desirable to decouple the relative motion of the core/shell pair, which is an imaginary degree of freedom, from the real physical system. To do that, the "compute temp/cs"_compute_temp_cs.html command can be used, in conjunction with any of the thermostat fixes, such as "fix nvt"_fix_nh.html or "fix Loading Loading @@ -2704,6 +2707,22 @@ fix thermostatequ all nve # integrator as needed f fix_modify thermoberendsen temp CSequ thermo_modify temp CSequ # output of center-of-mass derived temperature :pre The pressure for the core/shell system is computed via the regular LAMMPS convention by "treating the cores and shells as individual particles"_#MitchellFincham2. For the thermo output of the pressure as well as for the application of a barostat, it is necessary to use an additional "pressure"_compute_pressure compute based on the default "temperature"_compute_temp and specifying it as a second argument in "fix modify"_fix_modify.html and "thermo_modify"_thermo_modify.html resulting in: (...) compute CSequ all temp/cs cores shells compute thermo_press_lmp all pressure thermo_temp # pressure for individual particles thermo_modify temp CSequ press thermo_press_lmp # modify thermo to regular pressure fix press_bar all npt temp 300 300 0.04 iso 0 0 0.4 fix_modify press_bar temp CSequ press thermo_press_lmp # pressure modification for correct kinetic scalar :pre If "compute temp/cs"_compute_temp_cs.html is used, the decoupled relative motion of the core and the shell should in theory be stable. However numerical fluctuation can introduce a small Loading @@ -2724,24 +2743,18 @@ temp/cs"_compute_temp_cs.html command to the {temp} keyword of the velocity all create 1427 134 bias yes temp CSequ velocity all scale 1427 temp CSequ :pre It is important to note that the polarizability of the core/shell pairs is based on their relative motion. Therefore the choice of spring force and mass ratio need to ensure much faster relative motion of the 2 atoms within the core/shell pair than their center-of-mass velocity. This allow the shells to effectively react instantaneously to the electrostatic environment. This fast movement also limits the timestep size that can be used. To maintain the correct polarizability of the core/shell pairs, the kinetic energy of the internal motion shall remain nearly constant. Therefore the choice of spring force and mass ratio need to ensure much faster relative motion of the 2 atoms within the core/shell pair than their center-of-mass velocity. This allows the shells to effectively react instantaneously to the electrostatic environment and limits energy transfer to or from the core/shell oscillators. This fast movement also dictates the timestep that can be used. The primary literature of the adiabatic core/shell model suggests that the fast relative motion of the core/shell pairs only allows negligible energy transfer to the environment. Therefore it is not intended to decouple the core/shell degree of freedom from the physical system during production runs. In other words, the "compute temp/cs"_compute_temp_cs.html command should not be used during production runs and is only required during equilibration. This way one is consistent with literature (based on the code packages DL_POLY or GULP for instance). energy transfer to the environment. The mentioned energy transfer will typically lead to a small drift in total energy over time. This internal energy can be monitored using the "compute chunk/atom"_compute_chunk_atom.html and "compute Loading @@ -2761,15 +2774,21 @@ command, to use as input to the "compute chunk/atom"_compute_chunk_atom.html command to define the core/shell pairs as chunks. For example, For example if core/shell pairs are the only molecules: fix csinfo all property/atom i_CSID # property/atom command read_data NaCl_CS_x0.1_prop.data fix csinfo NULL CS-Info # atom property added in the data-file compute prop all property/atom i_CSID read_data NaCl_CS_x0.1_prop.data compute prop all property/atom molecule compute cs_chunk all chunk/atom c_prop compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0 # note the chosen degrees of freedom for the core/shell pairs fix ave_chunk all ave/time 10 1 10 c_cstherm file chunk.dump mode vector :pre For example if core/shell pairs and other molecules are present: fix csinfo all property/atom i_CSID # property/atom command read_data NaCl_CS_x0.1_prop.data fix csinfo NULL CS-Info # atom property added in the data-file compute prop all property/atom i_CSID (...) :pre The additional section in the date file would be formatted like this: CS-Info # header of additional section :pre Loading Loading @@ -2890,9 +2909,13 @@ Phys, 79, 926 (1983). :link(Shinoda) [(Shinoda)] Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004). :link(MitchellFinchham) [(Mitchell and Finchham)] Mitchell, Finchham, J Phys Condensed Matter, :link(MitchellFincham) [(Mitchell and Fincham)] Mitchell, Fincham, J Phys Condensed Matter, 5, 1031-1038 (1993). :link(MitchellFincham2) [(Fincham)] Fincham, Mackrodt and Mitchell, J Phys Condensed Matter, 6, 393-404 (1994). :link(howto-Lamoureux) [(Lamoureux and Roux)] G. Lamoureux, B. Roux, J. Chem. Phys 119, 3025 (2003)
doc/src/angle_class2.txt +1 −0 Original line number Diff line number Diff line Loading @@ -8,6 +8,7 @@ angle_style class2 command :h3 angle_style class2/omp command :h3 angle_style class2/kk command :h3 [Syntax:] Loading
doc/src/bond_class2.txt +1 −0 Original line number Diff line number Diff line Loading @@ -8,6 +8,7 @@ bond_style class2 command :h3 bond_style class2/omp command :h3 bond_style class2/kk command :h3 [Syntax:] Loading
