Loading doc/fix_rigid.html +15 −17 Original line number Diff line number Diff line Loading @@ -68,24 +68,22 @@ to the motion. The <A HREF = "neigh_modify.html">neigh_modify exclude</A> and includes all the desired rigid bodies. LAMMPS will allow multiple rigid fixes to be defined, but it is more expensive. </P> <P>This fix uses constant-energy integration, so you may need to impose additional constraints to control the temperature of an ensemble of rigid bodies. You can use <A HREF = "fix_langevin.html">fix langevin</A> for this purpose to treat the system as effectively immersed in an implicit solvent, i.e. a Brownian dynamics model. Or you can thermostat additional atoms of an explicit solvent directly. </P> <P>The degrees-of-freedom removed by rigid bodies are accounted for in temperature and pressure computations. Similary, the rigid body contribution to the pressure virial is also accounted for. The latter is only correct if forces within the bodies have been turned off, and there is only a single fix rigid defined. For each linear rigid body of three or more atoms, one degree-of-freedom must be subtracted using a <A HREF = "compute_modify.html">compute_modify</A> command (i.e. for a simulation temperature and pressure computations. Similarly, the rigid body contribution to the pressure of the system (virial) is also accounted for. For linear rigid bodies of three or more atoms, one additional degree-of-freedom must be subtracted manually using the <A HREF = "compute_modify.html">compute_modify</A> command. E.g. for a simulation of 10 such rigid bodies, use "compute_modify thermo_temp extra 13", after the thermo_style command, where 3 is the default setting and an additional 10 degrees-of-freedom are subtracted). </P> <P>Note that this fix uses constant-energy integration, so you may need to impose additional constraints to control the temperature of an ensemble of rigid bodies. You can use <A HREF = "fix_langevin.html">fix langevin</A> for this purpose to treat the system as effectively immersed in an implicit solvent, i.e. a Brownian dynamics model. Or you can thermostat additional atoms of an explicit solvent directly. after the thermo_style command, where 3 is the default setting and an additional 10 degrees-of-freedom are subtracted. </P> <P>IMPORTANT NOTE: The periodic image flags of atoms in rigid bodies are modified when the center-of-mass of the rigid body moves across a Loading doc/fix_rigid.txt +15 −17 Original line number Diff line number Diff line Loading @@ -61,24 +61,22 @@ For computational efficiency, you should define one fix rigid which includes all the desired rigid bodies. LAMMPS will allow multiple rigid fixes to be defined, but it is more expensive. This fix uses constant-energy integration, so you may need to impose additional constraints to control the temperature of an ensemble of rigid bodies. You can use "fix langevin"_fix_langevin.html for this purpose to treat the system as effectively immersed in an implicit solvent, i.e. a Brownian dynamics model. Or you can thermostat additional atoms of an explicit solvent directly. The degrees-of-freedom removed by rigid bodies are accounted for in temperature and pressure computations. Similary, the rigid body contribution to the pressure virial is also accounted for. The latter is only correct if forces within the bodies have been turned off, and there is only a single fix rigid defined. For each linear rigid body of three or more atoms, one degree-of-freedom must be subtracted using a "compute_modify"_compute_modify.html command (i.e. for a simulation temperature and pressure computations. Similarly, the rigid body contribution to the pressure of the system (virial) is also accounted for. For linear rigid bodies of three or more atoms, one additional degree-of-freedom must be subtracted manually using the "compute_modify"_compute_modify.html command. E.g. for a simulation of 10 such rigid bodies, use "compute_modify thermo_temp extra 13", after the thermo_style command, where 3 is the default setting and an additional 10 degrees-of-freedom are subtracted). Note that this fix uses constant-energy integration, so you may need to impose additional constraints to control the temperature of an ensemble of rigid bodies. You can use "fix langevin"_fix_langevin.html for this purpose to treat the system as effectively immersed in an implicit solvent, i.e. a Brownian dynamics model. Or you can thermostat additional atoms of an explicit solvent directly. after the thermo_style command, where 3 is the default setting and an additional 10 degrees-of-freedom are subtracted. IMPORTANT NOTE: The periodic image flags of atoms in rigid bodies are modified when the center-of-mass of the rigid body moves across a Loading Loading
doc/fix_rigid.html +15 −17 Original line number Diff line number Diff line Loading @@ -68,24 +68,22 @@ to the motion. The <A HREF = "neigh_modify.html">neigh_modify exclude</A> and includes all the desired rigid bodies. LAMMPS will allow multiple rigid fixes to be defined, but it is more expensive. </P> <P>This fix uses constant-energy integration, so you may need to impose additional constraints to control the temperature of an ensemble of rigid bodies. You can use <A HREF = "fix_langevin.html">fix langevin</A> for this purpose to treat the system as effectively immersed in an implicit solvent, i.e. a Brownian dynamics model. Or you can thermostat additional atoms of an explicit solvent directly. </P> <P>The degrees-of-freedom removed by rigid bodies are accounted for in temperature and pressure computations. Similary, the rigid body contribution to the pressure virial is also accounted for. The latter is only correct if forces within the bodies have been turned off, and there is only a single fix rigid defined. For each linear rigid body of three or more atoms, one degree-of-freedom must be subtracted using a <A HREF = "compute_modify.html">compute_modify</A> command (i.e. for a simulation temperature and pressure computations. Similarly, the rigid body contribution to the pressure of the system (virial) is also accounted for. For linear rigid bodies of three or more atoms, one additional degree-of-freedom must be subtracted manually using the <A HREF = "compute_modify.html">compute_modify</A> command. E.g. for a simulation of 10 such rigid bodies, use "compute_modify thermo_temp extra 13", after the thermo_style command, where 3 is the default setting and an additional 10 degrees-of-freedom are subtracted). </P> <P>Note that this fix uses constant-energy integration, so you may need to impose additional constraints to control the temperature of an ensemble of rigid bodies. You can use <A HREF = "fix_langevin.html">fix langevin</A> for this purpose to treat the system as effectively immersed in an implicit solvent, i.e. a Brownian dynamics model. Or you can thermostat additional atoms of an explicit solvent directly. after the thermo_style command, where 3 is the default setting and an additional 10 degrees-of-freedom are subtracted. </P> <P>IMPORTANT NOTE: The periodic image flags of atoms in rigid bodies are modified when the center-of-mass of the rigid body moves across a Loading
doc/fix_rigid.txt +15 −17 Original line number Diff line number Diff line Loading @@ -61,24 +61,22 @@ For computational efficiency, you should define one fix rigid which includes all the desired rigid bodies. LAMMPS will allow multiple rigid fixes to be defined, but it is more expensive. This fix uses constant-energy integration, so you may need to impose additional constraints to control the temperature of an ensemble of rigid bodies. You can use "fix langevin"_fix_langevin.html for this purpose to treat the system as effectively immersed in an implicit solvent, i.e. a Brownian dynamics model. Or you can thermostat additional atoms of an explicit solvent directly. The degrees-of-freedom removed by rigid bodies are accounted for in temperature and pressure computations. Similary, the rigid body contribution to the pressure virial is also accounted for. The latter is only correct if forces within the bodies have been turned off, and there is only a single fix rigid defined. For each linear rigid body of three or more atoms, one degree-of-freedom must be subtracted using a "compute_modify"_compute_modify.html command (i.e. for a simulation temperature and pressure computations. Similarly, the rigid body contribution to the pressure of the system (virial) is also accounted for. For linear rigid bodies of three or more atoms, one additional degree-of-freedom must be subtracted manually using the "compute_modify"_compute_modify.html command. E.g. for a simulation of 10 such rigid bodies, use "compute_modify thermo_temp extra 13", after the thermo_style command, where 3 is the default setting and an additional 10 degrees-of-freedom are subtracted). Note that this fix uses constant-energy integration, so you may need to impose additional constraints to control the temperature of an ensemble of rigid bodies. You can use "fix langevin"_fix_langevin.html for this purpose to treat the system as effectively immersed in an implicit solvent, i.e. a Brownian dynamics model. Or you can thermostat additional atoms of an explicit solvent directly. after the thermo_style command, where 3 is the default setting and an additional 10 degrees-of-freedom are subtracted. IMPORTANT NOTE: The periodic image flags of atoms in rigid bodies are modified when the center-of-mass of the rigid body moves across a Loading
