Loading doc/src/fix_cmap.txt +5 −0 Original line number Diff line number Diff line Loading @@ -97,6 +97,11 @@ The "fix_modify"_fix_modify.html {energy} option is supported by this fix to add the potential "energy" of the CMAP interactions system's potential energy as part of "thermodynamic output"_thermo_style.html. The "fix_modify"_fix_modify.html {virial} option is supported by this fix to add the contribution due to the interaction between atoms and each wall to the system's virial as part of "thermodynamic output"_thermo_style.html. The default is {virial yes} This fix computes a global scalar which can be accessed by various "output commands"_Section_howto.html#howto_15. The scalar is the potential energy discussed above. The scalar value calculated by this Loading doc/src/fix_efield.txt +5 −0 Original line number Diff line number Diff line Loading @@ -124,6 +124,11 @@ can include the forces added by this fix in a consistent manner. I.e. there is a decrease in potential energy when atoms move in the direction of the added force due to the electric field. The "fix_modify"_fix_modify.html {virial} option is supported by this fix to add the contribution due to the interaction between atoms and each wall to the system's virial as part of "thermodynamic output"_thermo_style.html. The default is {virial no} The "fix_modify"_fix_modify.html {respa} option is supported by this fix. This allows to set at which level of the "r-RESPA"_run_style.html integrator the fix adding its forces. Default is the outermost level. Loading doc/src/fix_external.txt +5 −0 Original line number Diff line number Diff line Loading @@ -131,6 +131,11 @@ forces added by this fix in a consistent manner. I.e. there is a decrease in potential energy when atoms move in the direction of the added force. The "fix_modify"_fix_modify.html {virial} option is supported by this fix to add the contribution due to the interaction between atoms and each wall to the system's virial as part of "thermodynamic output"_thermo_style.html. The default is {virial yes} This fix computes a global scalar which can be accessed by various "output commands"_Section_howto.html#howto_15. The scalar is the potential energy discussed above. The scalar stored by this fix Loading doc/src/fix_modify.txt +26 −7 Original line number Diff line number Diff line Loading @@ -14,10 +14,11 @@ fix_modify fix-ID keyword value ... :pre fix-ID = ID of the fix to modify :ulb,l one or more keyword/value pairs may be appended :l keyword = {temp} or {press} or {energy} or {respa} or {dynamic/dof} :l keyword = {temp} or {press} or {energy} or {virial} or {respa} or {dynamic/dof} :l {temp} value = compute ID that calculates a temperature {press} value = compute ID that calculates a pressure {energy} value = {yes} or {no} {virial} value = {yes} or {no} {respa} value = {1} to {max respa level} or {0} (for outermost level) {dynamic/dof} value = {yes} or {no} yes/no = do or do not recompute the number of degrees of freedom (DOF) contributing to the temperature :pre Loading Loading @@ -52,11 +53,10 @@ define their own compute by default, as described in their documentation. Thus this option allows the user to override the default method for computing P. For fixes that calculate a contribution to the potential energy of the system, the {energy} keyword will include that contribution in thermodynamic output of potential energy. This is because the {energy yes} setting must be specified to include the fix's global or per-atom energy in the calculation performed by the "compute The {energy} keyword can be used with fixes that support it. {energy yes} adds a contribution to the potential energy of the system. The fix's global and per-atom energy is included in the calculation performed by the "compute pe"_compute_pe.html or "compute pe/atom"_compute_pe_atom.html commands. See the "thermo_style"_thermo_style.html command for info on how potential energy is output. For fixes that tally a global Loading @@ -69,6 +69,25 @@ are using it when performing an "energy minimization"_minimize.html and if you want the energy and forces it produces to be part of the optimization criteria. The {virial} keyword can be used with fixes that support it. {virial yes} adds a contribution to the virial of the system. The fix's global and per-atom virial is included in the calculation performed by the "compute pressure"_compute_pressure.html or "compute stress/atom"_compute_stress_atom.html commands. See the "thermo_style"_thermo_style.html command for info on how pressure is output. NOTE: You must specify the {virial yes} setting for a fix if you are doing "box relaxation"_fix_box_relax.html and if you want virial contribution of the fix to be part of the relaxation criteria, although this seems unlikely. NOTE: This option is only supported by fixes that explicitly say so. For some of these (e.g. the "fix shake"_fix_shake.html command) the default setting is {virial yes}, for others it is {virial no}. For fixes that set or modify forces, it may be possible to select at which "r-RESPA"_run_style.html level the fix operates via the {respa} keyword. The RESPA level at which the fix is active can be selected. Loading Loading @@ -111,4 +130,4 @@ pressure"_compute_pressure.html, "thermo_style"_thermo_style.html [Default:] The option defaults are temp = ID defined by fix, press = ID defined by fix, energy = no, respa = 0. by fix, energy = no, virial = different for each fix style, respa = 0. doc/src/fix_rigid.txt +5 −0 Original line number Diff line number Diff line Loading @@ -703,6 +703,11 @@ NVT, NPT, NPH rigid styles to add the energy change induced by the thermostatting to the system's potential energy as part of "thermodynamic output"_thermo_style.html. The "fix_modify"_fix_modify.html {virial} option is supported by this fix to add the contribution due to the interaction between atoms and each wall to the system's virial as part of "thermodynamic output"_thermo_style.html. The default is {virial yes} The "fix_modify"_fix_modify.html {temp} and {press} options are supported by the 4 NPT and NPH rigid styles to change the computes used to calculate the instantaneous pressure tensor. Note that the 2 Loading Loading
doc/src/fix_cmap.txt +5 −0 Original line number Diff line number Diff line Loading @@ -97,6 +97,11 @@ The "fix_modify"_fix_modify.html {energy} option is supported by this fix to add the potential "energy" of the CMAP interactions system's potential energy as part of "thermodynamic output"_thermo_style.html. The "fix_modify"_fix_modify.html {virial} option is supported by this fix to add the contribution due to the interaction between atoms and each wall to the system's virial as part of "thermodynamic output"_thermo_style.html. The default is {virial yes} This fix computes a global scalar which can be accessed by various "output commands"_Section_howto.html#howto_15. The scalar is the potential energy discussed above. The scalar value calculated by this Loading
doc/src/fix_efield.txt +5 −0 Original line number Diff line number Diff line Loading @@ -124,6 +124,11 @@ can include the forces added by this fix in a consistent manner. I.e. there is a decrease in potential energy when atoms move in the direction of the added force due to the electric field. The "fix_modify"_fix_modify.html {virial} option is supported by this fix to add the contribution due to the interaction between atoms and each wall to the system's virial as part of "thermodynamic output"_thermo_style.html. The default is {virial no} The "fix_modify"_fix_modify.html {respa} option is supported by this fix. This allows to set at which level of the "r-RESPA"_run_style.html integrator the fix adding its forces. Default is the outermost level. Loading
doc/src/fix_external.txt +5 −0 Original line number Diff line number Diff line Loading @@ -131,6 +131,11 @@ forces added by this fix in a consistent manner. I.e. there is a decrease in potential energy when atoms move in the direction of the added force. The "fix_modify"_fix_modify.html {virial} option is supported by this fix to add the contribution due to the interaction between atoms and each wall to the system's virial as part of "thermodynamic output"_thermo_style.html. The default is {virial yes} This fix computes a global scalar which can be accessed by various "output commands"_Section_howto.html#howto_15. The scalar is the potential energy discussed above. The scalar stored by this fix Loading
doc/src/fix_modify.txt +26 −7 Original line number Diff line number Diff line Loading @@ -14,10 +14,11 @@ fix_modify fix-ID keyword value ... :pre fix-ID = ID of the fix to modify :ulb,l one or more keyword/value pairs may be appended :l keyword = {temp} or {press} or {energy} or {respa} or {dynamic/dof} :l keyword = {temp} or {press} or {energy} or {virial} or {respa} or {dynamic/dof} :l {temp} value = compute ID that calculates a temperature {press} value = compute ID that calculates a pressure {energy} value = {yes} or {no} {virial} value = {yes} or {no} {respa} value = {1} to {max respa level} or {0} (for outermost level) {dynamic/dof} value = {yes} or {no} yes/no = do or do not recompute the number of degrees of freedom (DOF) contributing to the temperature :pre Loading Loading @@ -52,11 +53,10 @@ define their own compute by default, as described in their documentation. Thus this option allows the user to override the default method for computing P. For fixes that calculate a contribution to the potential energy of the system, the {energy} keyword will include that contribution in thermodynamic output of potential energy. This is because the {energy yes} setting must be specified to include the fix's global or per-atom energy in the calculation performed by the "compute The {energy} keyword can be used with fixes that support it. {energy yes} adds a contribution to the potential energy of the system. The fix's global and per-atom energy is included in the calculation performed by the "compute pe"_compute_pe.html or "compute pe/atom"_compute_pe_atom.html commands. See the "thermo_style"_thermo_style.html command for info on how potential energy is output. For fixes that tally a global Loading @@ -69,6 +69,25 @@ are using it when performing an "energy minimization"_minimize.html and if you want the energy and forces it produces to be part of the optimization criteria. The {virial} keyword can be used with fixes that support it. {virial yes} adds a contribution to the virial of the system. The fix's global and per-atom virial is included in the calculation performed by the "compute pressure"_compute_pressure.html or "compute stress/atom"_compute_stress_atom.html commands. See the "thermo_style"_thermo_style.html command for info on how pressure is output. NOTE: You must specify the {virial yes} setting for a fix if you are doing "box relaxation"_fix_box_relax.html and if you want virial contribution of the fix to be part of the relaxation criteria, although this seems unlikely. NOTE: This option is only supported by fixes that explicitly say so. For some of these (e.g. the "fix shake"_fix_shake.html command) the default setting is {virial yes}, for others it is {virial no}. For fixes that set or modify forces, it may be possible to select at which "r-RESPA"_run_style.html level the fix operates via the {respa} keyword. The RESPA level at which the fix is active can be selected. Loading Loading @@ -111,4 +130,4 @@ pressure"_compute_pressure.html, "thermo_style"_thermo_style.html [Default:] The option defaults are temp = ID defined by fix, press = ID defined by fix, energy = no, respa = 0. by fix, energy = no, virial = different for each fix style, respa = 0.
doc/src/fix_rigid.txt +5 −0 Original line number Diff line number Diff line Loading @@ -703,6 +703,11 @@ NVT, NPT, NPH rigid styles to add the energy change induced by the thermostatting to the system's potential energy as part of "thermodynamic output"_thermo_style.html. The "fix_modify"_fix_modify.html {virial} option is supported by this fix to add the contribution due to the interaction between atoms and each wall to the system's virial as part of "thermodynamic output"_thermo_style.html. The default is {virial yes} The "fix_modify"_fix_modify.html {temp} and {press} options are supported by the 4 NPT and NPH rigid styles to change the computes used to calculate the instantaneous pressure tensor. Note that the 2 Loading
