Loading doc/src/fix_cmap.txt +5 −0 Original line number Original line 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 fix to add the potential "energy" of the CMAP interactions system's potential energy as part of "thermodynamic output"_thermo_style.html. 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 This fix computes a global scalar which can be accessed by various "output commands"_Section_howto.html#howto_15. The scalar is the "output commands"_Section_howto.html#howto_15. The scalar is the potential energy discussed above. The scalar value calculated by this potential energy discussed above. The scalar value calculated by this Loading doc/src/fix_efield.txt +5 −0 Original line number Original line 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 I.e. there is a decrease in potential energy when atoms move in the direction of the added force due to the electric field. 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 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 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. integrator the fix adding its forces. Default is the outermost level. Loading doc/src/fix_external.txt +5 −0 Original line number Original line 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 decrease in potential energy when atoms move in the direction of the added force. 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 This fix computes a global scalar which can be accessed by various "output commands"_Section_howto.html#howto_15. The scalar is the "output commands"_Section_howto.html#howto_15. The scalar is the potential energy discussed above. The scalar stored by this fix potential energy discussed above. The scalar stored by this fix Loading doc/src/fix_modify.txt +26 −7 Original line number Original line 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 fix-ID = ID of the fix to modify :ulb,l one or more keyword/value pairs may be appended :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 {temp} value = compute ID that calculates a temperature {press} value = compute ID that calculates a pressure {press} value = compute ID that calculates a pressure {energy} value = {yes} or {no} {energy} value = {yes} or {no} {virial} value = {yes} or {no} {respa} value = {1} to {max respa level} or {0} (for outermost level) {respa} value = {1} to {max respa level} or {0} (for outermost level) {dynamic/dof} value = {yes} or {no} {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 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 documentation. Thus this option allows the user to override the default method for computing P. default method for computing P. For fixes that calculate a contribution to the potential energy of the The {energy} keyword can be used with fixes that support it. system, the {energy} keyword will include that contribution in {energy yes} adds a contribution to the potential energy of the thermodynamic output of potential energy. This is because the {energy system. The fix's global and per-atom yes} setting must be specified to include the fix's global or per-atom energy is included in the calculation performed by the "compute energy in the calculation performed by the "compute pe"_compute_pe.html or "compute pe/atom"_compute_pe_atom.html pe"_compute_pe.html or "compute pe/atom"_compute_pe_atom.html commands. See the "thermo_style"_thermo_style.html command for info commands. See the "thermo_style"_thermo_style.html command for info on how potential energy is output. For fixes that tally a global 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 and if you want the energy and forces it produces to be part of the optimization criteria. 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 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} 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. 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:] [Default:] The option defaults are temp = ID defined by fix, press = ID defined 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 Original line 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 thermostatting to the system's potential energy as part of "thermodynamic output"_thermo_style.html. "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 The "fix_modify"_fix_modify.html {temp} and {press} options are supported by the 4 NPT and NPH rigid styles to change the computes supported by the 4 NPT and NPH rigid styles to change the computes used to calculate the instantaneous pressure tensor. Note that the 2 used to calculate the instantaneous pressure tensor. Note that the 2 Loading Loading
doc/src/fix_cmap.txt +5 −0 Original line number Original line 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 fix to add the potential "energy" of the CMAP interactions system's potential energy as part of "thermodynamic output"_thermo_style.html. 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 This fix computes a global scalar which can be accessed by various "output commands"_Section_howto.html#howto_15. The scalar is the "output commands"_Section_howto.html#howto_15. The scalar is the potential energy discussed above. The scalar value calculated by this potential energy discussed above. The scalar value calculated by this Loading
doc/src/fix_efield.txt +5 −0 Original line number Original line 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 I.e. there is a decrease in potential energy when atoms move in the direction of the added force due to the electric field. 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 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 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. integrator the fix adding its forces. Default is the outermost level. Loading
doc/src/fix_external.txt +5 −0 Original line number Original line 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 decrease in potential energy when atoms move in the direction of the added force. 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 This fix computes a global scalar which can be accessed by various "output commands"_Section_howto.html#howto_15. The scalar is the "output commands"_Section_howto.html#howto_15. The scalar is the potential energy discussed above. The scalar stored by this fix potential energy discussed above. The scalar stored by this fix Loading
doc/src/fix_modify.txt +26 −7 Original line number Original line 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 fix-ID = ID of the fix to modify :ulb,l one or more keyword/value pairs may be appended :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 {temp} value = compute ID that calculates a temperature {press} value = compute ID that calculates a pressure {press} value = compute ID that calculates a pressure {energy} value = {yes} or {no} {energy} value = {yes} or {no} {virial} value = {yes} or {no} {respa} value = {1} to {max respa level} or {0} (for outermost level) {respa} value = {1} to {max respa level} or {0} (for outermost level) {dynamic/dof} value = {yes} or {no} {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 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 documentation. Thus this option allows the user to override the default method for computing P. default method for computing P. For fixes that calculate a contribution to the potential energy of the The {energy} keyword can be used with fixes that support it. system, the {energy} keyword will include that contribution in {energy yes} adds a contribution to the potential energy of the thermodynamic output of potential energy. This is because the {energy system. The fix's global and per-atom yes} setting must be specified to include the fix's global or per-atom energy is included in the calculation performed by the "compute energy in the calculation performed by the "compute pe"_compute_pe.html or "compute pe/atom"_compute_pe_atom.html pe"_compute_pe.html or "compute pe/atom"_compute_pe_atom.html commands. See the "thermo_style"_thermo_style.html command for info commands. See the "thermo_style"_thermo_style.html command for info on how potential energy is output. For fixes that tally a global 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 and if you want the energy and forces it produces to be part of the optimization criteria. 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 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} 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. 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:] [Default:] The option defaults are temp = ID defined by fix, press = ID defined 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 Original line 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 thermostatting to the system's potential energy as part of "thermodynamic output"_thermo_style.html. "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 The "fix_modify"_fix_modify.html {temp} and {press} options are supported by the 4 NPT and NPH rigid styles to change the computes supported by the 4 NPT and NPH rigid styles to change the computes used to calculate the instantaneous pressure tensor. Note that the 2 used to calculate the instantaneous pressure tensor. Note that the 2 Loading
