git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1195 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
@ -2,10 +2,16 @@
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\begin{document}
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\begin{document}
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$$
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\begin{eqnarray*}
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S_{ab} = - \left[ m v_a v_b +
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S_{ab} & = & - \left[ m v_a v_b +
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\frac{1}{2} \sum_{j = 1}^{N_p} (a_i - a_j) F_{p_{ij}} +
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\frac{1}{2} \sum_{n = 1}^{N_p} (r_{1_a} F_{1_b} + r_{2_a} F_{2_b}) +
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\frac{1}{2} \sum_{j = 1}^{N_b} (a_i - a_j) F_{b_{ij}} \right]
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\frac{1}{2} \sum_{n = 1}^{N_b} (r_{1_a} F_{1_b} + r_{2_a} F_{2_b}) +
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$$
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\frac{1}{3} \sum_{n = 1}^{N_a} (r_{1_a} F_{1_b} + r_{2_a} F_{2_b} +
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r_{3_a} F_{3_b}) + \\
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&& \frac{1}{4} \sum_{n = 1}^{N_d} (r_{1_a} F_{1_b} + r_{2_a} F_{2_b} +
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r_{3_a} F_{3_b} + r_{4_a} F_{4_b}) +
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\frac{1}{4} \sum_{n = 1}^{N_i} (r_{1_a} F_{1_b} + r_{2_a} F_{2_b} +
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r_{3_a} F_{3_b} + r_{4_a} F_{4_b}) \right]
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\end{eqnarray*}
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\end{document}
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\end{document}
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@ -318,12 +318,12 @@ of each style or click on the style itself for a full description:
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</P>
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</P>
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<DIV ALIGN=center><TABLE BORDER=1 >
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<DIV ALIGN=center><TABLE BORDER=1 >
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<TR ALIGN="center"><TD ><A HREF = "fix_addforce.html">addforce</A></TD><TD ><A HREF = "fix_aveforce.html">aveforce</A></TD><TD ><A HREF = "fix_ave_atom.html">ave/atom</A></TD><TD ><A HREF = "fix_ave_spatial.html">ave/spatial</A></TD><TD ><A HREF = "fix_ave_time.html">ave/time</A></TD><TD ><A HREF = "fix_com.html">com</A></TD><TD ><A HREF = "fix_deform.html">deform</A></TD><TD ><A HREF = "fix_deposit.html">deposit</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "fix_addforce.html">addforce</A></TD><TD ><A HREF = "fix_aveforce.html">aveforce</A></TD><TD ><A HREF = "fix_ave_atom.html">ave/atom</A></TD><TD ><A HREF = "fix_ave_spatial.html">ave/spatial</A></TD><TD ><A HREF = "fix_ave_time.html">ave/time</A></TD><TD ><A HREF = "fix_com.html">com</A></TD><TD ><A HREF = "fix_deform.html">deform</A></TD><TD ><A HREF = "fix_deposit.html">deposit</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "fix_drag.html">drag</A></TD><TD ><A HREF = "fix_dt_reset.html">dt/reset</A></TD><TD ><A HREF = "fix_efield.html">efield</A></TD><TD ><A HREF = "fix_enforce2d.html">enforce2d</A></TD><TD ><A HREF = "fix_freeze.html">freeze</A></TD><TD ><A HREF = "fix_gran_diag.html">gran/diag</A></TD><TD ><A HREF = "fix_gravity.html">gravity</A></TD><TD ><A HREF = "fix_gyration.html">gyration</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "fix_drag.html">drag</A></TD><TD ><A HREF = "fix_dt_reset.html">dt/reset</A></TD><TD ><A HREF = "fix_efield.html">efield</A></TD><TD ><A HREF = "fix_enforce2d.html">enforce2d</A></TD><TD ><A HREF = "fix_freeze.html">freeze</A></TD><TD ><A HREF = "fix_gravity.html">gravity</A></TD><TD ><A HREF = "fix_gyration.html">gyration</A></TD><TD ><A HREF = "fix_heat.html">heat</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "fix_heat.html">heat</A></TD><TD ><A HREF = "fix_indent.html">indent</A></TD><TD ><A HREF = "fix_langevin.html">langevin</A></TD><TD ><A HREF = "fix_lineforce.html">lineforce</A></TD><TD ><A HREF = "fix_msd.html">msd</A></TD><TD ><A HREF = "fix_momentum.html">momentum</A></TD><TD ><A HREF = "fix_nph.html">nph</A></TD><TD ><A HREF = "fix_npt.html">npt</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "fix_indent.html">indent</A></TD><TD ><A HREF = "fix_langevin.html">langevin</A></TD><TD ><A HREF = "fix_lineforce.html">lineforce</A></TD><TD ><A HREF = "fix_msd.html">msd</A></TD><TD ><A HREF = "fix_momentum.html">momentum</A></TD><TD ><A HREF = "fix_nph.html">nph</A></TD><TD ><A HREF = "fix_npt.html">npt</A></TD><TD ><A HREF = "fix_npt_asphere.html">npt/asphere</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "fix_npt_asphere.html">npt/asphere</A></TD><TD ><A HREF = "fix_nve.html">nve</A></TD><TD ><A HREF = "fix_nve_asphere.html">nve/asphere</A></TD><TD ><A HREF = "fix_nve_dipole.html">nve/dipole</A></TD><TD ><A HREF = "fix_nve_gran.html">nve/gran</A></TD><TD ><A HREF = "fix_nve_limit.html">nve/limit</A></TD><TD ><A HREF = "fix_nve_noforce.html">nve/noforce</A></TD><TD ><A HREF = "fix_nvt.html">nvt</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "fix_nve.html">nve</A></TD><TD ><A HREF = "fix_nve_asphere.html">nve/asphere</A></TD><TD ><A HREF = "fix_nve_dipole.html">nve/dipole</A></TD><TD ><A HREF = "fix_nve_gran.html">nve/gran</A></TD><TD ><A HREF = "fix_nve_limit.html">nve/limit</A></TD><TD ><A HREF = "fix_nve_noforce.html">nve/noforce</A></TD><TD ><A HREF = "fix_nvt.html">nvt</A></TD><TD ><A HREF = "fix_nvt_asphere.html">nvt/asphere</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "fix_nvt_asphere.html">nvt/asphere</A></TD><TD ><A HREF = "fix_nvt_sllod.html">nvt/sllod</A></TD><TD ><A HREF = "fix_orient_fcc.html">orient/fcc</A></TD><TD ><A HREF = "fix_planeforce.html">planeforce</A></TD><TD ><A HREF = "fix_poems.html">poems</A></TD><TD ><A HREF = "fix_pour.html">pour</A></TD><TD ><A HREF = "fix_print.html">print</A></TD><TD ><A HREF = "fix_rdf.html">rdf</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "fix_nvt_sllod.html">nvt/sllod</A></TD><TD ><A HREF = "fix_orient_fcc.html">orient/fcc</A></TD><TD ><A HREF = "fix_planeforce.html">planeforce</A></TD><TD ><A HREF = "fix_poems.html">poems</A></TD><TD ><A HREF = "fix_pour.html">pour</A></TD><TD ><A HREF = "fix_print.html">print</A></TD><TD ><A HREF = "fix_rdf.html">rdf</A></TD><TD ><A HREF = "fix_recenter.html">recenter</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "fix_recenter.html">recenter</A></TD><TD ><A HREF = "fix_rigid.html">rigid</A></TD><TD ><A HREF = "fix_setforce.html">setforce</A></TD><TD ><A HREF = "fix_shake.html">shake</A></TD><TD ><A HREF = "fix_spring.html">spring</A></TD><TD ><A HREF = "fix_spring_rg.html">spring/rg</A></TD><TD ><A HREF = "fix_spring_self.html">spring/self</A></TD><TD ><A HREF = "fix_temp_rescale.html">temp/rescale</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "fix_rigid.html">rigid</A></TD><TD ><A HREF = "fix_setforce.html">setforce</A></TD><TD ><A HREF = "fix_shake.html">shake</A></TD><TD ><A HREF = "fix_spring.html">spring</A></TD><TD ><A HREF = "fix_spring_rg.html">spring/rg</A></TD><TD ><A HREF = "fix_spring_self.html">spring/self</A></TD><TD ><A HREF = "fix_temp_rescale.html">temp/rescale</A></TD><TD ><A HREF = "fix_tmd.html">tmd</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "fix_tmd.html">tmd</A></TD><TD ><A HREF = "fix_viscosity.html">viscosity</A></TD><TD ><A HREF = "fix_viscous.html">viscous</A></TD><TD ><A HREF = "fix_wall_gran.html">wall/gran</A></TD><TD ><A HREF = "fix_wall_lj126.html">wall/lj126</A></TD><TD ><A HREF = "fix_wall_lj93.html">wall/lj93</A></TD><TD ><A HREF = "fix_wall_reflect.html">wall/reflect</A></TD><TD ><A HREF = "fix_wiggle.html">wiggle</A>
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<TR ALIGN="center"><TD ><A HREF = "fix_viscosity.html">viscosity</A></TD><TD ><A HREF = "fix_viscous.html">viscous</A></TD><TD ><A HREF = "fix_wall_gran.html">wall/gran</A></TD><TD ><A HREF = "fix_wall_lj126.html">wall/lj126</A></TD><TD ><A HREF = "fix_wall_lj93.html">wall/lj93</A></TD><TD ><A HREF = "fix_wall_reflect.html">wall/reflect</A></TD><TD ><A HREF = "fix_wiggle.html">wiggle</A>
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</TD></TR></TABLE></DIV>
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</TD></TR></TABLE></DIV>
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<HR>
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<HR>
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@ -333,10 +333,10 @@ descriptions of each style or click on the style itself for a full
|
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description:
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description:
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</P>
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</P>
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<DIV ALIGN=center><TABLE BORDER=1 >
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<DIV ALIGN=center><TABLE BORDER=1 >
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<TR ALIGN="center"><TD ><A HREF = "compute_attribute_atom.html">attribute/atom</A></TD><TD ><A HREF = "compute_centro_atom.html">centro/atom</A></TD><TD ><A HREF = "compute_coord_atom.html">coord/atom</A></TD><TD ><A HREF = "compute_ebond_atom.html">ebond/atom</A></TD><TD ><A HREF = "compute_epair_atom.html">epair/atom</A></TD><TD ><A HREF = "compute_ke_atom.html">ke/atom</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "compute_attribute_atom.html">attribute/atom</A></TD><TD ><A HREF = "compute_centro_atom.html">centro/atom</A></TD><TD ><A HREF = "compute_coord_atom.html">coord/atom</A></TD><TD ><A HREF = "compute_ke_atom.html">ke/atom</A></TD><TD ><A HREF = "compute_pe.html">pe</A></TD><TD ><A HREF = "compute_pe_atom.html">pe/atom</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "compute_pe.html">pe</A></TD><TD ><A HREF = "compute_pressure.html">pressure</A></TD><TD ><A HREF = "compute_rotate_dipole.html">rotate/dipole</A></TD><TD ><A HREF = "compute_rotate_gran.html">rotate/gran</A></TD><TD ><A HREF = "compute_stress_atom.html">stress/atom</A></TD><TD ><A HREF = "compute_sum.html">sum</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "compute_pressure.html">pressure</A></TD><TD ><A HREF = "compute_rotate_dipole.html">rotate/dipole</A></TD><TD ><A HREF = "compute_rotate_gran.html">rotate/gran</A></TD><TD ><A HREF = "compute_stress_atom.html">stress/atom</A></TD><TD ><A HREF = "compute_sum.html">sum</A></TD><TD ><A HREF = "compute_sum_atom.html">sum/atom</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "compute_sum_atom.html">sum/atom</A></TD><TD ><A HREF = "compute_temp.html">temp</A></TD><TD ><A HREF = "compute_temp_asphere.html">temp/asphere</A></TD><TD ><A HREF = "compute_temp_deform.html">temp/deform</A></TD><TD ><A HREF = "compute_temp_dipole.html">temp/dipole</A></TD><TD ><A HREF = "compute_temp_partial.html">temp/partial</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "compute_temp.html">temp</A></TD><TD ><A HREF = "compute_temp_asphere.html">temp/asphere</A></TD><TD ><A HREF = "compute_temp_deform.html">temp/deform</A></TD><TD ><A HREF = "compute_temp_dipole.html">temp/dipole</A></TD><TD ><A HREF = "compute_temp_partial.html">temp/partial</A></TD><TD ><A HREF = "compute_temp_ramp.html">temp/ramp</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "compute_temp_ramp.html">temp/ramp</A></TD><TD ><A HREF = "compute_temp_region.html">temp/region</A></TD><TD ><A HREF = "compute_variable.html">variable</A></TD><TD ><A HREF = "compute_variable_atom.html">variable/atom</A>
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<TR ALIGN="center"><TD ><A HREF = "compute_temp_region.html">temp/region</A></TD><TD ><A HREF = "compute_variable.html">variable</A></TD><TD ><A HREF = "compute_variable_atom.html">variable/atom</A>
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</TD></TR></TABLE></DIV>
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</TD></TR></TABLE></DIV>
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<P>These are compute styles contributed by users, which can be used if
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<P>These are compute styles contributed by users, which can be used if
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@ -93,10 +93,9 @@ defined in LAMMPS:
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<UL><LI><A HREF = "compute_attribute_atom.html">attribute/atom</A> - attribute (x,v,f,etc) of each atom
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<UL><LI><A HREF = "compute_attribute_atom.html">attribute/atom</A> - attribute (x,v,f,etc) of each atom
|
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<LI><A HREF = "compute_centro_atom.html">centro/atom</A> - centro-symmetry parameter for each atom
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<LI><A HREF = "compute_centro_atom.html">centro/atom</A> - centro-symmetry parameter for each atom
|
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<LI><A HREF = "compute_coord_atom.html">coord/atom</A> - coordination number for each atom
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<LI><A HREF = "compute_coord_atom.html">coord/atom</A> - coordination number for each atom
|
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<LI><A HREF = "compute_ebond_atom.html">ebond/atom</A> - bond energy for each atom
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<LI><A HREF = "compute_epair_atom.html">epair/atom</A> - pairwise energy for each atom
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<LI><A HREF = "compute_ke_atom.html">ke/atom</A> - kinetic energy for each atom
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<LI><A HREF = "compute_ke_atom.html">ke/atom</A> - kinetic energy for each atom
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<LI><A HREF = "compute_pe.html">pe</A> - potential energy
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<LI><A HREF = "compute_pe.html">pe</A> - potential energy
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<LI><A HREF = "compute_pe.html">pe</A> - potential energy for each atom
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<LI><A HREF = "compute_pressure.html">pressure</A> - total pressure and pressure tensor
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<LI><A HREF = "compute_pressure.html">pressure</A> - total pressure and pressure tensor
|
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<LI><A HREF = "compute_rotate_dipole.html">rotate/dipole</A> - rotational energy of dipolar atoms
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<LI><A HREF = "compute_rotate_dipole.html">rotate/dipole</A> - rotational energy of dipolar atoms
|
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<LI><A HREF = "compute_rotate_gran.html">rotate/gran</A> - rotational energy of granular atoms
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<LI><A HREF = "compute_rotate_gran.html">rotate/gran</A> - rotational energy of granular atoms
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@ -23,14 +23,13 @@
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<P><B>Examples:</B>
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<P><B>Examples:</B>
|
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</P>
|
</P>
|
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<PRE>compute 1 all pe
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<PRE>compute 1 all pe
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compute molPE all bond angle dihedral improper
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compute molPE all pe bond angle dihedral improper
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</PRE>
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</PRE>
|
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<P><B>Description:</B>
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<P><B>Description:</B>
|
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</P>
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</P>
|
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<P>Define a computation that calculates the potential energy of the
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<P>Define a computation that calculates the potential energy of the
|
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entire system of atoms. The specified group must be "all". See the
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entire system of atoms. The specified group must be "all". See the
|
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<A HREF = "compute_epair_atom.html">compute epair/atom</A> and <A HREF = "compute_ebond_atom.html">compute
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<A HREF = "compute_pe_atom.html">compute pe/atom</A> command if you want per-atom
|
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ebond/atom</A> commands if you want per-atom
|
|
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energies. These per-atom values could be summed for a group of atoms
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energies. These per-atom values could be summed for a group of atoms
|
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via the <A HREF = "compute_sum.html">compute sum</A> command.
|
via the <A HREF = "compute_sum.html">compute sum</A> command.
|
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</P>
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</P>
|
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@ -57,7 +56,9 @@ LAMMPS starts up, as if this command were in the input script:
|
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</P>
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</P>
|
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<P><B>Restrictions:</B> none
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<P><B>Restrictions:</B> none
|
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</P>
|
</P>
|
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<P><B>Related commands:</B> none
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<P><B>Related commands:</B>
|
||||||
|
</P>
|
||||||
|
<P><A HREF = "compute_pe_atom.html">compute pe/atom</A>
|
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</P>
|
</P>
|
||||||
<P><B>Default:</B> none
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<P><B>Default:</B> none
|
||||||
</P>
|
</P>
|
||||||
|
|||||||
@ -20,14 +20,13 @@ keyword = {pair} or {bond} or {angle} or {dihedral} or {improper} or {kspace} :u
|
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[Examples:]
|
[Examples:]
|
||||||
|
|
||||||
compute 1 all pe
|
compute 1 all pe
|
||||||
compute molPE all bond angle dihedral improper :pre
|
compute molPE all pe bond angle dihedral improper :pre
|
||||||
|
|
||||||
[Description:]
|
[Description:]
|
||||||
|
|
||||||
Define a computation that calculates the potential energy of the
|
Define a computation that calculates the potential energy of the
|
||||||
entire system of atoms. The specified group must be "all". See the
|
entire system of atoms. The specified group must be "all". See the
|
||||||
"compute epair/atom"_compute_epair_atom.html and "compute
|
"compute pe/atom"_compute_pe_atom.html command if you want per-atom
|
||||||
ebond/atom"_compute_ebond_atom.html commands if you want per-atom
|
|
||||||
energies. These per-atom values could be summed for a group of atoms
|
energies. These per-atom values could be summed for a group of atoms
|
||||||
via the "compute sum"_compute_sum.html command.
|
via the "compute sum"_compute_sum.html command.
|
||||||
|
|
||||||
@ -54,6 +53,8 @@ See the "thermo_style" command for more details.
|
|||||||
|
|
||||||
[Restrictions:] none
|
[Restrictions:] none
|
||||||
|
|
||||||
[Related commands:] none
|
[Related commands:]
|
||||||
|
|
||||||
|
"compute pe/atom"_compute_pe_atom.html
|
||||||
|
|
||||||
[Default:] none
|
[Default:] none
|
||||||
|
|||||||
@ -13,15 +13,18 @@
|
|||||||
</H3>
|
</H3>
|
||||||
<P><B>Syntax:</B>
|
<P><B>Syntax:</B>
|
||||||
</P>
|
</P>
|
||||||
<PRE>compute ID group-ID pressure compute-ID
|
<PRE>compute ID group-ID pressure temp-ID keyword ...
|
||||||
</PRE>
|
</PRE>
|
||||||
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
|
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
|
||||||
<LI>pressure = style name of this compute command
|
<LI>pressure = style name of this compute command
|
||||||
<LI>compute-ID = ID of compute that calculates temperature
|
<LI>temp-ID = ID of compute that calculates temperature
|
||||||
|
<LI>zero or more keywords may be appended
|
||||||
|
<LI>keyword = <I>ke</I> or <I>pair</I> or <I>bond</I> or <I>angle</I> or <I>dihedral</I> or <I>improper</I> or <I>kspace</I> or <I>fix</I>
|
||||||
</UL>
|
</UL>
|
||||||
<P><B>Examples:</B>
|
<P><B>Examples:</B>
|
||||||
</P>
|
</P>
|
||||||
<PRE>compute 1 all pressure myTemp
|
<PRE>compute 1 all pressure myTemp
|
||||||
|
compute 1 all pressure thermo_temp pair bond
|
||||||
</PRE>
|
</PRE>
|
||||||
<P><B>Description:</B>
|
<P><B>Description:</B>
|
||||||
</P>
|
</P>
|
||||||
@ -39,26 +42,35 @@ of atoms via the <A HREF = "compute_sum.html">compute sum</A> command.
|
|||||||
below), Kb is the Boltzmann constant, T is the temperature, d is the
|
below), Kb is the Boltzmann constant, T is the temperature, d is the
|
||||||
dimensionality of the system (2 or 3 for 2d/3d), V is the system
|
dimensionality of the system (2 or 3 for 2d/3d), V is the system
|
||||||
volume (or area in 2d), and the second term is the virial, computed
|
volume (or area in 2d), and the second term is the virial, computed
|
||||||
within LAMMPS for all pairwise as well as 2-body, 3-body, 4-body, and
|
within LAMMPS for all pairwise as well as 2-body, 3-body, and 4-body,
|
||||||
long-range interactions. <A HREF = "fix.html">Fixes</A> that impose constraints
|
and long-range interactions. <A HREF = "fix.html">Fixes</A> that impose constraints
|
||||||
(e.g. the <A HREF = "fix_shake.html">fix shake</A> command) also contribute to the
|
(e.g. the <A HREF = "fix_shake.html">fix shake</A> command) also contribute to the
|
||||||
virial term.
|
virial term.
|
||||||
</P>
|
</P>
|
||||||
<P>A 6-component pressure tensor is also calculated by this compute which
|
<P>A 6-component pressure tensor is also calculated by this compute whose
|
||||||
can be output by the <A HREF = "thermo_style.html">thermo_style custom</A> command.
|
componenents can be output by the <A HREF = "thermo_style.html">thermo_style
|
||||||
The formula for the components of the tensor is the same as in above
|
custom</A> command or accessed by other
|
||||||
formula, except that the first term uses the components of the kinetic
|
<A HREF = "compute.html">compute</A> and <A HREF = "fix.html">fix</A> commands. The equation for
|
||||||
energy tensor (vx * vy instead of v^2 for temperature) and the second
|
the components of the tensor is the same as in above formula, except
|
||||||
term uses Rx * Fy for the Wxy component of the virial tensor, etc.
|
that the first term uses the components of the kinetic energy tensor
|
||||||
|
(vx * vy instead of v^2 for temperature) and the second term uses Rx *
|
||||||
|
Fy for the Wxy component of the virial tensor, etc.
|
||||||
|
</P>
|
||||||
|
<P>If no extra keywords are listed, the entire equation above is
|
||||||
|
calculated which includes a temperature term (or kinetic energy
|
||||||
|
tensor) and the virial as the sum of pair, bond, angle, dihedral,
|
||||||
|
improper, kspace (long-range), and fix contributions. If any extra
|
||||||
|
keywords are listed, then only those components are summed to compute
|
||||||
|
ke and/or the virial.
|
||||||
</P>
|
</P>
|
||||||
<P>The temperature and kinetic energy tensor is not calculated by this
|
<P>The temperature and kinetic energy tensor is not calculated by this
|
||||||
compute, but rather by the temperature compute specified as the last
|
compute, but rather by the temperature compute specified with the
|
||||||
argument of the command. Normally this compute should calculate the
|
command. Normally this compute should calculate the temperature of
|
||||||
temperature of all atoms for consistency with the virial term, but any
|
all atoms for consistency with the virial term, but any compute style
|
||||||
compute style that calculates temperature can be used, e.g. one that
|
that calculates temperature can be used, e.g. one that excludes frozen
|
||||||
excludes frozen atoms or other degrees of freedom.
|
atoms or other degrees of freedom.
|
||||||
</P>
|
</P>
|
||||||
<P>Note that the N is the above formula is really degrees-of-freedom/d
|
<P>Note that the N is the above formula is really degrees-of-freedom
|
||||||
where the DOF is specified by the temperature compute. See the
|
where the DOF is specified by the temperature compute. See the
|
||||||
various <A HREF = "compute.html">compute temperature</A> styles for details.
|
various <A HREF = "compute.html">compute temperature</A> styles for details.
|
||||||
</P>
|
</P>
|
||||||
@ -74,7 +86,9 @@ LAMMPS starts up, as if this command were in the input script:
|
|||||||
</P>
|
</P>
|
||||||
<P><B>Related commands:</B>
|
<P><B>Related commands:</B>
|
||||||
</P>
|
</P>
|
||||||
<P><A HREF = "compute_temp.html">compute temp</A>, <A HREF = "themo_style.html">thermo_style</A>
|
<P><A HREF = "compute_temp.html">compute temp</A>, <A HREF = "compute_stress_atom.html">compute
|
||||||
|
stress/atom</A>,
|
||||||
|
<A HREF = "themo_style.html">thermo_style</A>,
|
||||||
</P>
|
</P>
|
||||||
<P><B>Default:</B> none
|
<P><B>Default:</B> none
|
||||||
</P>
|
</P>
|
||||||
|
|||||||
@ -10,15 +10,18 @@ compute pressure command :h3
|
|||||||
|
|
||||||
[Syntax:]
|
[Syntax:]
|
||||||
|
|
||||||
compute ID group-ID pressure compute-ID :pre
|
compute ID group-ID pressure temp-ID keyword ... :pre
|
||||||
|
|
||||||
ID, group-ID are documented in "compute"_compute.html command
|
ID, group-ID are documented in "compute"_compute.html command
|
||||||
pressure = style name of this compute command
|
pressure = style name of this compute command
|
||||||
compute-ID = ID of compute that calculates temperature :ul
|
temp-ID = ID of compute that calculates temperature
|
||||||
|
zero or more keywords may be appended
|
||||||
|
keyword = {ke} or {pair} or {bond} or {angle} or {dihedral} or {improper} or {kspace} or {fix} :ul
|
||||||
|
|
||||||
[Examples:]
|
[Examples:]
|
||||||
|
|
||||||
compute 1 all pressure myTemp :pre
|
compute 1 all pressure myTemp
|
||||||
|
compute 1 all pressure thermo_temp pair bond :pre
|
||||||
|
|
||||||
[Description:]
|
[Description:]
|
||||||
|
|
||||||
@ -36,26 +39,35 @@ where N is the number of atoms in the system (see discussion of DOF
|
|||||||
below), Kb is the Boltzmann constant, T is the temperature, d is the
|
below), Kb is the Boltzmann constant, T is the temperature, d is the
|
||||||
dimensionality of the system (2 or 3 for 2d/3d), V is the system
|
dimensionality of the system (2 or 3 for 2d/3d), V is the system
|
||||||
volume (or area in 2d), and the second term is the virial, computed
|
volume (or area in 2d), and the second term is the virial, computed
|
||||||
within LAMMPS for all pairwise as well as 2-body, 3-body, 4-body, and
|
within LAMMPS for all pairwise as well as 2-body, 3-body, and 4-body,
|
||||||
long-range interactions. "Fixes"_fix.html that impose constraints
|
and long-range interactions. "Fixes"_fix.html that impose constraints
|
||||||
(e.g. the "fix shake"_fix_shake.html command) also contribute to the
|
(e.g. the "fix shake"_fix_shake.html command) also contribute to the
|
||||||
virial term.
|
virial term.
|
||||||
|
|
||||||
A 6-component pressure tensor is also calculated by this compute which
|
A 6-component pressure tensor is also calculated by this compute whose
|
||||||
can be output by the "thermo_style custom"_thermo_style.html command.
|
componenents can be output by the "thermo_style
|
||||||
The formula for the components of the tensor is the same as in above
|
custom"_thermo_style.html command or accessed by other
|
||||||
formula, except that the first term uses the components of the kinetic
|
"compute"_compute.html and "fix"_fix.html commands. The equation for
|
||||||
energy tensor (vx * vy instead of v^2 for temperature) and the second
|
the components of the tensor is the same as in above formula, except
|
||||||
term uses Rx * Fy for the Wxy component of the virial tensor, etc.
|
that the first term uses the components of the kinetic energy tensor
|
||||||
|
(vx * vy instead of v^2 for temperature) and the second term uses Rx *
|
||||||
|
Fy for the Wxy component of the virial tensor, etc.
|
||||||
|
|
||||||
|
If no extra keywords are listed, the entire equation above is
|
||||||
|
calculated which includes a temperature term (or kinetic energy
|
||||||
|
tensor) and the virial as the sum of pair, bond, angle, dihedral,
|
||||||
|
improper, kspace (long-range), and fix contributions. If any extra
|
||||||
|
keywords are listed, then only those components are summed to compute
|
||||||
|
ke and/or the virial.
|
||||||
|
|
||||||
The temperature and kinetic energy tensor is not calculated by this
|
The temperature and kinetic energy tensor is not calculated by this
|
||||||
compute, but rather by the temperature compute specified as the last
|
compute, but rather by the temperature compute specified with the
|
||||||
argument of the command. Normally this compute should calculate the
|
command. Normally this compute should calculate the temperature of
|
||||||
temperature of all atoms for consistency with the virial term, but any
|
all atoms for consistency with the virial term, but any compute style
|
||||||
compute style that calculates temperature can be used, e.g. one that
|
that calculates temperature can be used, e.g. one that excludes frozen
|
||||||
excludes frozen atoms or other degrees of freedom.
|
atoms or other degrees of freedom.
|
||||||
|
|
||||||
Note that the N is the above formula is really degrees-of-freedom/d
|
Note that the N is the above formula is really degrees-of-freedom
|
||||||
where the DOF is specified by the temperature compute. See the
|
where the DOF is specified by the temperature compute. See the
|
||||||
various "compute temperature"_compute.html styles for details.
|
various "compute temperature"_compute.html styles for details.
|
||||||
|
|
||||||
@ -71,6 +83,8 @@ where "thermo_temp" is the ID of a similarly defined compute of style
|
|||||||
|
|
||||||
[Related commands:]
|
[Related commands:]
|
||||||
|
|
||||||
"compute temp"_compute_temp.html, "thermo_style"_themo_style.html
|
"compute temp"_compute_temp.html, "compute
|
||||||
|
stress/atom"_compute_stress_atom.html,
|
||||||
|
"thermo_style"_themo_style.html,
|
||||||
|
|
||||||
[Default:] none
|
[Default:] none
|
||||||
|
|||||||
@ -13,97 +13,99 @@
|
|||||||
</H3>
|
</H3>
|
||||||
<P><B>Syntax:</B>
|
<P><B>Syntax:</B>
|
||||||
</P>
|
</P>
|
||||||
<PRE>compute ID group-ID stress/atom keyword value ...
|
<PRE>compute ID group-ID stress/atom keyword ...
|
||||||
</PRE>
|
</PRE>
|
||||||
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
|
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
|
||||||
|
<LI>stress/atom = style name of this compute command
|
||||||
<LI>stress/atom = style name of this compute command
|
<LI>zero or more keywords may be appended
|
||||||
|
<LI>keyword = <I>ke</I> or <I>pair</I> or <I>bond</I> or <I>angle</I> or <I>dihedral</I> or <I>improper</I>
|
||||||
<LI>zero or more keyword/arg pairs may be appended
|
|
||||||
|
|
||||||
<LI>keyword = <I>ke</I> or <I>pair</I> or <I>bond</I>
|
|
||||||
|
|
||||||
<PRE> <I>ke</I> arg = <I>yes</I> or <I>no</I>
|
|
||||||
yes/no = include/exclude kinetic energy contribution to stress
|
|
||||||
<I>pair</I> arg = <I>yes</I> or <I>no</I>
|
|
||||||
yes/no = include/exclude pairwise energy contribution to stress
|
|
||||||
<I>bond</I> arg = <I>yes</I> or <I>no</I>
|
|
||||||
yes/no = include/exclude bond energy contribution to stress
|
|
||||||
</PRE>
|
|
||||||
|
|
||||||
</UL>
|
</UL>
|
||||||
<P><B>Examples:</B>
|
<P><B>Examples:</B>
|
||||||
</P>
|
</P>
|
||||||
<PRE>compute 1 mobile stress/atom
|
<PRE>compute 1 mobile stress/atom
|
||||||
</PRE>
|
</PRE>
|
||||||
<PRE>compute 1 all stress/atom ke no
|
<PRE>compute 1 all stress/atom pair bond
|
||||||
</PRE>
|
</PRE>
|
||||||
<P><B>Description:</B>
|
<P><B>Description:</B>
|
||||||
</P>
|
</P>
|
||||||
<P>Define a computation that computes the per-atom stress tensor for each
|
<P>Define a computation that computes the symmetric per-atom stress
|
||||||
atom in a group. The tensor for each atom has 6 components: xx, yy,
|
tensor for each atom in a group. The tensor for each atom has 6
|
||||||
zz, xy, xz, yz. The resulting values can be accessed by indices 1-6
|
components: xx, yy, zz, xy, xz, yz. See the <A HREF = "compute_pressure.html">compute
|
||||||
by any command that uses per-atom computes, e.g. the <A HREF = "dump.html">dump
|
pressure</A> command if you want the stress tensor
|
||||||
|
(pressure) of the entire system. The 6 components can be accessed by
|
||||||
|
indices 1-6 by any command that uses per-atom computes, e.g. the <A HREF = "dump.html">dump
|
||||||
custom</A> command or <A HREF = "fix_ave_spatial.html">fix ave/spatial</A>
|
custom</A> command or <A HREF = "fix_ave_spatial.html">fix ave/spatial</A>
|
||||||
command or <A HREF = "fix_ave_atom.html">fix ave/atom</A> command.
|
command or <A HREF = "fix_ave_atom.html">fix ave/atom</A> command. See <A HREF = "Section_howto.html#4_15">this
|
||||||
|
section</A> for an overview.
|
||||||
</P>
|
</P>
|
||||||
<P>The stress tensor for each atom is the sum of 3 terms in the following
|
<P>The stress tensor for each atom is given by the following formula.
|
||||||
formula. Any of the terms can be excluded by setting the <I>ke</I>,
|
where the ab component of stress on atom <I>I</I> is as shown where <I>a</I> and
|
||||||
<I>pair</I>, or <I>bond</I> keywords to <I>no</I>. The ab component of stress on
|
<I>b</I> take on values x,y,z to generate the 6 components of the symmetric
|
||||||
atom <I>I</I> is as follows, where <I>a</I> and <I>b</I> take on values x,y,z to
|
tensor:
|
||||||
generate the 6 components of the symmetric tensor:
|
|
||||||
</P>
|
</P>
|
||||||
<CENTER><IMG SRC = "Eqs/stress_tensor.jpg">
|
<CENTER><IMG SRC = "Eqs/stress_tensor.jpg">
|
||||||
</CENTER>
|
</CENTER>
|
||||||
<P>The first term is a kinetic energy contribution for atom <I>I</I>. The
|
<P>The first term is a kinetic energy contribution for atom <I>I</I>. The
|
||||||
second term is a pairwise energy contribution where <I>J</I> loops over the
|
second term is a pairwise energy contribution where <I>N</I> loops over the
|
||||||
<I>Np</I> neighbors of atom <I>I</I>, and <I>Fp</I> is one of 3 components of force
|
<I>Np</I> neighbors of atom <I>I</I>, <I>r1</I> and <I>r2</I> are the positions of the 2
|
||||||
on atom <I>I</I> due to the pairwise interaction with atom <I>J</I>. The third
|
atoms, and <I>F1</I> and <I>F2</I> are the forces on the 2 atoms. The third
|
||||||
term is a bond energy contribution where <I>J</I> loops over the <I>Nb</I> bonds
|
term is a bond contribution for the <I>Nb</I> bonds whihc atom <I>I</I> is part
|
||||||
which atom <I>I</I> is part of, and <I>Fb</I> is one of 3 components of force on
|
of. And similarly for the <I>Na</I> angle, <I>Nd</I> dihedral, and <I>Ni</I>
|
||||||
atom <I>I</I> due to the bonded interaction with atom <I>J</I>.
|
improper interactions atom <I>I</I> is part of.
|
||||||
</P>
|
</P>
|
||||||
<P>If two atoms interact, either pairwise or in a bond, and only one of
|
<P>As the formula implies, a virial contribution produced by a small set
|
||||||
them is in the compute group, the interaction is included in the
|
of atoms (e.g. 4 atoms in a dihedral or 3 atoms in a Tersoff 3-body
|
||||||
per-atom stress of the atom in the group.
|
interaction) is assigned in equal portions to each atom in the set.
|
||||||
|
E.g. 1/4 of the dihedral virial to each of the 4 atoms.
|
||||||
</P>
|
</P>
|
||||||
<P>For force fields that include a contribution to the pairwise
|
<P>If no extra keywords are listed, all of the terms in this formula are
|
||||||
interaction that is computed as part of dihedral terms (i.e. 1-4
|
included in the per-atom stress tensor. If any extra keywords are
|
||||||
interactions), this contribution is NOT included in the per-atom
|
listed, only those terms are summed to compute the tensor.
|
||||||
pairwise stress.
|
|
||||||
</P>
|
</P>
|
||||||
<P>IMPORTANT NOTE: The per-atom stress does NOT include contributions due
|
<P>Note that the stress for each atom is due to its interaction with all
|
||||||
to angles, dihedrals, impropers that the atom is part of, or a
|
other atoms in the simulation, not just with other atoms in the group.
|
||||||
long-range Coulombic contribution. Currently, there is no way in
|
|
||||||
LAMMPS to calculate per-atom stress from angles, dihedrals, improper,
|
|
||||||
or long-range interactions.
|
|
||||||
</P>
|
</P>
|
||||||
<P>Note that as defined above, per-atom stress is the negative of the
|
<P>The <A HREF = "dihedral_charmm.html">dihedral_style charmm</A> style calculates
|
||||||
per-atom pressure tensor. It is also really a stress-volume
|
pairwise interactions between 1-4 atoms. The virial contribution of
|
||||||
|
these terms is included in the pair virial, not the dihedral virial.
|
||||||
|
</P>
|
||||||
|
<P>Note that as defined in the formula, per-atom stress is the negative
|
||||||
|
of the per-atom pressure tensor. It is also really a stress-volume
|
||||||
formulation. It would need to be divided by a per-atom volume to have
|
formulation. It would need to be divided by a per-atom volume to have
|
||||||
units of stress, but an individual atom's volume is not easy to
|
units of stress, but an individual atom's volume is not easy to
|
||||||
compute in a deformed solid. Thus, if you sum the diagonal components
|
compute in a deformed solid or a liquid. Thus, if the diagonal
|
||||||
of the per-atom stress tensor for all atoms in the system and divide
|
components of the per-atom stress tensor are summed for all atoms in
|
||||||
the sum by 3V, where V is the volume of the system, you should get -P,
|
the system and the sum is divided by 3V, where V is the volume of the
|
||||||
where P is the total pressure of the system (assuming there is no
|
system, the result should be -P, where P is the total pressure of the
|
||||||
angle, dihedral, improper, or long-range contribution to the total
|
system.
|
||||||
pressure).
|
|
||||||
</P>
|
</P>
|
||||||
<P>Computation of per-atom stress tensor components requires a loop thru
|
<P>These lines in an input script should yield that result (assuming
|
||||||
the pairwise and bond neighbor lists and inter-processor
|
there is no fix or long-range contribution to the stress):
|
||||||
communication, so it can be inefficient to compute/dump this quantity
|
</P>
|
||||||
too frequently or to have multiple compute/dump commands, each of a
|
<PRE>compute global all pressure thermo_temp
|
||||||
<I>stress/atom</I> style.
|
compute peratom all stress/atom
|
||||||
|
compute p all sum peratom
|
||||||
|
variable p equal div(add(add(c_p<B>1</B>,c_p<B>2</B>),c_p<B>3</B>),mult(3.0,vol))
|
||||||
|
thermo_style custom step temp etotal c_global v_p
|
||||||
|
</PRE>
|
||||||
|
<P>IMPORTANT NOTE: The per-atom stress does NOT include contributions due
|
||||||
|
to fixes (e.g. <A HREF = "fix_shake.html">SHAKE</A>) or long-range Coulombic
|
||||||
|
interactions (via the <A HREF = "kspace_style.html">kspace_style</A> command). The
|
||||||
|
former needs to be added to LAMMPS. We're not sure if the latter is
|
||||||
|
possible to compute. There are also a few pair styles for manybody
|
||||||
|
potentials that are not yet instrumented to yield per-atom stress.
|
||||||
|
See the Restrictions below.
|
||||||
</P>
|
</P>
|
||||||
<P><B>Restrictions:</B>
|
<P><B>Restrictions:</B>
|
||||||
</P>
|
</P>
|
||||||
<P>Some pair potentials do not allow the calculation of per-atom stress
|
<P>These pair styles do not yet work with this compute: "airebo", "meam",
|
||||||
via this command. An error will be generated if this is the case.
|
and "TIP4P".
|
||||||
</P>
|
</P>
|
||||||
<P><B>Related commands:</B> none
|
<P><B>Related commands:</B>
|
||||||
</P>
|
</P>
|
||||||
<P><B>Default:</B>
|
<P><A HREF = "compute_pe.html">compute pe</A>, <A HREF = "compute_stress_atom.html">compute
|
||||||
|
stress/atom</A>
|
||||||
</P>
|
</P>
|
||||||
<P>The option defaults are ke = yes, pair = yes, bond = yes.
|
<P><B>Default:</B> none
|
||||||
</P>
|
</P>
|
||||||
</HTML>
|
</HTML>
|
||||||
|
|||||||
@ -10,89 +10,96 @@ compute stress/atom command :h3
|
|||||||
|
|
||||||
[Syntax:]
|
[Syntax:]
|
||||||
|
|
||||||
compute ID group-ID stress/atom keyword value ... :pre
|
compute ID group-ID stress/atom keyword ... :pre
|
||||||
|
|
||||||
ID, group-ID are documented in "compute"_compute.html command :ulb,l
|
ID, group-ID are documented in "compute"_compute.html command
|
||||||
stress/atom = style name of this compute command :l
|
stress/atom = style name of this compute command
|
||||||
zero or more keyword/arg pairs may be appended :l
|
zero or more keywords may be appended
|
||||||
keyword = {ke} or {pair} or {bond} :l
|
keyword = {ke} or {pair} or {bond} or {angle} or {dihedral} or {improper} :ul
|
||||||
{ke} arg = {yes} or {no}
|
|
||||||
yes/no = include/exclude kinetic energy contribution to stress
|
|
||||||
{pair} arg = {yes} or {no}
|
|
||||||
yes/no = include/exclude pairwise energy contribution to stress
|
|
||||||
{bond} arg = {yes} or {no}
|
|
||||||
yes/no = include/exclude bond energy contribution to stress :pre
|
|
||||||
:ule
|
|
||||||
|
|
||||||
[Examples:]
|
[Examples:]
|
||||||
|
|
||||||
compute 1 mobile stress/atom :pre
|
compute 1 mobile stress/atom :pre
|
||||||
compute 1 all stress/atom ke no :pre
|
compute 1 all stress/atom pair bond :pre
|
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[Description:]
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[Description:]
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Define a computation that computes the per-atom stress tensor for each
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Define a computation that computes the symmetric per-atom stress
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atom in a group. The tensor for each atom has 6 components: xx, yy,
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tensor for each atom in a group. The tensor for each atom has 6
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zz, xy, xz, yz. The resulting values can be accessed by indices 1-6
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components: xx, yy, zz, xy, xz, yz. See the "compute
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by any command that uses per-atom computes, e.g. the "dump
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pressure"_compute_pressure.html command if you want the stress tensor
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(pressure) of the entire system. The 6 components can be accessed by
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indices 1-6 by any command that uses per-atom computes, e.g. the "dump
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custom"_dump.html command or "fix ave/spatial"_fix_ave_spatial.html
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custom"_dump.html command or "fix ave/spatial"_fix_ave_spatial.html
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command or "fix ave/atom"_fix_ave_atom.html command.
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command or "fix ave/atom"_fix_ave_atom.html command. See "this
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section"_Section_howto.html#4_15 for an overview.
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The stress tensor for each atom is the sum of 3 terms in the following
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The stress tensor for each atom is given by the following formula.
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formula. Any of the terms can be excluded by setting the {ke},
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where the ab component of stress on atom {I} is as shown where {a} and
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{pair}, or {bond} keywords to {no}. The ab component of stress on
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{b} take on values x,y,z to generate the 6 components of the symmetric
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atom {I} is as follows, where {a} and {b} take on values x,y,z to
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tensor:
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generate the 6 components of the symmetric tensor:
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:c,image(Eqs/stress_tensor.jpg)
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:c,image(Eqs/stress_tensor.jpg)
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The first term is a kinetic energy contribution for atom {I}. The
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The first term is a kinetic energy contribution for atom {I}. The
|
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second term is a pairwise energy contribution where {J} loops over the
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second term is a pairwise energy contribution where {N} loops over the
|
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{Np} neighbors of atom {I}, and {Fp} is one of 3 components of force
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{Np} neighbors of atom {I}, {r1} and {r2} are the positions of the 2
|
||||||
on atom {I} due to the pairwise interaction with atom {J}. The third
|
atoms, and {F1} and {F2} are the forces on the 2 atoms. The third
|
||||||
term is a bond energy contribution where {J} loops over the {Nb} bonds
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term is a bond contribution for the {Nb} bonds whihc atom {I} is part
|
||||||
which atom {I} is part of, and {Fb} is one of 3 components of force on
|
of. And similarly for the {Na} angle, {Nd} dihedral, and {Ni}
|
||||||
atom {I} due to the bonded interaction with atom {J}.
|
improper interactions atom {I} is part of.
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|
||||||
If two atoms interact, either pairwise or in a bond, and only one of
|
As the formula implies, a virial contribution produced by a small set
|
||||||
them is in the compute group, the interaction is included in the
|
of atoms (e.g. 4 atoms in a dihedral or 3 atoms in a Tersoff 3-body
|
||||||
per-atom stress of the atom in the group.
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interaction) is assigned in equal portions to each atom in the set.
|
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E.g. 1/4 of the dihedral virial to each of the 4 atoms.
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||||||
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|
||||||
For force fields that include a contribution to the pairwise
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If no extra keywords are listed, all of the terms in this formula are
|
||||||
interaction that is computed as part of dihedral terms (i.e. 1-4
|
included in the per-atom stress tensor. If any extra keywords are
|
||||||
interactions), this contribution is NOT included in the per-atom
|
listed, only those terms are summed to compute the tensor.
|
||||||
pairwise stress.
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|
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|
||||||
IMPORTANT NOTE: The per-atom stress does NOT include contributions due
|
Note that the stress for each atom is due to its interaction with all
|
||||||
to angles, dihedrals, impropers that the atom is part of, or a
|
other atoms in the simulation, not just with other atoms in the group.
|
||||||
long-range Coulombic contribution. Currently, there is no way in
|
|
||||||
LAMMPS to calculate per-atom stress from angles, dihedrals, improper,
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|
||||||
or long-range interactions.
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|
||||||
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|
||||||
Note that as defined above, per-atom stress is the negative of the
|
The "dihedral_style charmm"_dihedral_charmm.html style calculates
|
||||||
per-atom pressure tensor. It is also really a stress-volume
|
pairwise interactions between 1-4 atoms. The virial contribution of
|
||||||
|
these terms is included in the pair virial, not the dihedral virial.
|
||||||
|
|
||||||
|
Note that as defined in the formula, per-atom stress is the negative
|
||||||
|
of the per-atom pressure tensor. It is also really a stress-volume
|
||||||
formulation. It would need to be divided by a per-atom volume to have
|
formulation. It would need to be divided by a per-atom volume to have
|
||||||
units of stress, but an individual atom's volume is not easy to
|
units of stress, but an individual atom's volume is not easy to
|
||||||
compute in a deformed solid. Thus, if you sum the diagonal components
|
compute in a deformed solid or a liquid. Thus, if the diagonal
|
||||||
of the per-atom stress tensor for all atoms in the system and divide
|
components of the per-atom stress tensor are summed for all atoms in
|
||||||
the sum by 3V, where V is the volume of the system, you should get -P,
|
the system and the sum is divided by 3V, where V is the volume of the
|
||||||
where P is the total pressure of the system (assuming there is no
|
system, the result should be -P, where P is the total pressure of the
|
||||||
angle, dihedral, improper, or long-range contribution to the total
|
system.
|
||||||
pressure).
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|
||||||
|
|
||||||
Computation of per-atom stress tensor components requires a loop thru
|
These lines in an input script should yield that result (assuming
|
||||||
the pairwise and bond neighbor lists and inter-processor
|
there is no fix or long-range contribution to the stress):
|
||||||
communication, so it can be inefficient to compute/dump this quantity
|
|
||||||
too frequently or to have multiple compute/dump commands, each of a
|
compute global all pressure thermo_temp
|
||||||
{stress/atom} style.
|
compute peratom all stress/atom
|
||||||
|
compute p all sum peratom
|
||||||
|
variable p equal div(add(add(c_p[1],c_p[2]),c_p[3]),mult(3.0,vol))
|
||||||
|
thermo_style custom step temp etotal c_global v_p :pre
|
||||||
|
|
||||||
|
IMPORTANT NOTE: The per-atom stress does NOT include contributions due
|
||||||
|
to fixes (e.g. "SHAKE"_fix_shake.html) or long-range Coulombic
|
||||||
|
interactions (via the "kspace_style"_kspace_style.html command). The
|
||||||
|
former needs to be added to LAMMPS. We're not sure if the latter is
|
||||||
|
possible to compute. There are also a few pair styles for manybody
|
||||||
|
potentials that are not yet instrumented to yield per-atom stress.
|
||||||
|
See the Restrictions below.
|
||||||
|
|
||||||
[Restrictions:]
|
[Restrictions:]
|
||||||
|
|
||||||
Some pair potentials do not allow the calculation of per-atom stress
|
These pair styles do not yet work with this compute: "airebo", "meam",
|
||||||
via this command. An error will be generated if this is the case.
|
and "TIP4P".
|
||||||
|
|
||||||
[Related commands:] none
|
[Related commands:]
|
||||||
|
|
||||||
[Default:]
|
"compute pe"_compute_pe.html, "compute
|
||||||
|
stress/atom"_compute_stress_atom.html
|
||||||
|
|
||||||
The option defaults are ke = yes, pair = yes, bond = yes.
|
[Default:] none
|
||||||
|
|||||||
@ -94,7 +94,6 @@ for individual fixes for info on which ones can be restarted.
|
|||||||
<LI><A HREF = "fix_efield.html">efield</A> - impose electric field on system
|
<LI><A HREF = "fix_efield.html">efield</A> - impose electric field on system
|
||||||
<LI><A HREF = "fix_enforce2d.html">enforce2d</A> - zero out z-dimension velocity and force
|
<LI><A HREF = "fix_enforce2d.html">enforce2d</A> - zero out z-dimension velocity and force
|
||||||
<LI><A HREF = "fix_freeze.html">freeze</A> - freeze atoms in a granular simulation
|
<LI><A HREF = "fix_freeze.html">freeze</A> - freeze atoms in a granular simulation
|
||||||
<LI><A HREF = "fix_gran_diag.html">gran/diag</A> - compute granular diagnostics
|
|
||||||
<LI><A HREF = "fix_gravity.html">gravity</A> - add gravity to atoms in a granular simulation
|
<LI><A HREF = "fix_gravity.html">gravity</A> - add gravity to atoms in a granular simulation
|
||||||
<LI><A HREF = "fix_gyration.html">gyration</A> - compute radius of gyration
|
<LI><A HREF = "fix_gyration.html">gyration</A> - compute radius of gyration
|
||||||
<LI><A HREF = "fix_heat.html">heat</A> - add/subtract momentum-conserving heat
|
<LI><A HREF = "fix_heat.html">heat</A> - add/subtract momentum-conserving heat
|
||||||
|
|||||||
Reference in New Issue
Block a user