I am not sure whether the way I measure the stress is right

Please post to the list, not to me personally.

(3) The constant NPT time integration via Nose/Hoover is used to release the
initial stress of the model. The initial stress is released to about 60 MPa.
It cannot be smaller. Is there any other ways to do it better or is the way
I did right?

If you run long enough, with an appropriate damping constant,
the pressure (suitably time averaged) should go to the target value.

A detailed explanation of the input file is as follows, which may
explain the answer I am looking for and what the doc page says more clearly.
Could please read it and reply me?

I don't have time to read through people's long input scripts looking
for issues. That
is your job. Your original Q was whether pzz was measuring what you
want. I have no answer to that, since I don't know what you want. All
I can tell you is that Pzz is calculated the way the doc page says that
it is. Whether that is what you want or not is a question you have
to answer.

Steve

Thank you. Your suggestions are very helpful.

Best regards,
Liu Bo

At 2013-03-07 23:18:43,“Steve Plimpton” [email protected] wrote: >Please post to the list, not to me personally. > >> (3) The constant NPT time integration via Nose/Hoover is used to release the >> initial stress of the model. The initial stress is released to about 60 MPa. >> It cannot be smaller. Is there any other ways to do it better or is the way >> I did right? > >If you run long enough, with an appropriate damping constant, >the pressure (suitably time averaged) should go to the target value. > >> A detailed explanation of the input file is as follows, which may >> explain the answer I am looking for and what the doc page says more clearly. >> Could please read it and reply me? > >I don’t have time to read through people’s long input scripts looking >for issues. That >is your job. Your original Q was whether pzz was measuring what you >want. I have no answer to that, since I don’t know what you want. All >I can tell you is that Pzz is calculated the way the doc page says that >it is. Whether that is what you want or not is a question you have >to answer. > >Steve > >On Wed, Mar 6, 2013 at 6:55 PM, Liu Bo <[email protected]…4002…> wrote: >> Dear Steve, >> >> >> >> Thank you. A detailed explanation of the input file is as follows, which may >> explain the answer I am looking for and what the doc page says more clearly. >> Could please read it and reply me? Thanks a lot. >> >> >> >> (1) The read_data commad reads in a model that has three layers that are >> stacked along z-coordinate. >> >> (2) Then I defined two regions that include part of the two layers at the >> two ends of model. The two regions will be dragged to opposite directions to >> deform the model >> >> (3) The constant NPT time integration via Nose/Hoover is used to release the >> initial stress of the model. The initial stress is released to about 60 MPa. >> It cannot be smaller. Is there any other ways to do it better or is the way >> I did right? >> >> (4) The two regions are dragged to opposite directions to deform the model. >> Constant NPT time integration via Nose/Hoover is used while the model is >> being deformed. >> >> (5) Output the results. >> >> >> >> Best regards, >> >> Liu Bo >> >> >> >> ###################################### >> >> # Input file for uniaxial tensile loading of nanoparticle composites >> >> # This input file using (at least partly) one of the evo wiki tutorials >> >> # https://icme.hpc.msstate.edu/mediawiki/index.php/Uniaxial_Tension >> >> >> >> # Units >> >> units real >> >> dimension 3 >> >> atom_style full >> >> boundary p p p >> >> >> >> timestep 1 >> >> >> >> # Force field >> >> pair_style lj/class2/coul/long 10 10 >> >> bond_style class2 >> >> angle_style class2 >> >> dihedral_style class2 >> >> improper_style class2 >> >> kspace_style pppm 1e-4 >> >> >> >> dielectric 1.0 >> >> special_bonds lj 0 0 1 coul 0 0 1 dihedral yes >> >> >> >> # Atom definition >> >> # The model has three layers that are stacked along z-coordinate >> >> read_data data.LayerOH >> >> >> >> ###################################### >> >> # Define two regions that include part of the two layers at the two ends of >> model >> >> # The two regions are dragged to opposite directions to deform the model >> >> region 1 block 0 21.608 0 19.64 43.0 53.0 units box >> >> region 2 block 0 21.608 0 19.64 -2.0 8.0 units box >> >> >> >> group fixedtop region 1 >> >> group fixedbottom region 2 >> >> group boundary union fixedtop fixedbottom >> >> group mobilezone subtract all boundary >> >> >> >> ###################################### >> >> # Initialize velocity. >> >> velocity all create 1 7655 rot yes dist gaussian >> >> velocity all zero linear >> >> >> >> # Modify >> >> Neighbor 0.3 bin >> >> neigh_modify every 2 delay 10 check yes >> >> >> >> # Thermo setting >> >> thermo 500 >> >> thermo_style custom step temp press pe ke etotal vol lx ly lz pxx pyy pzz >> pxy pxz pyz >> >> timestep 1 >> >> >> >> ###################################### >> >> # Minimization >> >> minimize 1e-16 1e-16 1000000000 10000000000000 >> >> >> >> # Quench (Run for at least 10 picosecond) >> >> # Constant NPT time integration via Nose/Hoover >> >> # This step is used to release the initial stress of the model. Is it right? >> >> reset_timestep 0 >> >> fix 1 all npt temp 300 300 1 iso 0 0 1 drag 1 >> >> run 30000 >> >> unfix 1 >> >> >> >> ###################################### >> >> # Deformation. >> >> # The two regions are dragged to opposite directions to deform the model. >> >> variable vmove equal 0.0001 >> >> reset_timestep 0 >> >> fix 1 all npt temp 300 300 1 x 0 0 1 y 0 0 1 drag 1 >> >> fix 2 fixedtop move linear 0.0 0.0 {vmove} units box >> >> fix 3 fixedbottom move linear 0.0 0.0 -{vmove} units box >> >> >> >> ###################################### >> >> # Output strain and stress info to file >> >> # for units real, pressure is in [atmospheres] = 101.325 [kPa] = >> 1.01325/10000 [GPa] >> >> # p2, p3, p4 are in GPa >> >> variable disp equal “2stepv_vmove” >> >> variable p1 equal “v_disp” >> >> variable p2 equal “-pxx1.01325/10000" >> >> variable p3 equal "-pyy1.01325/10000” >> >> variable p4 equal “-pzz1.01325/10000" >> >> fix def1 all print 1 “{p1} {p2} {p3} {p4}” file Al_SC_100.def1.txt >> screen no >> >> >> >> # Prepare data for VMD >> >> dump 1 all atom 100 dump.LayerOHimage >> >> dump_modify 1 image yes >> >> >> >> dump 2 all atom 100 dump.LayerOH >> >> >> >> # Display thermo >> >> thermo 100 >> >> thermo_style custom step v_disp temp v_p2 v_p3 v_p4 ke pe etotal press >> >> run 40000 >> >> >> >> ###################################### >> >> # SIMULATION DONE >> >> print “All done” >> >> >> >> At 2013-03-07 00:24:26,“Steve Plimpton” [email protected] >> wrote: >>>What answer are you looking for other than what the doc >>>page says that it calculates? >>> >>>Steve >>> >>>On Wed, Mar 6, 2013 at 3:37 AM, Liu Bo <[email protected]…4002…> wrote: >>>> Dear all, >>>> >>>> I deformed a parallel hexahedron cell by dragging the two ends toward two >>>> opposite directions along z-coordinate with a constant velocity. Then I >>>> use >>>> pzz as the stress in z-coordinate. I am not sure whether it is right. >>>> >>>> Best regards, >>>> >>>> Liu Bo >>>> >>>> >>>> >>>> # Input file for uniaxial tensile loading of nano-partical composites >>>> >>>> # Mark Tschopp, November 2010 >>>> >>>> # --------------------------- units ---------------------------------- >>>> >>>> units real >>>> >>>> dimension 3 >>>> >>>> atom_style full >>>> >>>> boundary p p p >>>> >>>> >>>> >>>> timestep 1 >>>> >>>> >>>> >>>> # --------------------------- force field ---------------------------- >>>> >>>> pair_style lj/class2/coul/long 10 10 >>>> >>>> bond_style class2 >>>> >>>> angle_style class2 >>>> >>>> dihedral_style class2 >>>> >>>> improper_style class2 >>>> >>>> kspace_style pppm 1e-4 >>>> >>>> >>>> >>>> dielectric 1.0 >>>> >>>> special_bonds lj 0 0 1 coul 0 0 1 dihedral yes >>>> >>>> >>>> >>>> # ----------------------- atom definitionh --------------------------- >>>> >>>> read_data data.LayerOH >>>> >>>> >>>> >>>> region 1 block 0 21.608 0 19.64 43.0 53.0 units box >>>> >>>> region 2 block 0 21.608 0 19.64 -2.0 8.0 units box >>>> >>>> >>>> >>>> group fixedtop region 1 >>>> >>>> group fixedbottom region 2 >>>> >>>> group boundary union fixedtop fixedbottom >>>> >>>> group mobilezone subtract all boundary >>>> >>>> >>>> >>>> # ----------------------- initialize velocity ------------------------ >>>> >>>> velocity all create 1 7655 rot yes dist gaussian >>>> >>>> velocity all zero linear >>>> >>>> >>>> >>>> # ----------------------------- modify ------------------------------- >>>> >>>> neighbor 0.3 bin >>>> >>>> neigh_modify every 2 delay 10 check yes >>>> >>>> >>>> >>>> # ----------------------- thermo setting ----------------------------- >>>> >>>> thermo 500 >>>> >>>> thermo_style custom step temp press pe ke etotal vol lx ly lz pxx pyy pzz >>>> pxy pxz pyz >>>> >>>> timestep 1 >>>> >>>> >>>> >>>> # ------------------------- EQUILIBRATION ---------------------------- >>>> >>>> minimize 1e-16 1e-16 1000000000 10000000000000 >>>> >>>> >>>> >>>> # ------------- quench (Run for at least 10 picosecond) -------------- >>>> >>>> # Constant NPT time integration via Nose/Hoover >>>> >>>> >>>> >>>> reset_timestep 0 >>>> >>>> fix 1 all npt temp 300 300 1 iso 0 0 1 drag 1 >>>> >>>> run 30000 >>>> >>>> unfix 1 >>>> >>>> >>>> >>>> ###################################### >>>> >>>> # DEFORMATION >>>> >>>> variable vmove equal 0.0001 >>>> >>>> reset_timestep 0 >>>> >>>> fix 1 all npt temp 300 300 1 x 0 0 1 y 0 0 1 drag 1 >>>> >>>> fix 2 fixedtop move linear 0.0 0.0 {vmove} units box >>>> >>>> fix 3 fixedbottom move linear 0.0 0.0 -{vmove} units box >>>> >>>> >>>> >>>> # Output strain and stress info to file >>>> >>>> # for units metal, pressure is in [bars] = 100 [kPa] = 1/10000 [GPa] >>>> >>>> # p2, p3, p4 are in GPa >>>> >>>> variable disp equal "2stepv_vmove" >>>> >>>> variable p1 equal “v_disp” >>>> >>>> variable p2 equal "-pxx1.01325/10000” >>>> >>>> variable p3 equal “-pyy1.01325/10000" >>>> >>>> variable p4 equal "-pzz1.01325/10000” >>>> >>>> fix def1 all print 1 “{p1} {p2} {p3} {p4}” file Al_SC_100.def1.txt >>>> screen no >>>> >>>> >>>> >>>> # Prepare data for VMD >>>> >>>> dump 1 all atom 100 dump.LayerOHimage >>>> >>>> dump_modify 1 image yes >>>> >>>> >>>> >>>> dump 2 all atom 100 dump.LayerOH >>>> >>>> >>>> >>>> # Display thermo >>>> >>>> thermo 100 >>>> >>>> thermo_style custom step v_disp temp v_p2 v_p3 v_p4 ke pe etotal press >>>> >>>> run 40000 >>>> >>>> >>>> >>>> ###################################### >>>> >>>> # SIMULATION DONE >>>> >>>> print “All done” >>>> >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> Symantec Endpoint Protection 12 positioned as A LEADER in The Forrester >>>> Wave™: Endpoint Security, Q1 2013 and “remains a good choice” in the >>>> endpoint security space. For insight on selecting the right partner to >>>> tackle endpoint security challenges, access the full report. >>>> http://p.sf.net/sfu/symantec-dev2dev >>>> _______________________________________________ >>>> lammps-users mailing list >>>> [email protected] >>>> https://lists.sourceforge.net/lists/listinfo/lammps-users >>>>