diff --git a/doc/fix_msst.html b/doc/fix_msst.html index 8be90641a8..60f2daffe7 100644 --- a/doc/fix_msst.html +++ b/doc/fix_msst.html @@ -155,7 +155,7 @@ all.

Related commands:

-

fix deform +

fix nphug, fix deform

Default:

diff --git a/doc/fix_msst.txt b/doc/fix_msst.txt index 0a606bf814..60dbc1f20d 100644 --- a/doc/fix_msst.txt +++ b/doc/fix_msst.txt @@ -145,7 +145,7 @@ all. [Related commands:] -"fix deform"_fix_deform.html +"fix nphug"_fix_nphug.html, "fix deform"_fix_deform.html [Default:] diff --git a/doc/fix_nh.html b/doc/fix_nh.html index 49165c16ce..6bf376ba76 100644 --- a/doc/fix_nh.html +++ b/doc/fix_nh.html @@ -28,7 +28,7 @@
  • style_name = nvt or npt or nph 
    one or more keyword value pairs may be appended
-keyword = temp or iso or aniso or tri or x or y or z or xy or yz or xz or couple or tchain or pchain or mtk or tloop or ploop or nreset or drag or dilate
+keyword = temp or iso or aniso or tri or x or y or z or xy or yz or xz or couple or tchain or pchain or mtk or tloop or ploop or nreset or drag or dilate or scaleyz or scalexz or scalexy
   temp values = Tstart Tstop Tdamp
     Tstart,Tstop = external temperature at start/end of run
     Tdamp = temperature damping parameter (time units)
diff --git a/doc/fix_nh.txt b/doc/fix_nh.txt
index 4b4ea236e5..f7dd7f2561 100644
--- a/doc/fix_nh.txt
+++ b/doc/fix_nh.txt
@@ -19,7 +19,7 @@ fix ID group-ID style_name keyword value ... :pre
 ID, group-ID are documented in "fix"_fix.html command :ulb,l
 style_name = {nvt} or {npt} or {nph} :l
 one or more keyword value pairs may be appended
-keyword = {temp} or {iso} or {aniso} or {tri} or {x} or {y} or {z} or {xy} or {yz} or {xz} or {couple} or {tchain} or {pchain} or {mtk} or {tloop} or {ploop} or {nreset} or {drag} or {dilate}
+keyword = {temp} or {iso} or {aniso} or {tri} or {x} or {y} or {z} or {xy} or {yz} or {xz} or {couple} or {tchain} or {pchain} or {mtk} or {tloop} or {ploop} or {nreset} or {drag} or {dilate} or {scaleyz} or {scalexz} or {scalexy}
   {temp} values = Tstart Tstop Tdamp
     Tstart,Tstop = external temperature at start/end of run
     Tdamp = temperature damping parameter (time units)
diff --git a/doc/fix_nphug.html b/doc/fix_nphug.html
new file mode 100644
index 0000000000..e4ad3a3f2e
--- /dev/null
+++ b/doc/fix_nphug.html
@@ -0,0 +1,219 @@
+
+
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands 
+
    
+
+
+
+
+
+
+
    
+
+
    fix nphug command 
+
    
+
    Syntax:
+
    
+
    fix ID group-ID nphug keyword value ... 
+
    
+
+
    Examples:
+
    
+
    fix myhug all nphug temp 1.0 1.0 10.0 z 40.0 40.0 70.0
+fix myhug all nphug temp 1.0 1.0 10.0 iso 40.0 40.0 70.0 drag 200.0 tchain 1 pchain 0 
+
    
+
    Description:
+
    
+
    This command is a variant of the Nose-Hoover
+fix npt fix style.
+It performs time integration of the Hugoniostat equations
+of motion developed by Ravelo et al. (Ravelo).
+These equations compress the system to a state with average
+axial stress or pressure equal to the specified target value 
+and that satisfies the Rankine-Hugoniot (RH)
+jump conditions for steady shocks.
+
    
+
    The compression can be performed 
+either
+hydrostatically (using keyword iso, aniso, or tri) or uniaxially
+(using keywords x, y, or z).  In the hydrostatic case,
+the cell dimensions change dynamically so that the average axial stress
+in all three directions converges towards the specified target value. 
+In the uniaxial case, the chosen cell dimension changes dynamically 
+so that the average
+axial stress in that direction converges towards the target value. The
+other two cell dimensions are kept fixed (zero lateral strain).
+
    
+
    This leads to the following additional restrictions on the keywords:
+
    
+
    One and only one of the following keywords should be used: iso, aniso, tri, x, y, z, 
+
    
+
    The specified initial and final target pressures must be the same.
+
    
+
    The keywords xy, xz, yz may not be used.
+
    
+
    The only admissible value for the couple keyword is xyz, 
+which has the same effect as keyword iso 
+
    
+
+
    Essentially, a Hugoniostat simulation is an NPT simulation in which the
+user-specified target temperature is replaced with a time-dependent 
+target temperature Tt obtained from the following equation:
+
    
+
    Tt - T = (0.5*(P+P0)(V0-V)+E0-E)/(Ndof kB) = Delta
+
    
+
    where T and Tt are the instantaneous and target temperatures,
+P and P0 are the instantaneous and reference pressure or axial stress,
+depending on whether hydrostatic or uniaxial compression is being 
+performed, V and V0 are the instantaneous and reference volumes,
+E and E0 are the instantaneous and reference internal energy (potential
+plus kinetic), Ndof is the number of degrees of freedom used in the
+definition of temperature, and kB is the Boltzmann constant. Delta is the 
+negative deviation of the instantaneous temperature from the target temperature.
+The values of E0, V0, and P0 are the instantaneous values at the start of
+the simulation. These can be overridden using the fix_modify keywords e0,
+v0, and p0 described below.
+
    
+
    
+
+
    IMPORTANT NOTE: Unlike the fix
+temp/berendsen command which performs
+thermostatting but NO time integration, this fix performs
+thermostatting/barostatting AND time integration.  Thus you should not
+use any other time integration fix, such as fix nve on
+atoms to which this fix is applied.  Likewise, this fix should not be 
+used on atoms that have their temperature controlled by another fix 
+- e.g. by fix langevin or fix temp/rescale
+commands.
+
    
+
    
+
+
    This fix compute a temperature and pressure each timestep.  To do
+this, the fix creates its own computes of style "temp" and "pressure",
+as if one of these two sets of commands had been issued:
+
    
+
    compute fix-ID_temp group-ID temp
+compute fix-ID_press group-ID pressure fix-ID_temp 
+
    
+
    compute fix-ID_temp all temp
+compute fix-ID_press all pressure fix-ID_temp 
+
    
+
    See the compute temp and compute
+pressure commands for details.  Note that the
+IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID
++ underscore + "press".  For fix nvt, the group for the new computes
+is the same as the fix group.  For fix nph and fix npt, the group for
+the new computes is "all" since pressure is computed for the entire
+system.
+
    
+
    Note that these are NOT the computes used by thermodynamic output (see
+the thermo_style command) with ID = thermo_temp
+and thermo_press.  This means you can change the attributes of this
+fix's temperature or pressure via the
+compute_modify command or print this temperature
+or pressure during thermodynamic output via the thermo_style
+custom command using the appropriate compute-ID.
+It also means that changing attributes of thermo_temp or
+thermo_press will have no effect on this fix.
+
    
+
    
+
+
    Restart, fix_modify, output, run start/stop, minimize info:
+
    
+
    This fix writes the values of E0, V0, and P0, as well as the 
+state of all the thermostat and barostat
+variables to binary restart files.  See the
+read_restart command for info on how to re-specify
+a fix in an input script that reads a restart file, so that the
+operation of the fix continues in an uninterrupted fashion.
+
    
+
    The fix_modify e0, v0 and p0 keywords
+can be used to define the values of these quantities. Note the
+the values for e0 and v0 are extensive, and so must correspond
+to the total energy and volume of the entire system, not energy and 
+volume per atom. If any of these quantities are not specified, then the
+instanteous value in the system at the start of the simulation is used.
+
    
+
    The fix_modify temp and press options are
+supported by these fixes.  You can use them to assign a
+compute you have defined to this fix which will be used
+in its thermostatting or barostatting procedure, as described above.
+If you do this, note that the kinetic energy derived from the compute
+temperature should be consistent with the virial term computed using
+all atoms for the pressure.  LAMMPS will warn you if you choose to
+compute temperature on a subset of atoms.
+
    
+
    The fix_modify energy option is supported by these
+fixes to add the energy change induced by Nose/Hoover thermostatting
+and barostatting to the system's potential energy as part of
+thermodynamic output. Either way, this energy is *not*
+included in the definition of internal energy E when calculating the value
+of Delta in the above equation.
+
    
+
    These fixes compute a global scalar and a global vector of quantities,
+which can be accessed by various output
+commands.  The scalar value calculated by
+these fixes is "extensive"; the vector values are "intensive".
+
    
+
    The scalar is the cumulative energy change due to the fix.
+
    
+
    The vector stores three quantities unique to this fix (Delta, Us, and up),
+followed by all the internal Nose/Hoover thermostat and barostat
+variables defined for fix_style npt. Delta is the deviation
+of the temperature from the target temperature, given by the above equation.
+Us and up are the shock and particle velocity correspponding to a steady
+shock calculated from the Rh conditions. They have units of distance/time.
+
    
+
    Restrictions:
+
    
+
    This fix style is part of the SHOCK package.  It is only enabled if
+LAMMPS was built with that package. See the Making
+LAMMPS section for more info.
+
    
+
    All the usual restrictions for fix_style npt apply,
+plus the additional ones mentioned above.
+
    
+
    Related commands:
+
    
+
    fix msst, fix npt, fix_modify
+
    
+
    Default:
+
    
+
    The keyword defaults are the same as those for fix npt
+
    
+
    
+
+
+
+
    (Ravelo) Ravelo, Holian, Germann and Lomdahl, Phys Rev B, 70, 014103 (2004).
+
    
+
diff --git a/doc/fix_nphug.txt b/doc/fix_nphug.txt
new file mode 100644
index 0000000000..6bb5664302
--- /dev/null
+++ b/doc/fix_nphug.txt
@@ -0,0 +1,211 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+fix nphug command :h3
+
+[Syntax:]
+
+fix ID group-ID nphug keyword value ... :pre
+
+ID, group-ID are documented in "fix"_fix.html command :ulb,l
+one or more keyword value pairs may be appended
+keyword = {temp} or {iso} or {aniso} or {tri} or {x} or {y} or {z} or {couple} or {tchain} or {pchain} or {mtk} or {tloop} or {ploop} or {nreset} or {drag} or {dilate} or {scaleyz} or {scalexz} or {scalexy}
+  {temp} values = Value1 Value2 Tdamp
+    Value1, Value2 = Nose-Hoover target temperatures, ignored by Hugoniostat
+    Tdamp = temperature damping parameter (time units)
+  {iso} or {aniso} or {tri} values = Pstart Pstop Pdamp
+    Pstart,Pstop = scalar external pressures, must be equal (pressure units)
+    Pdamp = pressure damping parameter (time units)
+  {x} or {y} or {z} or {xy} or {yz} or {xz} values = Pstart Pstop Pdamp
+    Pstart,Pstop = external stress tensor components, must be equal (pressure units)
+    Pdamp = stress damping parameter (time units)
+  {couple} = {none} or {xyz} or {xy} or {yz} or {xz}
+  {tchain} value = length of thermostat chain (1 = single thermostat)
+  {pchain} values = length of thermostat chain on barostat (0 = no thermostat)
+  {mtk} value = {yes} or {no} = add in MTK adjustment term or not
+  {tloop} value = number of sub-cycles to perform on thermostat
+  {ploop} value = number of sub-cycles to perform on barostat thermostat
+  {nreset} value = reset reference cell every this many timesteps
+  {drag} value = drag factor added to barostat/thermostat (0.0 = no drag)
+  {dilate} value = {all} or {partial}
+  {scaleyz} value = {yes} or {no} = scale yz with lz
+  {scalexz} value = {yes} or {no} = scale xz with lz
+  {scalexy} value = {yes} or {no} = scale xy with ly :pre
+:ule
+
+[Examples:]
+
+fix myhug all nphug temp 1.0 1.0 10.0 z 40.0 40.0 70.0
+fix myhug all nphug temp 1.0 1.0 10.0 iso 40.0 40.0 70.0 drag 200.0 tchain 1 pchain 0 
+
+[Description:]
+
+This command is a variant of the Nose-Hoover
+"fix npt"_fix_nh.html fix style.
+It performs time integration of the Hugoniostat equations
+of motion developed by Ravelo et al. "(Ravelo)"_#Ravelo.
+These equations compress the system to a state with average
+axial stress or pressure equal to the specified target value 
+and that satisfies the Rankine-Hugoniot (RH)
+jump conditions for steady shocks.
+
+The compression can be performed 
+either
+hydrostatically (using keyword iso, aniso, or tri) or uniaxially
+(using keywords x, y, or z).  In the hydrostatic case,
+the cell dimensions change dynamically so that the average axial stress
+in all three directions converges towards the specified target value. 
+In the uniaxial case, the chosen cell dimension changes dynamically 
+so that the average
+axial stress in that direction converges towards the target value. The
+other two cell dimensions are kept fixed (zero lateral strain).
+
+This leads to the following additional restrictions on the keywords:
+
+One and only one of the following keywords should be used: iso, aniso, tri, x, y, z, 
+
+The specified initial and final target pressures must be the same.
+
+The keywords xy, xz, yz may not be used.
+
+The only admissible value for the couple keyword is xyz, 
+which has the same effect as keyword iso 
+
+The temp keyword must be used in order to specify the time constant for 
+kinetic energy relaxation, but initial and final target temperature values
+are ignored.  :ul
+
+Essentially, a Hugoniostat simulation is an NPT simulation in which the
+user-specified target temperature is replaced with a time-dependent 
+target temperature Tt obtained from the following equation:
+
+Tt - T = (0.5*(P+P0)(V0-V)+E0-E)/(Ndof kB) = Delta
+
+where T and Tt are the instantaneous and target temperatures,
+P and P0 are the instantaneous and reference pressure or axial stress,
+depending on whether hydrostatic or uniaxial compression is being 
+performed, V and V0 are the instantaneous and reference volumes,
+E and E0 are the instantaneous and reference internal energy (potential
+plus kinetic), Ndof is the number of degrees of freedom used in the
+definition of temperature, and kB is the Boltzmann constant. Delta is the 
+negative deviation of the instantaneous temperature from the target temperature.
+The values of E0, V0, and P0 are the instantaneous values at the start of
+the simulation. These can be overridden using the fix_modify keywords {e0},
+{v0}, and {p0} described below.
+
+:line
+
+IMPORTANT NOTE: Unlike the "fix
+temp/berendsen"_fix_temp_berendsen.html command which performs
+thermostatting but NO time integration, this fix performs
+thermostatting/barostatting AND time integration.  Thus you should not
+use any other time integration fix, such as "fix nve"_fix_nve.html on
+atoms to which this fix is applied.  Likewise, this fix should not be 
+used on atoms that have their temperature controlled by another fix 
+- e.g. by "fix langevin"_fix_nh.html or "fix temp/rescale"_fix_temp_rescale.html
+commands.
+
+:line
+
+This fix compute a temperature and pressure each timestep.  To do
+this, the fix creates its own computes of style "temp" and "pressure",
+as if one of these two sets of commands had been issued:
+
+compute fix-ID_temp group-ID temp
+compute fix-ID_press group-ID pressure fix-ID_temp :pre
+
+compute fix-ID_temp all temp
+compute fix-ID_press all pressure fix-ID_temp :pre
+
+See the "compute temp"_compute_temp.html and "compute
+pressure"_compute_pressure.html commands for details.  Note that the
+IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID
++ underscore + "press".  For fix nvt, the group for the new computes
+is the same as the fix group.  For fix nph and fix npt, the group for
+the new computes is "all" since pressure is computed for the entire
+system.
+
+Note that these are NOT the computes used by thermodynamic output (see
+the "thermo_style"_thermo_style.html command) with ID = {thermo_temp}
+and {thermo_press}.  This means you can change the attributes of this
+fix's temperature or pressure via the
+"compute_modify"_compute_modify.html command or print this temperature
+or pressure during thermodynamic output via the "thermo_style
+custom"_thermo_style.html command using the appropriate compute-ID.
+It also means that changing attributes of {thermo_temp} or
+{thermo_press} will have no effect on this fix.
+
+:line
+
+[Restart, fix_modify, output, run start/stop, minimize info:]
+
+This fix writes the values of E0, V0, and P0, as well as the 
+state of all the thermostat and barostat
+variables to "binary restart files"_restart.html.  See the
+"read_restart"_read_restart.html command for info on how to re-specify
+a fix in an input script that reads a restart file, so that the
+operation of the fix continues in an uninterrupted fashion.
+
+The "fix_modify"_fix_modify.html {e0}, {v0} and {p0} keywords
+can be used to define the values of these quantities. Note the
+the values for {e0} and {v0} are extensive, and so must correspond
+to the total energy and volume of the entire system, not energy and 
+volume per atom. If any of these quantities are not specified, then the
+instanteous value in the system at the start of the simulation is used.
+
+The "fix_modify"_fix_modify.html {temp} and {press} options are
+supported by these fixes.  You can use them to assign a
+"compute"_compute.html you have defined to this fix which will be used
+in its thermostatting or barostatting procedure, as described above.
+If you do this, note that the kinetic energy derived from the compute
+temperature should be consistent with the virial term computed using
+all atoms for the pressure.  LAMMPS will warn you if you choose to
+compute temperature on a subset of atoms.
+
+The "fix_modify"_fix_modify.html {energy} option is supported by these
+fixes to add the energy change induced by Nose/Hoover thermostatting
+and barostatting to the system's potential energy as part of
+"thermodynamic output"_thermo_style.html. Either way, this energy is *not*
+included in the definition of internal energy E when calculating the value
+of Delta in the above equation.
+
+These fixes compute a global scalar and a global vector of quantities,
+which can be accessed by various "output
+commands"_Section_howto.html#howto_15.  The scalar value calculated by
+these fixes is "extensive"; the vector values are "intensive".
+
+The scalar is the cumulative energy change due to the fix.
+
+The vector stores three quantities unique to this fix (Delta, Us, and up),
+followed by all the internal Nose/Hoover thermostat and barostat
+variables defined for "fix_style npt"_fix_nh.html. Delta is the deviation
+of the temperature from the target temperature, given by the above equation.
+Us and up are the shock and particle velocity correspponding to a steady
+shock calculated from the Rh conditions. They have units of distance/time.
+
+[Restrictions:]
+
+This fix style is part of the SHOCK package.  It is only enabled if
+LAMMPS was built with that package. See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
+
+All the usual restrictions for "fix_style npt"_fix_nh.html apply,
+plus the additional ones mentioned above.
+
+[Related commands:]
+
+"fix msst"_fix_msst.html, "fix npt"_fix_nh.html, "fix_modify"_fix_modify.html
+
+[Default:]
+
+The keyword defaults are the same as those for "fix npt"_fix_nh.html
+
+:line
+
+:link(Ravelo)
+[(Ravelo)] Ravelo, Holian, Germann and Lomdahl, Phys Rev B, 70, 014103 (2004).