diff --git a/doc/src/fix_brownian.rst b/doc/src/fix_brownian.rst index 6b65100375..c3b97446d2 100644 --- a/doc/src/fix_brownian.rst +++ b/doc/src/fix_brownian.rst @@ -40,9 +40,9 @@ Syntax *gamma_t_eigen* values = *gt1* and *gt2* and *gt3* for *brownian/asphere* *gt1*, *gt2*, and *gt3* = diagonal entries of body frame translational friction tensor *gamma_t* values = *gt* for *brownian* and *brownian/sphere* - *gt* = magnitude of the (isotropic) translational friction tensor + *gt* = magnitude of the (isotropic) translational friction tensor *rotation_temp* values = *T* for *brownian/sphere* and *brownian/asphere* - *T* = rotation temperature, which can be different then *temp* when out of equilibrium + *T* = rotation temperature, which can be different then *temp* when out of equilibrium *planar_rotation* values = none (constrains rotational diffusion to be in xy plane if in 3D) Examples diff --git a/doc/src/fix_colvars.rst b/doc/src/fix_colvars.rst index 21b235cb6b..ec7b33ce51 100644 --- a/doc/src/fix_colvars.rst +++ b/doc/src/fix_colvars.rst @@ -13,7 +13,7 @@ Syntax * ID, group-ID are documented in :doc:`fix ` command * colvars = style name of this fix command * configfile = the configuration file for the colvars module -* keyword = *input* or *output* or *seed* or *tstat* +* keyword = *input* or *output* or *seed* or *unwrap* or *tstat* .. parsed-literal:: diff --git a/doc/src/fix_deposit.rst b/doc/src/fix_deposit.rst index ad3c37b24c..cf28509f5e 100644 --- a/doc/src/fix_deposit.rst +++ b/doc/src/fix_deposit.rst @@ -17,7 +17,7 @@ Syntax * M = insert a single atom or molecule every M steps * seed = random # seed (positive integer) * one or more keyword/value pairs may be appended to args -* keyword = *region* or *id* or *global* or *local* or *near* or *gaussian* or *attempt* or *rate* or *vx* or *vy* or *vz* or *mol* or *rigid* or *shake* or *units* +* keyword = *region* or *id* or *global* or *local* or *near* or *gaussian* or *attempt* or *rate* or *vx* or *vy* or *vz* or *target* or *mol* or *molfrac* or *rigid* or *shake* or *orient* or *units* .. parsed-literal:: diff --git a/doc/src/fix_imd.rst b/doc/src/fix_imd.rst index e29da08c4c..cb1831d174 100644 --- a/doc/src/fix_imd.rst +++ b/doc/src/fix_imd.rst @@ -13,7 +13,7 @@ Syntax * ID, group-ID are documented in :doc:`fix ` command * imd = style name of this fix command * port = port number on which the fix listens for an IMD client -* keyword = *unwrap* or *fscale* or *trate* +* keyword = *unwrap* or *fscale* or *trate* or *nowait* .. parsed-literal:: diff --git a/doc/src/fix_langevin.rst b/doc/src/fix_langevin.rst index 50c1489d7c..396df2b926 100644 --- a/doc/src/fix_langevin.rst +++ b/doc/src/fix_langevin.rst @@ -20,7 +20,7 @@ Syntax * damp = damping parameter (time units) * seed = random number seed to use for white noise (positive integer) * zero or more keyword/value pairs may be appended -* keyword = *angmom* or *omega* or *scale* or *tally* or *zero* +* keyword = *angmom* or *gjf* or *omega* or *scale* or *tally* or *zero* .. parsed-literal:: diff --git a/doc/src/fix_lb_fluid.rst b/doc/src/fix_lb_fluid.rst index 0191f14b1c..5f20bb10b1 100644 --- a/doc/src/fix_lb_fluid.rst +++ b/doc/src/fix_lb_fluid.rst @@ -16,7 +16,7 @@ Syntax * viscosity = the fluid viscosity (units of mass/(time\*length)). * density = the fluid density. * zero or more keyword/value pairs may be appended -* keyword = *dx* or *dm* or *noise* or *stencil* or *read_restart* or *write_restart* or *zwall_velocity* or *pressurebcx* or *bodyforce* or *D3Q19* or *dumpxdmf* or *dof* or *scaleGamma* or *a0* or *npits* or *wp* or *sw* +* keyword = *dx* or *dm* or *noise* or *stencil* or *read_restart* or *write_restart* or *zwall_velocity* or *pressurebcx* or *bodyforce* or *D3Q19* or *dumpxdmf* or *linearInit* or *dof* or *scaleGamma* or *a0* or *npits* or *wp* or *sw* .. parsed-literal:: @@ -36,6 +36,7 @@ Syntax N = output the force and torque every N timesteps file = output file name timeI = 1 (use simulation time to index xdmf file), 0 (use output frame number to index xdmf file) + *linearInit* values = none = initialize density and velocity using linear interpolation (default is uniform density, no velocities) *dof* values = dof = specify the number of degrees of freedom for temperature calculation *scaleGamma* values = type gammaFactor type = atom type (1-N) diff --git a/doc/src/fix_modify.rst b/doc/src/fix_modify.rst index e0cf3a34c7..f4c5be6b12 100644 --- a/doc/src/fix_modify.rst +++ b/doc/src/fix_modify.rst @@ -12,7 +12,7 @@ Syntax * fix-ID = ID of the fix to modify * one or more keyword/value pairs may be appended -* keyword = *bodyforces* or *colname* or *dynamic/dof* or *energy* or *press* or *respa* or *temp* or *virial* +* keyword = *bodyforces* or *colname* or *dynamic/dof* or *energy* or *press* or *respa* or *temp* or *virial* .. parsed-literal:: diff --git a/doc/src/fix_npt_cauchy.rst b/doc/src/fix_npt_cauchy.rst index 6ff3dffba3..6bff29f9dd 100644 --- a/doc/src/fix_npt_cauchy.rst +++ b/doc/src/fix_npt_cauchy.rst @@ -13,7 +13,7 @@ Syntax * ID, group-ID are documented in :doc:`fix ` command * style_name = *npt/cauchy* * 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* or *scalexy* or *scaleyz* or *scalexz* or *flip* or *fixedpoint* +* 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 *scalexy* or *scaleyz* or *scalexz* or *flip* or *alpha* or *continue* or *fixedpoint* .. parsed-literal:: diff --git a/doc/src/fix_pour.rst b/doc/src/fix_pour.rst index 742648ac76..6ef18ea800 100644 --- a/doc/src/fix_pour.rst +++ b/doc/src/fix_pour.rst @@ -16,7 +16,7 @@ Syntax * type = atom type to assign to inserted particles (offset for molecule insertion) * seed = random # seed (positive integer) * one or more keyword/value pairs may be appended to args -* keyword = *region* or *diam* or *vol* or *rate* or *dens* or *vel* or *mol* or *rigid* or *shake* or *ignore* +* keyword = *region* or *diam* or *id* or *vol* or *rate* or *dens* or *vel* or *mol* or *molfrac* or *rigid* or *shake* or *ignore* .. parsed-literal:: diff --git a/doc/src/fix_rigid.rst b/doc/src/fix_rigid.rst index 445b86466c..9a3b6e4da3 100644 --- a/doc/src/fix_rigid.rst +++ b/doc/src/fix_rigid.rst @@ -80,7 +80,7 @@ Syntax groupID1, groupID2, ... = list of N group IDs * zero or more keyword/value pairs may be appended -* keyword = *langevin* or *reinit* or *temp* or *iso* or *aniso* or *x* or *y* or *z* or *couple* or *tparam* or *pchain* or *dilate* or *force* or *torque* or *infile* +* keyword = *langevin* or *reinit* or *temp* or *iso* or *aniso* or *x* or *y* or *z* or *couple* or *tparam* or *pchain* or *dilate* or *force* or *torque* or *infile* or *gravity* .. parsed-literal:: @@ -115,6 +115,11 @@ Syntax xflag,yflag,zflag = off/on if component of center-of-mass torque is active *infile* filename filename = file with per-body values of mass, center-of-mass, moments of inertia + *gravity* values = gravity-ID + gravity-ID = ID of fix gravity command to add gravitational forces + +.. + FIXME These don't seem to be included in the source code *mol* value = template-ID template-ID = ID of molecule template specified in a separate :doc:`molecule ` command diff --git a/doc/src/fix_viscosity.rst b/doc/src/fix_viscosity.rst index 204e435d6e..c99196e09b 100644 --- a/doc/src/fix_viscosity.rst +++ b/doc/src/fix_viscosity.rst @@ -17,7 +17,7 @@ Syntax * pdim = *x* or *y* or *z* = direction of momentum transfer * Nbin = # of layers in pdim direction (must be even number) * zero or more keyword/value pairs may be appended -* keyword = *swap* or *target* +* keyword = *swap* or *vtarget* .. parsed-literal:: diff --git a/doc/src/fix_wall.rst b/doc/src/fix_wall.rst index 3028588505..014c89cfd5 100644 --- a/doc/src/fix_wall.rst +++ b/doc/src/fix_wall.rst @@ -70,7 +70,7 @@ Syntax cutoff = distance from wall at which wall-particle interaction is cut off (distance units) * zero or more keyword/value pairs may be appended -* keyword = *units* or *fld* +* keyword = *units* or *fld* or *pbc* .. parsed-literal:: diff --git a/doc/src/fix_wall_piston.rst b/doc/src/fix_wall_piston.rst index af3dece2f5..1237d1ac7c 100644 --- a/doc/src/fix_wall_piston.rst +++ b/doc/src/fix_wall_piston.rst @@ -14,7 +14,7 @@ Syntax * wall/piston = style name of this fix command * face = *zlo* * zero or more keyword/value pairs may be appended -* keyword = *pos* or *vel* or *ramp* or *units* +* keyword = *pos* or *vel* or *ramp* or *temp* or *units* .. parsed-literal:: @@ -32,6 +32,10 @@ Syntax *lattice* = the wall position is defined in lattice units *box* = the wall position is defined in simulation box units +.. + FIXME: There are several "undocumented" key words for this fix: *rough*, + *rampNL1*, *rampNL2*, *rampNL3*, *rampNL4*, and *rampNL5*. + Examples """"""""