+ + -
-
fix_modify AtC output boundary_integral
-syntax
+fix_modify AtC output boundary_integral
+syntax
fix_modify AtC output boundary_integral [field] faceset [name]
- field (string) : name of hardy field
- name (string) : name of faceset
-examples
++examples
fix_modify AtC output boundary_integral stress faceset loop1
-description
++description
Calculates a surface integral of the given field dotted with the outward normal of the faces and puts output in the "GLOBALS" file
--restrictions
-Must be used with the hardy/field type of AtC fix ( see fix atc command )
--related
--default
++restrictions
+Must be used with the hardy/field type of AtC fix ( see fix atc command )
++related
++default
none
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_consistent_fe_initialization.html b/doc/src/USER/atc/man_consistent_fe_initialization.html index f4c33f5076..a731b09116 100644 --- a/doc/src/USER/atc/man_consistent_fe_initialization.html +++ b/doc/src/USER/atc/man_consistent_fe_initialization.html @@ -7,41 +7,39 @@ +
+ + -
-
fix_modify AtC consistent_fe_initialization
-syntax
+fix_modify AtC consistent_fe_initialization
+syntax
fix_modify AtC consistent_fe_initialization <on | off>
- <on|off> = switch to activiate/deactiviate the initial setting of FE intrinsic field to match the projected MD field
-examples
++examples
fix_modify atc consistent_fe_initialization on
-description
++description
Determines whether AtC initializes FE intrinsic fields (e.g., temperature) to match the projected MD values. This is particularly useful for fully overlapping simulations.
--restrictions
++restrictions
Can be used with: thermal, two_temperature. Cannot be used with time filtering on. Does not include boundary nodes.
--related
--default
++related
++default
Default is off
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_contour_integral.html b/doc/src/USER/atc/man_contour_integral.html index c321605e88..690f0fcc98 100644 --- a/doc/src/USER/atc/man_contour_integral.html +++ b/doc/src/USER/atc/man_contour_integral.html @@ -7,44 +7,42 @@ +
+ + -
-
fix_modify AtC output contour_integral
-syntax
+fix_modify AtC output contour_integral
+syntax
fix_modify AtC output contour_integral [field] faceset [name] <axis [x | y | z ]>
- field (string) : name of hardy field
- name (string) : name of faceset
- axis (string) : x or y or z
-examples
++examples
fix_modify AtC output contour_integral stress faceset loop1
-description
++description
Calculates a surface integral of the given field dotted with the outward normal of the faces and puts output in the "GLOBALS" file
--restrictions
-Must be used with the hardy/field type of AtC fix ( see fix atc command )
--related
--default
++restrictions
+Must be used with the hardy/field type of AtC fix ( see fix atc command )
++related
++default
none
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_control.html b/doc/src/USER/atc/man_control.html index af0236f30e..900952ba0b 100644 --- a/doc/src/USER/atc/man_control.html +++ b/doc/src/USER/atc/man_control.html @@ -7,24 +7,22 @@ +
+ + -
-tolerance (float) = relative tolerance to which matrix equations will be solved
-
diff --git a/doc/src/USER/atc/man_control_momentum.html b/doc/src/USER/atc/man_control_momentum.html
index 805c12567a..8f4f486595 100644
--- a/doc/src/USER/atc/man_control_momentum.html
+++ b/doc/src/USER/atc/man_control_momentum.html
@@ -7,24 +7,22 @@
+fix_modify AtC control
-syntax
+fix_modify AtC control
+syntax
fix_modify AtC control <physics_type> <solution_parameter>
-examples
++examples
fix_modify AtC control thermal max_iterations 10
fix_modify AtC control momentum tolerance 1.e-5
-description
++description
Sets the numerical parameters for the matrix solvers used in the specified control algorithm. Many solution approaches require iterative solvers, and these methods enable users to provide the maximum number of iterations and the relative tolerance.
--restrictions
++restrictions
only for be used with specific controllers : thermal, momentum
They are ignored if a lumped solution is requested
-related
--default
++related
++default
max_iterations is the number of rows in the matrix
tolerance is 1.e-10
+ + -
-face_set_id (string) = id of boundary face set, if not specified (or not possible when the atomic domain does not line up with mesh boundaries) defaults to an atomic-quadrature approximate evaulation
-
fix_modify AtC control momentum
-syntax
+fix_modify AtC control momentum
+syntax
fix_modify AtC control momentum none
fix_modify AtC control momentum rescale <frequency>
@@ -44,21 +42,21 @@ syntax
-examples
++examples
fix_modify AtC control momentum glc_velocity
fix_modify AtC control momentum flux faceset bndy_faces
-description
--restrictions
++description
++restrictions
only to be used with specific transfers : elastic
rescale not valid with time filtering activated
-related
--default
++related
++default
none
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_control_thermal.html b/doc/src/USER/atc/man_control_thermal.html index 301297f306..eab186f715 100644 --- a/doc/src/USER/atc/man_control_thermal.html +++ b/doc/src/USER/atc/man_control_thermal.html @@ -7,24 +7,22 @@ +
+ + -
-
+ LAMMPS Website
+ LAMMPS Manual
+ USER-AtC Manual
+ Commands
+
+
+
+ + -
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_decomposition.html b/doc/src/USER/atc/man_decomposition.html index 15725073d3..d54a201034 100644 --- a/doc/src/USER/atc/man_decomposition.html +++ b/doc/src/USER/atc/man_decomposition.html @@ -7,24 +7,22 @@ +
+ LAMMPS Website
+ LAMMPS Manual
+ USER-AtC Manual
+ Commands
+
+
+
+ + -
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_electron_integration.html b/doc/src/USER/atc/man_electron_integration.html index b14c14d86d..ab454c16d2 100644 --- a/doc/src/USER/atc/man_electron_integration.html +++ b/doc/src/USER/atc/man_electron_integration.html @@ -7,24 +7,22 @@ +
+ LAMMPS Website
+ LAMMPS Manual
+ USER-AtC Manual
+ Commands
+
+
+
+ + -
+ LAMMPS Website
+ LAMMPS Manual
+ USER-AtC Manual
+ Commands
+
+
+
+ + -
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_extrinsic_exchange.html b/doc/src/USER/atc/man_extrinsic_exchange.html index 8f6533ad64..4f1f5962d9 100644 --- a/doc/src/USER/atc/man_extrinsic_exchange.html +++ b/doc/src/USER/atc/man_extrinsic_exchange.html @@ -7,40 +7,38 @@ +
+ LAMMPS Website
+ LAMMPS Manual
+ USER-AtC Manual
+ Commands
+
+
+
+ + -
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_fe_md_boundary.html b/doc/src/USER/atc/man_fe_md_boundary.html index 06bca2b337..e517dd4855 100644 --- a/doc/src/USER/atc/man_fe_md_boundary.html +++ b/doc/src/USER/atc/man_fe_md_boundary.html @@ -7,40 +7,38 @@ +
+ LAMMPS Website
+ LAMMPS Manual
+ USER-AtC Manual
+ Commands
+
+
+
+ + -
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_fem_mesh.html b/doc/src/USER/atc/man_fem_mesh.html index 2abd84d6ce..b8ba584816 100644 --- a/doc/src/USER/atc/man_fem_mesh.html +++ b/doc/src/USER/atc/man_fem_mesh.html @@ -1,24 +1,45 @@ - - + + + +ATC: fix_modify AtC fem create mesh
-
-
-
-
+ LAMMPS Website
+ LAMMPS Manual
+ USER-AtC Manual
+ Commands
+
+
+
+ + + +
fix_modify AtC control thermal
-syntax
+fix_modify AtC control thermal
+syntax
fix_modify AtC control thermal <control_type> <optional_args>
- control_type (string) = none | rescale | hoover | flux
@@ -46,25 +44,25 @@ syntax - face_set_id (string), optional = id of boundary face set, if not specified (or not possible when the atomic domain does not line up with mesh boundaries) defaults to an atomic-quadrature approximate evaulation, does not work with interpolate
-examples
++examples
fix_modify AtC control thermal none
fix_modify AtC control thermal rescale 10
fix_modify AtC control thermal hoover
fix_modify AtC control thermal flux
fix_modify AtC control thermal flux faceset bndy_faces
-description
++description
Sets the energy exchange mechansim from the finite elements to the atoms, managed through a control algorithm. Rescale computes a scale factor for each atom to match the finite element temperature. Hoover is a Gaussian least-constraint isokinetic thermostat enforces that the nodal restricted atomic temperature matches the finite element temperature. Flux is a similar mode, but rather adds energy to the atoms based on conservation of energy. Hoover and flux allows the prescription of sources or fixed temperatures on the atoms.
--restrictions
++restrictions
only for be used with specific transfers : thermal (rescale, hoover, flux), two_temperature (flux)
rescale not valid with time filtering activated
-related
--default
++related
++default
none
rescale frequency is 1
flux boundary_integration_type is interpolate
+ + -
-
fix_modify AtC control thermal correction_max_iterations
-syntax
+fix_modify AtC control thermal correction_max_iterations
+syntax
fix_modify AtC control thermal correction_max_iterations <max_iterations>
- max_iterations (int) = maximum number of iterations that will be used by iterative matrix solvers
-examples
++examples
fix_modify AtC control thermal correction_max_iterations 10
-description
++description
Sets the maximum number of iterations to compute the 2nd order in time correction term for lambda with the fractional step method. The method uses the same tolerance as the controller's matrix solver.
--restrictions
++restrictions
only for use with thermal physics using the fractional step method.
--related
--default
++related
++default
correction_max_iterations is 20
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_decomposition.html b/doc/src/USER/atc/man_decomposition.html index 15725073d3..d54a201034 100644 --- a/doc/src/USER/atc/man_decomposition.html +++ b/doc/src/USER/atc/man_decomposition.html @@ -7,24 +7,22 @@ +
+ + -
-
fix_modify AtC decomposition
-syntax
+fix_modify AtC decomposition
+syntax
fix_modify AtC decomposition <type>
- <type> =
@@ -32,20 +30,20 @@ syntax distributed_memory: only owned nodal information on processor
-examples
++examples
fix_modify atc decomposition distributed_memory
-description
++description
Command for assigning the distribution of work and memory for parallel runs.
--restrictions
++restrictions
replicated_memory is appropriate for simulations were the number of nodes << number of atoms
--related
--default
++related
++default
replicated_memory
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_electron_integration.html b/doc/src/USER/atc/man_electron_integration.html index b14c14d86d..ab454c16d2 100644 --- a/doc/src/USER/atc/man_electron_integration.html +++ b/doc/src/USER/atc/man_electron_integration.html @@ -7,24 +7,22 @@ +
+ + -
-
diff --git a/doc/src/USER/atc/man_equilibrium_start.html b/doc/src/USER/atc/man_equilibrium_start.html
index 3723cf98bf..d01253c4b3 100644
--- a/doc/src/USER/atc/man_equilibrium_start.html
+++ b/doc/src/USER/atc/man_equilibrium_start.html
@@ -7,40 +7,38 @@
+fix_modify AtC extrinsic electron_integration
-syntax
+fix_modify AtC extrinsic electron_integration
+syntax
fix_modify AtC extrinsic electron_integration <integration_type> <num_subcyle_steps(optional)>
-
@@ -32,20 +30,20 @@ syntax
- num_subcycle_steps (int), optional = number of subcycle steps for the electron time integration
-examples
++examples
fix_modify AtC extrinsic electron_integration implicit
fix_modify AtC extrinsic electron_integration explicit 100
-description
++description
Switches between integration scheme for the electron temperature. The number of subcyling steps used to integrate the electron temperature 1 LAMMPS timestep can be manually adjusted to capture fast electron dynamics.
--restrictions
-For use only with two_temperature type of AtC fix ( see fix atc command )
+
+restrictions
+For use only with two_temperature type of AtC fix ( see fix atc command )
-default
++default
implicit
subcycle_steps = 1
+ + -
-
fix_modify AtC equilibrium_start
-syntax
+fix_modify AtC equilibrium_start
+syntax
fix_modify AtC equilibrium_start <on|off>
--examples
++examples
fix_modify atc equilibrium_start on
-description
++description
Starts filtered calculations assuming they start in equilibrium, i.e. perfect finite element force balance.
--restrictions
++restrictions
only needed before filtering is begun
--related
++related
--default
++default
on
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_extrinsic_exchange.html b/doc/src/USER/atc/man_extrinsic_exchange.html index 8f6533ad64..4f1f5962d9 100644 --- a/doc/src/USER/atc/man_extrinsic_exchange.html +++ b/doc/src/USER/atc/man_extrinsic_exchange.html @@ -7,40 +7,38 @@ +
+ + -
-
fix_modify AtC extrinsic exchange
-syntax
+fix_modify AtC extrinsic exchange
+syntax
fix_modify AtC extrinsic exchange <on|off>
--examples
++examples
fix_modify AtC extrinsic exchange on
-description
++description
Switches energy exchange between the MD system and electron system on and off
--restrictions
++restrictions
Only valid for use with two_temperature type of AtC fix.
--related
-see fix atc command
--default
++related
+see fix atc command
++default
on
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_fe_md_boundary.html b/doc/src/USER/atc/man_fe_md_boundary.html index 06bca2b337..e517dd4855 100644 --- a/doc/src/USER/atc/man_fe_md_boundary.html +++ b/doc/src/USER/atc/man_fe_md_boundary.html @@ -7,40 +7,38 @@ +
+ + -
-
fix_modify AtC fe_md_boundary
-syntax
+fix_modify AtC fe_md_boundary
+syntax
fix_modify AtC fe_md_boundary <faceset | interpolate | no_boundary> [args]
--examples
++examples
fix_modify atc fe_md_boundary interpolate
-description
++description
Specifies different methods for computing fluxes between between the MD and FE integration regions. Faceset defines a faceset separating the MD and FE regions and uses finite element face quadrature to compute the flux. Interpolate uses a reconstruction scheme to approximate the flux, which is more robust but less accurate if the MD/FE boundary does correspond to a faceset. No boundary results in no fluxes between the systems being computed.
--restrictions
++restrictions
If faceset is used, all the AtC non-boundary atoms must lie within and completely fill the domain enclosed by the faceset.
--related
++related
see for how to specify the faceset name.
--default
++default
Interpolate.
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_fem_mesh.html b/doc/src/USER/atc/man_fem_mesh.html index 2abd84d6ce..b8ba584816 100644 --- a/doc/src/USER/atc/man_fem_mesh.html +++ b/doc/src/USER/atc/man_fem_mesh.html @@ -1,24 +1,45 @@ - - + + + +
fix_modify AtC fem create mesh
-syntax
+ + + + ++ + + +
+
+
Generated on Mon Aug 17 09:35:16 2009 for ATC by +
Generated on Mon Aug 17 09:35:16 2009 for ATC by
1.3.9.1
diff --git a/doc/src/USER/atc/man_filter_scale.html b/doc/src/USER/atc/man_filter_scale.html
index 975f87e949..7a871f5c81 100644
--- a/doc/src/USER/atc/man_filter_scale.html
+++ b/doc/src/USER/atc/man_filter_scale.html
@@ -7,45 +7,43 @@
+
+ LAMMPS Website
+ LAMMPS Manual
+ USER-AtC Manual
+ Commands
+
+
+
+ + -
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_filter_type.html b/doc/src/USER/atc/man_filter_type.html index 8d9dbd3d12..2711d128e9 100644 --- a/doc/src/USER/atc/man_filter_type.html +++ b/doc/src/USER/atc/man_filter_type.html @@ -7,41 +7,39 @@ +
+ LAMMPS Website
+ LAMMPS Manual
+ USER-AtC Manual
+ Commands
+
+
+
+ + -
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_fix_atc.html b/doc/src/USER/atc/man_fix_atc.html index e710c28ed2..7cc6cfea5b 100644 --- a/doc/src/USER/atc/man_fix_atc.html +++ b/doc/src/USER/atc/man_fix_atc.html @@ -7,24 +7,22 @@ +
+ LAMMPS Website
+ LAMMPS Manual
+ USER-AtC Manual
+ Commands
+
+
+
+ + -
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_fix_flux.html b/doc/src/USER/atc/man_fix_flux.html index d8369a8785..42815def6b 100644 --- a/doc/src/USER/atc/man_fix_flux.html +++ b/doc/src/USER/atc/man_fix_flux.html @@ -7,44 +7,42 @@ +
+ LAMMPS Website
+ LAMMPS Manual
+ USER-AtC Manual
+ Commands
+
+
+
+ + -
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_fix_nodes.html b/doc/src/USER/atc/man_fix_nodes.html index cf5c93590a..03cf86eb92 100644 --- a/doc/src/USER/atc/man_fix_nodes.html +++ b/doc/src/USER/atc/man_fix_nodes.html @@ -7,46 +7,44 @@ +
+ LAMMPS Website
+ LAMMPS Manual
+ USER-AtC Manual
+ Commands
+
+
+
+ + -
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_hardy_computes.html b/doc/src/USER/atc/man_hardy_computes.html index c16550742b..b45b7dfb01 100644 --- a/doc/src/USER/atc/man_hardy_computes.html +++ b/doc/src/USER/atc/man_hardy_computes.html @@ -7,24 +7,22 @@ +
+ LAMMPS Website
+ LAMMPS Manual
+ USER-AtC Manual
+ Commands
+
+
+
+ + -
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_hardy_fields.html b/doc/src/USER/atc/man_hardy_fields.html index 1f55fd5e37..17903aabd0 100644 --- a/doc/src/USER/atc/man_hardy_fields.html +++ b/doc/src/USER/atc/man_hardy_fields.html @@ -7,24 +7,22 @@ +
+ LAMMPS Website
+ LAMMPS Manual
+ USER-AtC Manual
+ Commands
+
+
+
+ + -
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_hardy_gradients.html b/doc/src/USER/atc/man_hardy_gradients.html index 708fecbca1..00935f0ae2 100644 --- a/doc/src/USER/atc/man_hardy_gradients.html +++ b/doc/src/USER/atc/man_hardy_gradients.html @@ -7,24 +7,22 @@ +
+ LAMMPS Website
+ LAMMPS Manual
+ USER-AtC Manual
+ Commands
+
+
+
+ + -
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_hardy_kernel.html b/doc/src/USER/atc/man_hardy_kernel.html index 3d81b367dd..f97037784c 100644 --- a/doc/src/USER/atc/man_hardy_kernel.html +++ b/doc/src/USER/atc/man_hardy_kernel.html @@ -7,24 +7,22 @@ +
+ LAMMPS Website
+ LAMMPS Manual
+ USER-AtC Manual
+ Commands
+
+
+
+ + -
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_hardy_on_the_fly.html b/doc/src/USER/atc/man_hardy_on_the_fly.html index d140cf6840..79c1006c97 100644 --- a/doc/src/USER/atc/man_hardy_on_the_fly.html +++ b/doc/src/USER/atc/man_hardy_on_the_fly.html @@ -7,24 +7,22 @@ +
+ LAMMPS Website
+ LAMMPS Manual
+ USER-AtC Manual
+ Commands
+
+
+
+ + -
+ LAMMPS Website
+ LAMMPS Manual
+ USER-AtC Manual
+ Commands
+
+
+
+ + -
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_initial.html b/doc/src/USER/atc/man_initial.html index c0a0be3852..41ae06eb8c 100644 --- a/doc/src/USER/atc/man_initial.html +++ b/doc/src/USER/atc/man_initial.html @@ -7,41 +7,39 @@ +
+ LAMMPS Website
+ LAMMPS Manual
+ USER-AtC Manual
+ Commands
+
+
+
+ + -
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+ LAMMPS Website
+ LAMMPS Manual
+ USER-AtC Manual
+ Commands
+
+
+
+ + -
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_internal_element_set.html b/doc/src/USER/atc/man_internal_element_set.html index 31bee57860..849e8f0671 100644 --- a/doc/src/USER/atc/man_internal_element_set.html +++ b/doc/src/USER/atc/man_internal_element_set.html @@ -7,42 +7,40 @@ +
+ LAMMPS Website
+ LAMMPS Manual
+ USER-AtC Manual
+ Commands
+
+
+
+ + -
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_internal_quadrature.html b/doc/src/USER/atc/man_internal_quadrature.html index 172187c298..7f10e17076 100644 --- a/doc/src/USER/atc/man_internal_quadrature.html +++ b/doc/src/USER/atc/man_internal_quadrature.html @@ -7,40 +7,38 @@ +
+ LAMMPS Website
+ LAMMPS Manual
+ USER-AtC Manual
+ Commands
+
+
+
+ + -
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+ LAMMPS Website
+ LAMMPS Manual
+ USER-AtC Manual
+ Commands
+
+
+
+ + -
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_localized_lambda.html b/doc/src/USER/atc/man_localized_lambda.html index 5dadb9d730..fd845d0a71 100644 --- a/doc/src/USER/atc/man_localized_lambda.html +++ b/doc/src/USER/atc/man_localized_lambda.html @@ -7,38 +7,36 @@ +
+ LAMMPS Website
+ LAMMPS Manual
+ USER-AtC Manual
+ Commands
+
+
+
+ + -
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+ LAMMPS Website
+ LAMMPS Manual
+ USER-AtC Manual
+ Commands
+
+
+
+ + -
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_mask_direction.html b/doc/src/USER/atc/man_mask_direction.html index 01ca9d192b..31c18b4f1f 100644 --- a/doc/src/USER/atc/man_mask_direction.html +++ b/doc/src/USER/atc/man_mask_direction.html @@ -7,38 +7,36 @@ +
+ LAMMPS Website
+ LAMMPS Manual
+ USER-AtC Manual
+ Commands
+
+
+
+ + -
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Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_mesh_create_nodeset.html b/doc/src/USER/atc/man_mesh_create_nodeset.html index 9d5d155654..39bfffd119 100644 --- a/doc/src/USER/atc/man_mesh_create_nodeset.html +++ b/doc/src/USER/atc/man_mesh_create_nodeset.html @@ -7,41 +7,39 @@ +
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Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_mesh_delete_elements.html b/doc/src/USER/atc/man_mesh_delete_elements.html index cc269c8e65..60a2fe59a1 100644 --- a/doc/src/USER/atc/man_mesh_delete_elements.html +++ b/doc/src/USER/atc/man_mesh_delete_elements.html @@ -7,40 +7,38 @@ +
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Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_mesh_output.html b/doc/src/USER/atc/man_mesh_output.html index be1b4c194f..f768a29c41 100644 --- a/doc/src/USER/atc/man_mesh_output.html +++ b/doc/src/USER/atc/man_mesh_output.html @@ -7,39 +7,37 @@ +
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+ LAMMPS Manual
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+ LAMMPS Website
+ LAMMPS Manual
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Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_mesh_read.html b/doc/src/USER/atc/man_mesh_read.html index a497a2ed04..e0571ccf88 100644 --- a/doc/src/USER/atc/man_mesh_read.html +++ b/doc/src/USER/atc/man_mesh_read.html @@ -7,42 +7,40 @@ +
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+ LAMMPS Manual
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Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_mesh_write.html b/doc/src/USER/atc/man_mesh_write.html index 21754a1e68..756cf49922 100644 --- a/doc/src/USER/atc/man_mesh_write.html +++ b/doc/src/USER/atc/man_mesh_write.html @@ -7,41 +7,39 @@ +
+ LAMMPS Website
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+ LAMMPS Website
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Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_output.html b/doc/src/USER/atc/man_output.html index 3129ff30c9..aec1d5d55a 100644 --- a/doc/src/USER/atc/man_output.html +++ b/doc/src/USER/atc/man_output.html @@ -7,24 +7,22 @@ +
+ LAMMPS Website
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+ LAMMPS Website
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+ LAMMPS Website
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+ LAMMPS Website
+ LAMMPS Manual
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+ LAMMPS Website
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+ LAMMPS Website
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+ LAMMPS Manual
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+ LAMMPS Manual
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+ LAMMPS Website
+ LAMMPS Manual
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+ LAMMPS Website
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+ LAMMPS Website
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+ LAMMPS Website
+ LAMMPS Manual
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+ LAMMPS Website
+ LAMMPS Manual
+ USER-AtC Manual
+ Commands
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+ LAMMPS Website
+ LAMMPS Manual
+ USER-AtC Manual
+ Commands
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+ LAMMPS Website
+ LAMMPS Manual
+ USER-AtC Manual
+ Commands
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+ LAMMPS Website
+ LAMMPS Manual
+ USER-AtC Manual
+ Commands
+
+
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+ LAMMPS Website
+ LAMMPS Manual
+ USER-AtC Manual
+ Commands
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+ LAMMPS Website
+ LAMMPS Manual
+ USER-AtC Manual
+ Commands
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+ LAMMPS Website
+ LAMMPS Manual
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+ LAMMPS Website
+ LAMMPS Manual
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+ LAMMPS Website
+ LAMMPS Manual
+ USER-AtC Manual
+ Commands
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Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/body.txt b/doc/src/body.txt index 54ec157c74..344e5b1d65 100644 --- a/doc/src/body.txt +++ b/doc/src/body.txt @@ -6,7 +6,7 @@ :line -Body particles :h3 +Body particles :h1 [Overview:] diff --git a/doc/src/fix_atc.txt b/doc/src/fix_atc.txt index 75a82f063a..49014f0591 100644 --- a/doc/src/fix_atc.txt +++ b/doc/src/fix_atc.txt @@ -90,13 +90,11 @@ likewise for this post-processing example: run 1000 :pre the mesh's linear interpolation functions can be used as the localization function - by using the field option: +by using the field option: fix AtC internal atc field - fix_modify AtC mesh create 1 1 1 box p p p - - ... + ... :pre Note coupling and post-processing can be combined in the same simulations using separate fixes. @@ -108,11 +106,10 @@ No information about this fix is written to "binary restart files"_restart.html. [Restrictions:] -Thermal and two_temperature (coupling) types use a Verlet time-integration algorithm. The hardy type does not contain its own time-integrator and must be used with a separate fix that does contain one, e.g. nve, nvt, etc. +Thermal and two_temperature (coupling) types use a Verlet time-integration algorithm. The hardy type does not contain its own time-integrator and must be used with a separate fix that does contain one, e.g. nve, nvt, etc. In addition, currently: -Currently, -- the coupling is restricted to thermal physics -- the FE computations are done in serial on each processor. :ul +the coupling is restricted to thermal physics :ulb,l +the FE computations are done in serial on each processor. :l,ule [Related commands:] diff --git a/doc/src/fix_gcmc.txt b/doc/src/fix_gcmc.txt index c78142a999..38f0fb95ce 100644 --- a/doc/src/fix_gcmc.txt +++ b/doc/src/fix_gcmc.txt @@ -95,8 +95,8 @@ which will result in roughly one MC move per atom or molecule per MC cycle. All inserted particles are always added to two groups: the default -group "all" and the fix group specified in the fix command (which can -also be "all"). In addition, particles are also added to any groups +group "all" and the fix group specified in the fix command. +In addition, particles are also added to any groups specified by the {group} and {grouptype} keywords. If inserted particles are individual atoms, they are assigned the atom type given by the type argument. If they are molecules, the type argument has no @@ -104,6 +104,12 @@ effect and must be set to zero. Instead, the type of each atom in the inserted molecule is specified in the file read by the "molecule"_molecule.html command. +NOTE: Care should be taken to apply fix gcmc only to +a group that contains only those atoms and molecules +that you wish to manipulate using Monte Carlo. +Hence it is generally not a good idea to specify +the default group "all" in the fix command, although it is allowed. + This fix cannot be used to perform GCMC insertions of gas atoms or molecules other than the exchanged type, but GCMC deletions, and MC translations, and rotations can be performed on any atom/molecule in diff --git a/doc/src/group.txt b/doc/src/group.txt index afa218c5a3..dddb0459e3 100644 --- a/doc/src/group.txt +++ b/doc/src/group.txt @@ -13,11 +13,13 @@ group command :h3 group ID style args :pre ID = user-defined name of the group :ulb,l -style = {delete} or {region} or {type} or {id} or {molecule} or {variable} or \ +style = {delete} or {clear} or {empty} or {region} or \ + {type} or {id} or {molecule} or {variable} or \ {include} or {subtract} or {union} or {intersect} or \ {dynamic} or {static} :l {delete} = no args {clear} = no args + {empty} = no args {region} args = region-ID {type} or {id} or {molecule} args = list of one or more atom types, atom IDs, or molecule IDs @@ -41,6 +43,7 @@ style = {delete} or {region} or {type} or {id} or {molecule} or {variable} or \ keyword = {region} or {var} or {every} {region} value = region-ID {var} value = name of variable + {property} value = name of per-atom property {every} value = N = update group every this many timesteps {static} = no args :pre :ule @@ -99,6 +102,10 @@ e.g. using the "run every"_run.html command if a fix or compute or other operation expects the atoms in the group to remain constant, but LAMMPS does not check for this. +The {empty} style creates an empty group, which is useful for commands +like "fix gcmc"_fix_gcmc.html or with complex scripts that add atoms +to a group. + The {region} style puts all atoms in the region volume into the group. Note that this is a static one-time assignment. The atoms remain assigned (or not assigned) to the group even in they later move out of @@ -215,7 +222,11 @@ conditions are applied. If the {region} keyword is used, atoms not in the specified region are removed from the dynamic group. If the {var} keyword is used, the variable name must be an atom-style or atomfile-style variable. The variable is evaluated and atoms whose -per-atom values are 0.0, are removed from the dynamic group. +per-atom values are 0.0, are removed from the dynamic group. If the {property} +keyword is used, the per-atom property name must be a previously defined +per-atom property. The per-atom property is evaluated and atoms whose +values are 0.0 are removed from the dynamic group, otherwise they +are added to the group. The assignment of atoms to a dynamic group is done at the beginning of each run and on every timestep that is a multiple of {N}, which is the diff --git a/doc/src/lammps.book b/doc/src/lammps.book index d4e73453b0..878e4ad355 100644 --- a/doc/src/lammps.book +++ b/doc/src/lammps.book @@ -20,6 +20,7 @@ Section_python.html Section_errors.html Section_history.html +lammps_tutorials.html tutorial_bash_on_windows.html tutorial_drude.html tutorial_github.html @@ -28,6 +29,7 @@ tutorial_pylammps.html body.html manifolds.html +lammps_commands.html angle_coeff.html angle_style.html atom_modify.html @@ -138,7 +140,6 @@ fix_adapt_fep.html fix_addforce.html fix_addtorque.html fix_append_atoms.html -fix_atc.html fix_atom_swap.html fix_ave_atom.html fix_ave_chunk.html @@ -276,6 +277,7 @@ fix_spring_self.html fix_srd.html fix_store_force.html fix_store_state.html +fix_surface_global.html fix_temp_berendsen.html fix_temp_csvr.html fix_temp_rescale.html @@ -422,11 +424,13 @@ pair_airebo.html pair_awpmd.html pair_beck.html pair_body.html +pair_body_rounded_polygon.html pair_bop.html pair_born.html pair_brownian.html pair_buck.html pair_buck_long.html +pair_buck6d_coul_gauss.html pair_charmm.html pair_class2.html pair_colloid.html @@ -538,6 +542,7 @@ bond_zero.html angle_charmm.html angle_class2.html angle_cosine.html +angle_cosine_buck6d.html angle_cosine_delta.html angle_cosine_periodic.html angle_cosine_shift.html @@ -577,11 +582,13 @@ improper_distance.html improper_fourier.html improper_harmonic.html improper_hybrid.html +improper_inversion_harmonic.html improper_none.html improper_ring.html improper_umbrella.html improper_zero.html +fix_atc.html USER/atc/man_add_molecule.html USER/atc/man_add_species.html USER/atc/man_atom_element_map.html diff --git a/doc/src/lammps_commands.txt b/doc/src/lammps_commands.txt new file mode 100644 index 0000000000..f9c2e7366a --- /dev/null +++ b/doc/src/lammps_commands.txt @@ -0,0 +1,10 @@ + +LAMMPS Commands :h1 + +The following pages contain the detailed documentation of all +LAMMPS commands included in this version of LAMMPS. Generic +commands are listed first (in alphabetical order) followed by +command categories like compute styles or pair styles and so on. + +The documentation for the USER-ATC package fix_modify commands +follow at the very end of this manual. diff --git a/doc/src/lammps_tutorials.txt b/doc/src/lammps_tutorials.txt new file mode 100644 index 0000000000..5ceda65b60 --- /dev/null +++ b/doc/src/lammps_tutorials.txt @@ -0,0 +1,6 @@ + +Tutorials :h2 + +The following pages contain some in-depth tutorials for +selected topics, that did not fit into any other place +in the manual. diff --git a/doc/src/manifolds.txt b/doc/src/manifolds.txt index c9bb1ce57f..36c6caacb7 100644 --- a/doc/src/manifolds.txt +++ b/doc/src/manifolds.txt @@ -6,7 +6,7 @@ :line -Manifolds (surfaces) :h3 +Manifolds (surfaces) :h1 [Overview:] diff --git a/doc/src/pair_lj.txt b/doc/src/pair_lj.txt index 058d54fb59..e297d479bc 100644 --- a/doc/src/pair_lj.txt +++ b/doc/src/pair_lj.txt @@ -32,6 +32,8 @@ pair_style lj/cut/coul/long/omp command :h3 pair_style lj/cut/coul/msm command :h3 pair_style lj/cut/coul/msm/gpu command :h3 pair_style lj/cut/coul/msm/omp command :h3 +pair_style lj/cut/coul/wolf command :h3 +pair_style lj/cut/coul/wolf/omp command :h3 pair_style lj/cut/tip4p/cut command :h3 pair_style lj/cut/tip4p/cut/omp command :h3 pair_style lj/cut/tip4p/long command :h3 @@ -63,6 +65,10 @@ args = list of arguments for a particular style :ul {lj/cut/coul/msm} args = cutoff (cutoff2) cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units) cutoff2 = global cutoff for Coulombic (optional) (distance units) + {lj/cut/coul/wolf} args = alpha cutoff (cutoff2) + alpha = damping parameter (inverse distance units) + cutoff = global cutoff for LJ (and Coulombic if only 2 arg) (distance units) + cutoff2 = global cutoff for Coulombic (optional) (distance units) {lj/cut/tip4p/cut} args = otype htype btype atype qdist cutoff (cutoff2) otype,htype = atom types for TIP4P O and H btype,atype = bond and angle types for TIP4P waters @@ -115,6 +121,10 @@ pair_style lj/cut/tip4p/cut 1 2 7 8 0.15 12.0 10.0 pair_coeff * * 100.0 3.0 pair_coeff 1 1 100.0 3.5 9.0 :pre +pair_style lj/cut/coul/wolf 0.2 5. 10.0 +pair_coeff * * 1.0 1.0 +pair_coeff 1 1 1.0 1.0 2.5 :pre + pair_style lj/cut/tip4p/long 1 2 7 8 0.15 12.0 pair_style lj/cut/tip4p/long 1 2 7 8 0.15 12.0 10.0 pair_coeff * * 100.0 3.0 @@ -179,6 +189,24 @@ that a term is added for the "core/shell model"_Section_howto.html#howto_25 to allow charges on core and shell particles to be separated by r = 0.0. +Style {coul/wolf} adds a Coulombic pairwise interaction via the Wolf +summation method, described in "Wolf"_#Wolf1, given by: + +:c,image(Eqs/pair_coul_wolf.jpg) + +where {alpha} is the damping parameter, and erfc() is the +complementary error-function terms. This potential +is essentially a short-range, spherically-truncated, +charge-neutralized, shifted, pairwise {1/r} summation. With a +manipulation of adding and subtracting a self term (for i = j) to the +first and second term on the right-hand-side, respectively, and a +small enough {alpha} damping parameter, the second term shrinks and +the potential becomes a rapidly-converging real-space summation. With +a long enough cutoff and small enough alpha parameter, the energy and +forces calculated by the Wolf summation method approach those of the +Ewald sum. So it is a means of getting effective long-range +interactions with a short-range potential. + Styles {lj/cut/tip4p/cut} and {lj/cut/tip4p/long} implement the TIP4P water model of "(Jorgensen)"_#Jorgensen2, which introduces a massless site located a short distance away from the oxygen atom along the diff --git a/doc/src/read_data.txt b/doc/src/read_data.txt index 8c9aa02e22..fd297e36c1 100644 --- a/doc/src/read_data.txt +++ b/doc/src/read_data.txt @@ -15,10 +15,11 @@ read_data file keyword args ... :pre file = name of data file to read in :ulb,l zero or more keyword/arg pairs may be appended :l keyword = {add} or {offset} or {shift} or {extra/atom/types} or {extra/bond/types} or {extra/angle/types} or {extra/dihedral/types} or {extra/improper/types} or {extra/bond/per/atom} or {extra/angle/per/atom} or {extra/dihedral/per/atom} or {extra/improper/per/atom} or {group} or {nocoeff} or {fix} :l - {add} arg = {append} or {Nstart} or {merge} - append = add new atoms with IDs appended to current IDs - Nstart = add new atoms with IDs starting with Nstart - merge = add new atoms with their IDs unchanged + {add} arg = {append} or {IDoffset} or {IDoffset MOLoffset} or {merge} + append = add new atoms with atom IDs appended to current IDs + IDoffset = add new atoms with atom IDs having IDoffset added + MOLoffset = add new atoms with molecule IDs having MOLoffset added (only when molecule IDs are enabled) + merge = add new atoms with their atom IDs (and molecule IDs) unchanged {offset} args = toff boff aoff doff ioff toff = offset to add to atom types boff = offset to add to bond types @@ -120,20 +121,26 @@ boundary, then the atoms may become far apart if the box size grows. This will separate the atoms in the bond, which can lead to "lost" bond atoms or bad dynamics. -The three choices for the {add} argument affect how the IDs of atoms -in the data file are treated. If {append} is specified, atoms in the -data file are added to the current system, with their atom IDs reset -so that an atomID = M in the data file becomes atomID = N+M, where N -is the largest atom ID in the current system. This rule is applied to -all occurrences of atom IDs in the data file, e.g. in the Velocity or -Bonds section. If {Nstart} is specified, then {Nstart} is a numeric -value is given, e.g. 1000, so that an atomID = M in the data file -becomes atomID = 1000+M. If {merge} is specified, the data file atoms +The three choices for the {add} argument affect how the atom IDs and +molecule IDs of atoms in the data file are treated. If {append} is +specified, atoms in the data file are added to the current system, +with their atom IDs reset so that an atomID = M in the data file +becomes atomID = N+M, where N is the largest atom ID in the current +system. This rule is applied to all occurrences of atom IDs in the +data file, e.g. in the Velocity or Bonds section. This is also done +for molecule IDs, if the atom style does support molecule IDs or +they are enabled via fix property/atom. If {IDoffset} is specified, +then {IDoffset} is a numeric value is given, e.g. 1000, so that an +atomID = M in the data file becomes atomID = 1000+M. For systems +with enabled molecule IDs, another numerical argument {MOLoffset} +is required representing the equivalent offset for molecule IDs. +If {merge} is specified, the data file atoms are added to the current system without changing their IDs. They are assumed to merge (without duplication) with the currently defined atoms. It is up to you to insure there are no multiply defined atom IDs, as LAMMPS only performs an incomplete check that this is the case -by insuring the resulting max atomID >= the number of atoms. +by insuring the resulting max atomID >= the number of atoms. For +molecule IDs, there is no check done at all. The {offset} and {shift} keywords can only be used if the {add} keyword is also specified. @@ -547,7 +554,7 @@ charge: atom-ID atom-type q x y z dipole: atom-ID atom-type q x y z mux muy muz dpd: atom-ID atom-type theta x y z edpd: atom-ID atom-type edpd_temp edpd_cv x y z -mdpd: atom-ID atom-type x y z +mdpd: atom-ID atom-type rho x y z tdpd: atom-ID atom-type x y z cc1 cc2 ... ccNspecies electron: atom-ID atom-type q spin eradius x y z ellipsoid: atom-ID atom-type ellipsoidflag density x y z diff --git a/doc/src/tutorial_pylammps.txt b/doc/src/tutorial_pylammps.txt index 52eb6415db..11cddb3cbf 100644 --- a/doc/src/tutorial_pylammps.txt +++ b/doc/src/tutorial_pylammps.txt @@ -6,14 +6,14 @@ :line -PyLammps Tutorial :h1 +PyLammps Tutorial :h3 -Overview :h2 +Overview :h4 PyLammps is a Python wrapper class which can be created on its own or use an existing lammps Python object. It creates a simpler, Python-like interface to @@ -23,16 +23,16 @@ C++ code implementation. Finally, the IPyLammps wrapper builds on top of PyLammps and adds some additional features for IPython integration into IPython notebooks, e.g. for embedded visualization output from dump/image. -Comparison of lammps and PyLammps interfaces :h3 +Comparison of lammps and PyLammps interfaces :h5 -lammps.lammps :h4 +lammps.lammps :h6 uses C-Types direct memory access to native C++ data provides functions to send and receive data to LAMMPS requires knowledge of how LAMMPS internally works (C pointers, etc) :ul -lammps.PyLammps :h4 +lammps.PyLammps :h6 higher-level abstraction built on top of original C-Types interface manipulation of Python objects @@ -41,11 +41,11 @@ shorter, more concise Python better IPython integration, designed for quick prototyping :ul -Quick Start :h2 +Quick Start :h4 -System-wide Installation :h3 +System-wide Installation :h5 -Step 1: Building LAMMPS as a shared library :h4 +Step 1: Building LAMMPS as a shared library :h6 To use LAMMPS inside of Python it has to be compiled as shared library. This library is then loaded by the Python interface. In this example we enable the @@ -60,7 +60,7 @@ make yes-MOLECULE :pre # compile shared library using Makefile make mpi mode=shlib LMP_INC="-DLAMMPS_PNG -DLAMMPS_JPEG -DLAMMPS_FFMPEG -DLAMMPS_EXCEPTIONS" JPG_LIB="-lpng -ljpeg" :pre -Step 2: Installing the LAMMPS Python package :h4 +Step 2: Installing the LAMMPS Python package :h6 PyLammps is part of the lammps Python package. To install it simply install that package into your current Python installation. @@ -71,12 +71,12 @@ python install.py :pre NOTE: Recompiling the shared library requires reinstalling the Python package -Installation inside of a virtualenv :h3 +Installation inside of a virtualenv :h5 You can use virtualenv to create a custom Python environment specifically tuned for your workflow. -Benefits of using a virtualenv :h4 +Benefits of using a virtualenv :h6 isolation of your system Python installation from your development installation installation can happen in your user directory without root access (useful for HPC clusters) @@ -87,7 +87,7 @@ you can even install specific old versions of a package if necessary :ul apt-get install python-virtualenv :pre -Creating a virtualenv with lammps installed :h4 +Creating a virtualenv with lammps installed :h6 # create virtualenv name 'testing' :pre @@ -107,7 +107,7 @@ source testing/bin/activate :pre (testing) deactivate :pre -Creating a new instance of PyLammps :h2 +Creating a new instance of PyLammps :h4 To create a PyLammps object you need to first import the class from the lammps module. By using the default constructor, a new {lammps} instance is created. @@ -121,7 +121,7 @@ from lammps import lammps, PyLammps lmp = lammps() L = PyLammps(ptr=lmp) :pre -Commands :h2 +Commands :h4 Sending a LAMMPS command with the existing library interfaces is done using the command method of the lammps object instance. @@ -155,7 +155,7 @@ them automatically to a final command string. L.region("box block", xlo, xhi, ylo, yhi, zlo, zhi) :pre -System state :h2 +System state :h4 In addition to dispatching commands directly through the PyLammps object, it also provides several properties which allow you to query the system state. @@ -208,7 +208,7 @@ List of groups present in the current system :dd :dle -Working with LAMMPS variables :h2 +Working with LAMMPS variables :h4 LAMMPS variables can be both defined and accessed via the PyLammps interface. @@ -229,7 +229,7 @@ property of this object. print(a.value) a.value = 4 :pre -Retrieving the value of an arbitrary LAMMPS expressions :h2 +Retrieving the value of an arbitrary LAMMPS expressions :h4 LAMMPS expressions can be immediately evaluated by using the eval method. The passed string parameter can be any expression containing global thermo values, @@ -240,7 +240,7 @@ result = L.eval("pe") # potential energy :pre result = L.eval("v_t/2.0") :pre -Accessing atom data :h2 +Accessing atom data :h4 All atoms in the current simulation can be accessed by using the L.atoms list. Each element of this list is an object which exposes its properties (id, type, @@ -263,7 +263,7 @@ L.atoms\[0\].position = (1.0, 0.0) :pre # set position in 3D simulation L.atoms\[0\].position = (1.0, 0.0, 1.) :pre -Evaluating thermo data :h2 +Evaluating thermo data :h4 Each simulation run usually produces thermo output based on system state, computes, fixes or variables. The trajectories of these values can be queried @@ -291,7 +291,7 @@ steps = L.runs\[0\].step ke = L.runs\[0\].ke plt.plot(steps, ke) :pre -Error handling with PyLammps :h2 +Error handling with PyLammps :h4 Compiling the shared library with C++ exception support provides a better error handling experience. Without exceptions the LAMMPS code will terminate the @@ -304,7 +304,7 @@ current LAMMPS process is in an illegal state and must be terminated. It is advised to save your data and terminate the Python instance as quickly as possible. -Using PyLammps in IPython notebooks and Jupyter :h2 +Using PyLammps in IPython notebooks and Jupyter :h4 If the LAMMPS Python package is installed for the same Python interpreter as IPython, you can use PyLammps directly inside of an IPython notebook inside of @@ -320,7 +320,7 @@ Python environment (this assumes you followed the Quick Start instructions): jupyter notebook :pre -IPyLammps Examples :h2 +IPyLammps Examples :h4 Examples of IPython notebooks can be found in the python/examples/pylammps subdirectory. To open these notebooks launch {jupyter notebook} inside this @@ -328,7 +328,7 @@ directory and navigate to one of them. If you compiled and installed a LAMMPS shared library with exceptions, PNG, JPEG and FFMPEG support you should be able to rerun all of these notebooks. -Validating a dihedral potential :h3 +Validating a dihedral potential :h5 This example showcases how an IPython Notebook can be used to compare a simple LAMMPS simulation of a harmonic dihedral potential to its analytical solution. @@ -353,7 +353,7 @@ plot inside the IPython notebook. :c,image(JPG/pylammps_dihedral.jpg) -Running a Monte Carlo relaxation :h3 +Running a Monte Carlo relaxation :h5 This second example shows how to use PyLammps to create a 2D Monte Carlo Relaxation simulation, computing and plotting energy terms and even embedding video output. @@ -424,7 +424,7 @@ The energies of each iteration are collected in a Python list and finally plotte The IPython notebook also shows how to use dump commands and embed video files inside of the IPython notebook. -Using PyLammps and mpi4py (Experimental) :h2 +Using PyLammps and mpi4py (Experimental) :h4 PyLammps can be run in parallel using mpi4py. This python package can be installed using @@ -451,7 +451,7 @@ mpirun -np 4 python melt.py :pre IMPORTANT NOTE: Any command must be executed by all MPI processes. However, evaluations and querying the system state is only available on rank 0. -Feedback and Contributing :h2 +Feedback and Contributing :h4 If you find this Python interface useful, please feel free to provide feedback and ideas on how to improve it to Richard Berger (richard.berger@temple.edu). We also diff --git a/doc/src/variable.txt b/doc/src/variable.txt index e3b7c5de0d..c0851464c3 100644 --- a/doc/src/variable.txt +++ b/doc/src/variable.txt @@ -689,7 +689,7 @@ increase in increments of z, starting at x, until a is reached. At that point the timestep increases in increments of c, from a to b, then after b, increments by z are resumed until y is reached. For any current timestep, the next timestep in the sequence is returned. Thus -if stride(1000,2000,100,1350,1360,1) is used in a variable by the +if stride2(1000,2000,100,1350,1360,1) is used in a variable by the "dump_modify every"_dump_modify.html command, it will generate the sequence of output timesteps: diff --git a/examples/USER/meso/edpd/in.edpd b/examples/USER/meso/edpd/in.edpd index 316099bce3..af1a79d73d 100644 --- a/examples/USER/meso/edpd/in.edpd +++ b/examples/USER/meso/edpd/in.edpd @@ -1,54 +1,54 @@ -######################################################################## -### Heat conduction analog of periodic Poiseuille flow problem ### -### using energy-conserving DPD (eDPD) simulation ### -### ### -### Created : Zhen Li (zhen_li@brown.edu) ### -### Division of Applied Mathematics, Brown University. ### -### ### -### mDPD system setup follows Fig.12 in the publication: ### -### Z. Li, Y.-H. Tang, H. Lei, B. Caswell and G.E. Karniadakis. ### -### "Energy-conserving dissipative particle dynamics with ### -### temperature-dependent properties". J. Comput. Phys., ### -### 2014, 265: 113-127. DOI: 10.1016/j.jcp.2014.02.003 ### -######################################################################## -units lj -dimension 3 -boundary p p p -neighbor 0.2 bin -neigh_modify every 1 delay 0 check yes - -atom_style edpd - -region edpd block -10 10 -10 10 -5 5 units box -create_box 1 edpd -create_atoms 1 random 16000 276438 NULL -mass 1 1.0 -set atom * edpd/temp 1.0 -set atom * edpd/cv 1.0E5 - -pair_style edpd 1.58 9872598 -#pair_coeff 1 1 18.75 4.5 0.41 1.58 1.45E-5 2.0 1.58 -pair_coeff 1 1 18.75 4.5 0.41 1.58 1.41E-5 2.0 1.58 & - power 10.54 -3.66 3.44 -4.10 & - kappa -0.44 -3.21 5.04 0.00 - -compute mythermo all temp -thermo 100 -thermo_modify temp mythermo -thermo_modify flush yes - -velocity all create 1.0 432982 loop local dist gaussian - -fix mvv all mvv/edpd 0.5 -fix upper all edpd/source cuboid 0.0 5.0 0.0 20.0 10.0 10.0 0.01 -fix lower all edpd/source cuboid 0.0 -5.0 0.0 20.0 10.0 10.0 -0.01 - -timestep 0.01 -run 500 -reset_timestep 0 - -compute temp all edpd/temp/atom -compute ccT all chunk/atom bin/1d y 0.0 1.0 -fix stat all ave/chunk 1 500 500 ccT c_temp density/number norm sample file temp.profile - -run 500 +######################################################################## +### Heat conduction analog of periodic Poiseuille flow problem ### +### using energy-conserving DPD (eDPD) simulation ### +### ### +### Created : Zhen Li (zhen_li@brown.edu) ### +### Division of Applied Mathematics, Brown University. ### +### ### +### mDPD system setup follows Fig.12 in the publication: ### +### Z. Li, Y.-H. Tang, H. Lei, B. Caswell and G.E. Karniadakis. ### +### "Energy-conserving dissipative particle dynamics with ### +### temperature-dependent properties". J. Comput. Phys., ### +### 2014, 265: 113-127. DOI: 10.1016/j.jcp.2014.02.003 ### +######################################################################## +units lj +dimension 3 +boundary p p p +neighbor 0.2 bin +neigh_modify every 1 delay 0 check yes + +atom_style edpd + +region edpd block -10 10 -10 10 -5 5 units box +create_box 1 edpd +create_atoms 1 random 16000 276438 NULL +mass 1 1.0 +set atom * edpd/temp 1.0 +set atom * edpd/cv 1.0E5 + +pair_style edpd 1.58 9872598 +#pair_coeff 1 1 18.75 4.5 0.41 1.58 1.45E-5 2.0 1.58 +pair_coeff 1 1 18.75 4.5 0.41 1.58 1.41E-5 2.0 1.58 & + power 10.54 -3.66 3.44 -4.10 & + kappa -0.44 -3.21 5.04 0.00 + +compute mythermo all temp +thermo 100 +thermo_modify temp mythermo +thermo_modify flush yes + +velocity all create 1.0 432982 loop local dist gaussian + +fix mvv all mvv/edpd 0.5 +fix upper all edpd/source cuboid 0.0 5.0 0.0 20.0 10.0 10.0 0.01 +fix lower all edpd/source cuboid 0.0 -5.0 0.0 20.0 10.0 10.0 -0.01 + +timestep 0.01 +run 500 +reset_timestep 0 + +compute temp all edpd/temp/atom +compute ccT all chunk/atom bin/1d y 0.0 1.0 +fix stat all ave/chunk 1 500 500 ccT c_temp density/number norm sample file temp.profile + +run 500 diff --git a/examples/USER/meso/mdpd/in.mdpd b/examples/USER/meso/mdpd/in.mdpd index 201b4a340e..b0740c8227 100644 --- a/examples/USER/meso/mdpd/in.mdpd +++ b/examples/USER/meso/mdpd/in.mdpd @@ -1,52 +1,52 @@ -######################################################################## -#### 3D droplet oscilation using many-body DPD simulation ### -#### ### -#### Created : Zhen Li (zhen_li@brown.edu) ### -#### Division of Applied Mathematics, Brown University. ### -#### ### -#### mDPD parameters follow the choice of the publication: ### -#### Z. Li et al. "Three dimensional flow structures in a moving ### -#### droplet on substrate: a dissipative particle dynamics study" ### -#### Physics of Fluids, 2013, 25: 072103. DOI: 10.1063/1.4812366 ### -######################################################################## -units lj -dimension 3 -boundary p p p -neighbor 0.3 bin -neigh_modify every 1 delay 0 check yes - -atom_style mdpd - -region mdpd block -25 25 -10 10 -10 10 units box -create_box 1 mdpd - -lattice fcc 6 -region film block -20 20 -7.5 7.5 -2.0 2.0 units box -create_atoms 1 region film - -pair_style hybrid/overlay mdpd/rhosum mdpd 1.0 1.0 9872598 -pair_coeff 1 1 mdpd/rhosum 0.75 -pair_coeff 1 1 mdpd -40 25 18.0 1.0 0.75 -mass 1 1.0 - -compute mythermo all temp -thermo 100 -thermo_modify temp mythermo -thermo_modify flush yes - -velocity all create 1.0 38497 loop local dist gaussian - -fix mvv all mvv/dpd - -#dump mydump all atom 100 atom.lammpstrj - -#dump jpg all image 200 image.*.jpg type type zoom 5 adiam 0.5 & -# view 90 90 box no 0 size 600 200 -#dump_modify jpg pad 4 - -#dump avi all movie 200 movie.avi type type zoom 5 adiam 0.5 & -# view 90 90 box no 0 size 600 200 -#dump_modify avi pad 4 - -timestep 0.01 -run 4000 +######################################################################## +#### 3D droplet oscilation using many-body DPD simulation ### +#### ### +#### Created : Zhen Li (zhen_li@brown.edu) ### +#### Division of Applied Mathematics, Brown University. ### +#### ### +#### mDPD parameters follow the choice of the publication: ### +#### Z. Li et al. "Three dimensional flow structures in a moving ### +#### droplet on substrate: a dissipative particle dynamics study" ### +#### Physics of Fluids, 2013, 25: 072103. DOI: 10.1063/1.4812366 ### +######################################################################## +units lj +dimension 3 +boundary p p p +neighbor 0.3 bin +neigh_modify every 1 delay 0 check yes + +atom_style mdpd + +region mdpd block -25 25 -10 10 -10 10 units box +create_box 1 mdpd + +lattice fcc 6 +region film block -20 20 -7.5 7.5 -2.0 2.0 units box +create_atoms 1 region film + +pair_style hybrid/overlay mdpd/rhosum mdpd 1.0 1.0 9872598 +pair_coeff 1 1 mdpd/rhosum 0.75 +pair_coeff 1 1 mdpd -40 25 18.0 1.0 0.75 +mass 1 1.0 + +compute mythermo all temp +thermo 100 +thermo_modify temp mythermo +thermo_modify flush yes + +velocity all create 1.0 38497 loop local dist gaussian + +fix mvv all mvv/dpd + +#dump mydump all atom 100 atom.lammpstrj + +#dump jpg all image 200 image.*.jpg type type zoom 5 adiam 0.5 & +# view 90 90 box no 0 size 600 200 +#dump_modify jpg pad 4 + +#dump avi all movie 200 movie.avi type type zoom 5 adiam 0.5 & +# view 90 90 box no 0 size 600 200 +#dump_modify avi pad 4 + +timestep 0.01 +run 4000 diff --git a/examples/USER/meso/tdpd/in.tdpd b/examples/USER/meso/tdpd/in.tdpd index 748a4f5077..5107e7a454 100644 --- a/examples/USER/meso/tdpd/in.tdpd +++ b/examples/USER/meso/tdpd/in.tdpd @@ -1,54 +1,54 @@ -######################################################################## -### Pure diffusion with a reaction source term analog of a periodic ### -### Poiseuille flow problem using transport DPD (tDPD) simulation ### -### ### -### Created : Zhen Li (zhen_li@brown.edu) ### -### Division of Applied Mathematics, Brown University. ### -### ### -### tDPD system setup follows Fig.1 in the publication: ### -### Z. Li, A. Yazdani, A. Tartakovsky and G.E. Karniadakis. ### -### "Transport dissipative particle dynamics model for mesoscopic ### -### advection-diffusion-reaction problems. J. Chem. Phys., ### -### 2015, 143: 014101. DOI: 10.1063/1.4923254 ### -######################################################################## -units lj -dimension 3 -boundary p p p -neighbor 0.2 bin -neigh_modify every 1 delay 0 check yes - -atom_style tdpd 2 - -region tdpd block -10 10 -10 10 -5 5 units box -create_box 1 tdpd -create_atoms 1 random 16000 276438 NULL -mass 1 1.0 -set atom * cc 1 1.0 -set atom * cc 2 1.0 - -pair_style tdpd 1.0 1.58 9872598 -pair_coeff 1 1 18.75 4.5 0.41 1.58 1.58 1.0 1.0E-5 2.0 3.0 1.0E-5 2.0 - -compute mythermo all temp -thermo 50 -thermo_modify temp mythermo -thermo_modify flush yes - -velocity all create 1.0 432982 loop local dist gaussian - -fix mvv all mvv/tdpd 0.5 -fix upper1 all tdpd/source 1 cuboid 0.0 5.0 0.0 20.0 10.0 10.0 0.01 -fix lower1 all tdpd/source 1 cuboid 0.0 -5.0 0.0 20.0 10.0 10.0 -0.01 -fix upper2 all tdpd/source 2 cuboid 0.0 5.0 0.0 20.0 10.0 10.0 -0.01 -fix lower2 all tdpd/source 2 cuboid 0.0 -5.0 0.0 20.0 10.0 10.0 0.01 - -timestep 0.01 -run 500 -reset_timestep 0 - -compute cc1 all tdpd/cc/atom 1 -compute cc2 all tdpd/cc/atom 2 -compute bin all chunk/atom bin/1d y 0.0 1.0 -fix stat all ave/chunk 1 100 100 bin c_cc1 c_cc2 norm sample file cc.profile - -run 100 +######################################################################## +### Pure diffusion with a reaction source term analog of a periodic ### +### Poiseuille flow problem using transport DPD (tDPD) simulation ### +### ### +### Created : Zhen Li (zhen_li@brown.edu) ### +### Division of Applied Mathematics, Brown University. ### +### ### +### tDPD system setup follows Fig.1 in the publication: ### +### Z. Li, A. Yazdani, A. Tartakovsky and G.E. Karniadakis. ### +### "Transport dissipative particle dynamics model for mesoscopic ### +### advection-diffusion-reaction problems. J. Chem. Phys., ### +### 2015, 143: 014101. DOI: 10.1063/1.4923254 ### +######################################################################## +units lj +dimension 3 +boundary p p p +neighbor 0.2 bin +neigh_modify every 1 delay 0 check yes + +atom_style tdpd 2 + +region tdpd block -10 10 -10 10 -5 5 units box +create_box 1 tdpd +create_atoms 1 random 16000 276438 NULL +mass 1 1.0 +set atom * cc 1 1.0 +set atom * cc 2 1.0 + +pair_style tdpd 1.0 1.58 9872598 +pair_coeff 1 1 18.75 4.5 0.41 1.58 1.58 1.0 1.0E-5 2.0 3.0 1.0E-5 2.0 + +compute mythermo all temp +thermo 50 +thermo_modify temp mythermo +thermo_modify flush yes + +velocity all create 1.0 432982 loop local dist gaussian + +fix mvv all mvv/tdpd 0.5 +fix upper1 all tdpd/source 1 cuboid 0.0 5.0 0.0 20.0 10.0 10.0 0.01 +fix lower1 all tdpd/source 1 cuboid 0.0 -5.0 0.0 20.0 10.0 10.0 -0.01 +fix upper2 all tdpd/source 2 cuboid 0.0 5.0 0.0 20.0 10.0 10.0 -0.01 +fix lower2 all tdpd/source 2 cuboid 0.0 -5.0 0.0 20.0 10.0 10.0 0.01 + +timestep 0.01 +run 500 +reset_timestep 0 + +compute cc1 all tdpd/cc/atom 1 +compute cc2 all tdpd/cc/atom 2 +compute bin all chunk/atom bin/1d y 0.0 1.0 +fix stat all ave/chunk 1 100 100 bin c_cc1 c_cc2 norm sample file cc.profile + +run 100 diff --git a/examples/USER/mgpt/log.lammps b/examples/USER/mgpt/log.lammps deleted file mode 100644 index 9485c36e47..0000000000 --- a/examples/USER/mgpt/log.lammps +++ /dev/null @@ -1,78 +0,0 @@ -LAMMPS (23 Oct 2015) -# script for mgpt t=0 eos with relaxed vacancy in bcc structure: -# input for relaxed vacancy formation energy at constant pressure - -echo screen -Lattice spacing in x,y,z = 6.23812 6.23812 6.23812 -Created orthogonal box = (0 0 0) to (31.1906 31.1906 31.1906) - 1 by 1 by 1 MPI processor grid -Created 250 atoms -Deleted 1 atoms, new total = 249 -Reading potential file Ta6.8x.mgpt.potin with DATE: 2015-07-30 -Neighbor list info ... - 2 neighbor list requests - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 13.1712 - ghost atom cutoff = 13.1712 - binsize = 6.58562 -> bins = 5 5 5 -Memory usage per processor = 4.66978 Mbytes -Step Volume Temp PotEng TotEng Press - 0 30343.887 0 -73.994511 -73.994511 -1.0504398e+09 - 10 30343.887 0 -74.002332 -74.002332 -1.107516e+09 - 20 30343.887 0 -74.00485 -74.00485 -1.1316373e+09 - 30 30343.887 0 -74.005762 -74.005762 -1.143304e+09 - 40 30343.887 0 -74.006116 -74.006116 -1.149395e+09 - 50 30343.887 0 -74.006262 -74.006262 -1.1527914e+09 - 60 30343.887 0 -74.006323 -74.006323 -1.1547677e+09 - 70 30343.887 0 -74.00635 -74.00635 -1.1559529e+09 - 80 30343.887 0 -74.006361 -74.006361 -1.1566763e+09 - 90 30343.887 0 -74.006366 -74.006366 -1.1571256e+09 - 100 30343.887 0 -74.006369 -74.006369 -1.1574093e+09 - 110 30343.887 0 -74.00637 -74.00637 -1.1575908e+09 - 120 30343.887 0 -74.00637 -74.00637 -1.1577083e+09 - 130 30343.887 0 -74.00637 -74.00637 -1.1577849e+09 - 139 30343.887 0 -74.006371 -74.006371 -1.1578311e+09 -Loop time of 4.33109 on 1 procs for 139 steps with 249 atoms - -92.4% CPU use with 1 MPI tasks x no OpenMP threads - -Minimization stats: - Stopping criterion = energy tolerance - Energy initial, next-to-last, final = - -73.9945109564 -74.0063705487 -74.0063705557 - Force two-norm initial, final = 0.0366227 8.09081e-05 - Force max component initial, final = 0.00730948 8.05242e-06 - Final line search alpha, max atom move = 1 8.05242e-06 - Iterations, force evaluations = 139 139 - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 4.3064 | 4.3064 | 4.3064 | 0.0 | 99.43 -Neigh | 0.019113 | 0.019113 | 0.019113 | 0.0 | 0.44 -Comm | 0.0017624 | 0.0017624 | 0.0017624 | 0.0 | 0.04 -Output | 0.00084376 | 0.00084376 | 0.00084376 | 0.0 | 0.02 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0.00297 | | | 0.07 - -Nlocal: 249 ave 249 max 249 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 1479 ave 1479 max 1479 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 7936 ave 7936 max 7936 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 15872 ave 15872 max 15872 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 15872 -Ave neighs/atom = 63.743 -Neighbor list builds = 4 -Dangerous builds = 0 -number of atoms = 249 -atomic volume (a.u.) = 121.863 -total energy (ry/atom) = -0.594428679162064 -pressure (gpa) = -1.15783109519801 -249 121.863 -148.012741111354 -1.15783109519801 -121.863 -0.594428679162064 -1.15783109519801 -Total wall time: 0:00:04 diff --git a/examples/gcmc/in.gcmc.co2 b/examples/gcmc/in.gcmc.co2 index 128f05b489..bb6916fc48 100644 --- a/examples/gcmc/in.gcmc.co2 +++ b/examples/gcmc/in.gcmc.co2 @@ -58,21 +58,21 @@ timestep 1.0 # rigid constraints with thermostat -fix myrigidnvt all rigid/nvt/small molecule temp ${temp} ${temp} 100 mol co2mol +fix myrigidnvt co2 rigid/nvt/small molecule temp ${temp} ${temp} 100 mol co2mol fix_modify myrigidnvt dynamic/dof no # gcmc variable tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans) -fix mygcmc all gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol & +fix mygcmc co2 gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol & co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt # atom counts variable carbon atom "type==1" variable oxygen atom "type==2" -group carbon dynamic all var carbon -group oxygen dynamic all var oxygen +group carbon dynamic co2 var carbon +group oxygen dynamic co2 var oxygen variable nC equal count(carbon) variable nO equal count(oxygen) diff --git a/examples/gcmc/in.gcmc.lj b/examples/gcmc/in.gcmc.lj index 3fe78efb25..a1c7c6eb10 100644 --- a/examples/gcmc/in.gcmc.lj +++ b/examples/gcmc/in.gcmc.lj @@ -29,14 +29,18 @@ create_box 1 box pair_coeff * * 1.0 1.0 mass * 1.0 +# we recommend setting up a dedicated group for gcmc + +group gcmcgroup type 1 + # gcmc -fix mygcmc all gcmc 1 100 100 1 29494 ${temp} ${mu} ${disp} +fix mygcmc gcmcgroup gcmc 1 100 100 1 29494 ${temp} ${mu} ${disp} # atom count variable type1 atom "type==1" -group type1 dynamic all var type1 +group type1 dynamic gcmcgroup var type1 variable n1 equal count(type1) # averaging diff --git a/examples/latte/latte.in b/examples/latte/latte.in index 7df354a742..b8b214b78b 100644 --- a/examples/latte/latte.in +++ b/examples/latte/latte.in @@ -12,7 +12,7 @@ CONTROL{ xControl= 1 BASISTYPE= NONORTHO COORDSFILE= "./coords.dat" - PARAMPATH= "/home/user/LATTE/TBparam" + PARAMPATH= "./TBparam" KBT= 0.0 ENTROPYKIND= 1 PPOTON= 1 diff --git a/lib/colvars/colvar.cpp b/lib/colvars/colvar.cpp index ce76b3b9eb..5a4e8b617a 100644 --- a/lib/colvars/colvar.cpp +++ b/lib/colvars/colvar.cpp @@ -195,7 +195,7 @@ int colvar::init(std::string const &conf) // - it is homogeneous // - all cvcs are periodic // - all cvcs have the same period - if (cvcs[0]->b_periodic) { // TODO make this a CVC feature + if (is_enabled(f_cv_homogeneous) && cvcs[0]->b_periodic) { // TODO make this a CVC feature bool b_periodic = true; period = cvcs[0]->period; for (i = 1; i < cvcs.size(); i++) { diff --git a/lib/colvars/colvar.h b/lib/colvars/colvar.h index 20dad2771b..32c329460d 100644 --- a/lib/colvars/colvar.h +++ b/lib/colvars/colvar.h @@ -11,8 +11,6 @@ #define COLVAR_H #include
-#include
-#include
#include "colvarmodule.h"
#include "colvarvalue.h"
@@ -60,10 +58,13 @@ public:
/// \brief Current actual value (not extended DOF)
colvarvalue const & actual_value() const;
-
+
+ /// \brief Current running average (if calculated as set by analysis flag)
+ colvarvalue const & run_ave() const;
+
/// \brief Force constant of the spring
cvm::real const & force_constant() const;
-
+
/// \brief Current velocity (previously set by calc() or by read_traj())
colvarvalue const & velocity() const;
@@ -516,7 +517,7 @@ public:
// collective variable component base class
class cvc;
- // currently available collective variable components
+ // list of available collective variable components
// scalar colvar components
class distance;
@@ -611,12 +612,15 @@ inline colvarvalue const & colvar::value() const
return x_reported;
}
-
inline colvarvalue const & colvar::actual_value() const
{
return x;
}
+inline colvarvalue const & colvar::run_ave() const
+{
+ return runave;
+}
inline colvarvalue const & colvar::velocity() const
{
diff --git a/lib/colvars/colvar_UIestimator.h b/lib/colvars/colvar_UIestimator.h
index 7fc7f870a1..36ed938119 100644
--- a/lib/colvars/colvar_UIestimator.h
+++ b/lib/colvars/colvar_UIestimator.h
@@ -45,7 +45,7 @@ namespace UIestimator {
this->width = width;
this->dimension = lowerboundary.size();
this->y_size = y_size; // keep in mind the internal (spare) matrix is stored in diagonal form
- this->y_total_size = int(pow(double(y_size), dimension) + EPSILON);
+ this->y_total_size = int(std::pow(double(y_size), double(dimension)) + EPSILON);
// the range of the matrix is [lowerboundary, upperboundary]
x_total_size = 1;
@@ -121,7 +121,7 @@ namespace UIestimator {
int index = 0;
for (i = 0; i < dimension; i++) {
if (i + 1 < dimension)
- index += temp[i] * int(pow(double(y_size), dimension - i - 1) + EPSILON);
+ index += temp[i] * int(std::pow(double(y_size), double(dimension - i - 1)) + EPSILON);
else
index += temp[i];
}
diff --git a/lib/colvars/colvaratoms.cpp b/lib/colvars/colvaratoms.cpp
index d2a0f0a807..1be6f42e59 100644
--- a/lib/colvars/colvaratoms.cpp
+++ b/lib/colvars/colvaratoms.cpp
@@ -8,9 +8,11 @@
// Colvars repository at GitHub.
#include "colvarmodule.h"
+#include "colvarproxy.h"
#include "colvarparse.h"
#include "colvaratoms.h"
+
cvm::atom::atom()
{
index = -1;
diff --git a/lib/colvars/colvaratoms.h b/lib/colvars/colvaratoms.h
index 71c587e230..0dda6ab792 100644
--- a/lib/colvars/colvaratoms.h
+++ b/lib/colvars/colvaratoms.h
@@ -11,6 +11,7 @@
#define COLVARATOMS_H
#include "colvarmodule.h"
+#include "colvarproxy.h"
#include "colvarparse.h"
#include "colvardeps.h"
diff --git a/lib/colvars/colvarbias.cpp b/lib/colvars/colvarbias.cpp
index 301e83e730..29620fbee8 100644
--- a/lib/colvars/colvarbias.cpp
+++ b/lib/colvars/colvarbias.cpp
@@ -8,6 +8,7 @@
// Colvars repository at GitHub.
#include "colvarmodule.h"
+#include "colvarproxy.h"
#include "colvarvalue.h"
#include "colvarbias.h"
#include "colvargrid.h"
diff --git a/lib/colvars/colvarbias_abf.cpp b/lib/colvars/colvarbias_abf.cpp
index e4aea8eb86..b3b5b3eb16 100644
--- a/lib/colvars/colvarbias_abf.cpp
+++ b/lib/colvars/colvarbias_abf.cpp
@@ -8,6 +8,7 @@
// Colvars repository at GitHub.
#include "colvarmodule.h"
+#include "colvarproxy.h"
#include "colvar.h"
#include "colvarbias_abf.h"
@@ -18,16 +19,18 @@ colvarbias_abf::colvarbias_abf(char const *key)
b_CZAR_estimator(false),
system_force(NULL),
gradients(NULL),
+ pmf(NULL),
samples(NULL),
z_gradients(NULL),
z_samples(NULL),
czar_gradients(NULL),
+ czar_pmf(NULL),
last_gradients(NULL),
- last_samples(NULL)
+ last_samples(NULL),
+ pabf_freq(0)
{
}
-
int colvarbias_abf::init(std::string const &conf)
{
colvarbias::init(conf);
@@ -91,7 +94,7 @@ int colvarbias_abf::init(std::string const &conf)
// ************* checking the associated colvars *******************
- if (colvars.size() == 0) {
+ if (num_variables() == 0) {
cvm::error("Error: no collective variables specified for the ABF bias.\n");
return COLVARS_ERROR;
}
@@ -102,7 +105,8 @@ int colvarbias_abf::init(std::string const &conf)
}
bool b_extended = false;
- for (size_t i = 0; i < colvars.size(); i++) {
+ size_t i;
+ for (i = 0; i < num_variables(); i++) {
if (colvars[i]->value().type() != colvarvalue::type_scalar) {
cvm::error("Error: ABF bias can only use scalar-type variables.\n");
@@ -132,10 +136,10 @@ int colvarbias_abf::init(std::string const &conf)
}
if (get_keyval(conf, "maxForce", max_force)) {
- if (max_force.size() != colvars.size()) {
+ if (max_force.size() != num_variables()) {
cvm::error("Error: Number of parameters to maxForce does not match number of colvars.");
}
- for (size_t i = 0; i < colvars.size(); i++) {
+ for (i = 0; i < num_variables(); i++) {
if (max_force[i] < 0.0) {
cvm::error("Error: maxForce should be non-negative.");
}
@@ -145,9 +149,9 @@ int colvarbias_abf::init(std::string const &conf)
cap_force = false;
}
- bin.assign(colvars.size(), 0);
- force_bin.assign(colvars.size(), 0);
- system_force = new cvm::real [colvars.size()];
+ bin.assign(num_variables(), 0);
+ force_bin.assign(num_variables(), 0);
+ system_force = new cvm::real [num_variables()];
// Construct empty grids based on the colvars
if (cvm::debug()) {
@@ -159,14 +163,14 @@ int colvarbias_abf::init(std::string const &conf)
gradients->samples = samples;
samples->has_parent_data = true;
- // Data for eABF z-based estimator
- if (b_extended) {
+ // Data for eAB F z-based estimator
+ if ( b_extended ) {
get_keyval(conf, "CZARestimator", b_CZAR_estimator, true);
// CZAR output files for stratified eABF
get_keyval(conf, "writeCZARwindowFile", b_czar_window_file, false,
colvarparse::parse_silent);
- z_bin.assign(colvars.size(), 0);
+ z_bin.assign(num_variables(), 0);
z_samples = new colvar_grid_count(colvars);
z_samples->request_actual_value();
z_gradients = new colvar_grid_gradient(colvars);
@@ -176,6 +180,27 @@ int colvarbias_abf::init(std::string const &conf)
czar_gradients = new colvar_grid_gradient(colvars);
}
+ // For now, we integrate on-the-fly iff the grid is < 3D
+ if ( num_variables() <= 3 ) {
+ pmf = new integrate_potential(colvars, gradients);
+ if ( b_CZAR_estimator ) {
+ czar_pmf = new integrate_potential(colvars, czar_gradients);
+ }
+ get_keyval(conf, "integrate", b_integrate, true); // Integrate for output
+ if ( num_variables() > 1 ) {
+ // Projected ABF
+ get_keyval(conf, "pABFintegrateFreq", pabf_freq, 0);
+ // Parameters for integrating initial (and final) gradient data
+ get_keyval(conf, "integrateInitSteps", integrate_initial_steps, 1e4);
+ get_keyval(conf, "integrateInitTol", integrate_initial_tol, 1e-6);
+ // for updating the integrated PMF on the fly
+ get_keyval(conf, "integrateSteps", integrate_steps, 100);
+ get_keyval(conf, "integrateTol", integrate_tol, 1e-4);
+ }
+ } else {
+ b_integrate = false;
+ }
+
// For shared ABF, we store a second set of grids.
// This used to be only if "shared" was defined,
// but now we allow calling share externally (e.g. from Tcl).
@@ -188,6 +213,8 @@ int colvarbias_abf::init(std::string const &conf)
// If custom grids are provided, read them
if ( input_prefix.size() > 0 ) {
read_gradients_samples();
+ // Update divergence to account for input data
+ pmf->set_div();
}
// if extendedLangrangian is on, then call UI estimator
@@ -202,7 +229,7 @@ int colvarbias_abf::init(std::string const &conf)
bool UI_restart = (input_prefix.size() > 0);
- for (size_t i = 0; i < colvars.size(); i++)
+ for (i = 0; i < num_variables(); i++)
{
UI_lowerboundary.push_back(colvars[i]->lower_boundary);
UI_upperboundary.push_back(colvars[i]->upper_boundary);
@@ -238,6 +265,11 @@ colvarbias_abf::~colvarbias_abf()
gradients = NULL;
}
+ if (pmf) {
+ delete pmf;
+ pmf = NULL;
+ }
+
if (z_samples) {
delete z_samples;
z_samples = NULL;
@@ -253,6 +285,11 @@ colvarbias_abf::~colvarbias_abf()
czar_gradients = NULL;
}
+ if (czar_pmf) {
+ delete czar_pmf;
+ czar_pmf = NULL;
+ }
+
// shared ABF
// We used to only do this if "shared" was defined,
// but now we can call shared externally
@@ -278,44 +315,48 @@ colvarbias_abf::~colvarbias_abf()
int colvarbias_abf::update()
{
+ int iter;
+
if (cvm::debug()) cvm::log("Updating ABF bias " + this->name);
- if (cvm::step_relative() == 0) {
+ size_t i;
+ for (i = 0; i < num_variables(); i++) {
+ bin[i] = samples->current_bin_scalar(i);
+ }
+ if (cvm::proxy->total_forces_same_step()) {
+ // e.g. in LAMMPS, total forces are current
+ force_bin = bin;
+ }
- // At first timestep, do only:
- // initialization stuff (file operations relying on n_abf_biases
- // compute current value of colvars
+ if (cvm::step_relative() > 0 || cvm::proxy->total_forces_same_step()) {
- for (size_t i = 0; i < colvars.size(); i++) {
- bin[i] = samples->current_bin_scalar(i);
- }
+ if (update_bias) {
+// if (b_adiabatic_reweighting) {
+// // Update gradients non-locally based on conditional distribution of
+// // fictitious variable TODO
+//
+// } else
+ if (samples->index_ok(force_bin)) {
+ // Only if requested and within bounds of the grid...
- } else {
-
- for (size_t i = 0; i < colvars.size(); i++) {
- bin[i] = samples->current_bin_scalar(i);
- }
-
- if ( update_bias && samples->index_ok(force_bin) ) {
- // Only if requested and within bounds of the grid...
-
- for (size_t i = 0; i < colvars.size(); i++) {
- // get total forces (lagging by 1 timestep) from colvars
- // and subtract previous ABF force if necessary
- update_system_force(i);
+ for (i = 0; i < num_variables(); i++) {
+ // get total forces (lagging by 1 timestep) from colvars
+ // and subtract previous ABF force if necessary
+ update_system_force(i);
+ }
+ gradients->acc_force(force_bin, system_force);
+ if ( b_integrate ) {
+ pmf->update_div_neighbors(force_bin);
+ }
}
- if (cvm::proxy->total_forces_same_step()) {
- // e.g. in LAMMPS, total forces are current
- force_bin = bin;
- }
- gradients->acc_force(force_bin, system_force);
}
+
if ( z_gradients && update_bias ) {
- for (size_t i = 0; i < colvars.size(); i++) {
+ for (i = 0; i < num_variables(); i++) {
z_bin[i] = z_samples->current_bin_scalar(i);
}
if ( z_samples->index_ok(z_bin) ) {
- for (size_t i = 0; i < colvars.size(); i++) {
+ for (i = 0; i < num_variables(); i++) {
// If we are outside the range of xi, the force has not been obtained above
// the function is just an accessor, so cheap to call again anyway
update_system_force(i);
@@ -323,6 +364,14 @@ int colvarbias_abf::update()
z_gradients->acc_force(z_bin, system_force);
}
}
+
+ if ( b_integrate ) {
+ if ( pabf_freq && cvm::step_relative() % pabf_freq == 0 ) {
+ cvm::real err;
+ iter = pmf->integrate(integrate_steps, integrate_tol, err);
+ pmf->set_zero_minimum(); // TODO: do this only when necessary
+ }
+ }
}
if (!cvm::proxy->total_forces_same_step()) {
@@ -332,14 +381,14 @@ int colvarbias_abf::update()
}
// Reset biasing forces from previous timestep
- for (size_t i = 0; i < colvars.size(); i++) {
+ for (i = 0; i < num_variables(); i++) {
colvar_forces[i].reset();
}
// Compute and apply the new bias, if applicable
if (is_enabled(f_cvb_apply_force) && samples->index_ok(bin)) {
- size_t count = samples->value(bin);
+ cvm::real count = samples->value(bin);
cvm::real fact = 1.0;
// Factor that ensures smooth introduction of the force
@@ -348,21 +397,34 @@ int colvarbias_abf::update()
(cvm::real(count - min_samples)) / (cvm::real(full_samples - min_samples));
}
- const cvm::real * grad = &(gradients->value(bin));
+ std::vector grad(num_variables());
+ if ( pabf_freq ) {
+ // In projected ABF, the force is the PMF gradient estimate
+ pmf->vector_gradient_finite_diff(bin, grad);
+ } else {
+ // Normal ABF
+ gradients->vector_value(bin, grad);
+ }
+
+// if ( b_adiabatic_reweighting) {
+// // Average of force according to conditional distribution of fictitious variable
+// // need freshly integrated PMF, gradient TODO
+// } else
if ( fact != 0.0 ) {
- if ( (colvars.size() == 1) && colvars[0]->periodic_boundaries() ) {
+ if ( (num_variables() == 1) && colvars[0]->periodic_boundaries() ) {
// Enforce a zero-mean bias on periodic, 1D coordinates
// in other words: boundary condition is that the biasing potential is periodic
- colvar_forces[0].real_value = fact * (grad[0] / cvm::real(count) - gradients->average());
+ // This is enforced naturally if using integrated PMF
+ colvar_forces[0].real_value = fact * (grad[0] - gradients->average ());
} else {
- for (size_t i = 0; i < colvars.size(); i++) {
+ for (size_t i = 0; i < num_variables(); i++) {
// subtracting the mean force (opposite of the FE gradient) means adding the gradient
- colvar_forces[i].real_value = fact * grad[i] / cvm::real(count);
+ colvar_forces[i].real_value = fact * grad[i];
}
}
if (cap_force) {
- for (size_t i = 0; i < colvars.size(); i++) {
+ for (size_t i = 0; i < num_variables(); i++) {
if ( colvar_forces[i].real_value * colvar_forces[i].real_value > max_force[i] * max_force[i] ) {
colvar_forces[i].real_value = (colvar_forces[i].real_value > 0 ? max_force[i] : -1.0 * max_force[i]);
}
@@ -407,9 +469,9 @@ int colvarbias_abf::update()
// update UI estimator every step
if (b_UI_estimator)
{
- std::vector x(colvars.size(),0);
- std::vector y(colvars.size(),0);
- for (size_t i = 0; i < colvars.size(); i++)
+ std::vector x(num_variables(),0);
+ std::vector y(num_variables(),0);
+ for (size_t i = 0; i < num_variables(); i++)
{
x[i] = colvars[i]->actual_value();
y[i] = colvars[i]->value();
@@ -509,26 +571,60 @@ void colvarbias_abf::write_gradients_samples(const std::string &prefix, bool app
cvm::proxy->output_stream(samples_out_name, mode);
if (!samples_os) {
cvm::error("Error opening ABF samples file " + samples_out_name + " for writing");
+ return;
}
samples->write_multicol(*samples_os);
cvm::proxy->close_output_stream(samples_out_name);
+ // In dimension higher than 2, dx is easier to handle and visualize
+ if (num_variables() > 2) {
+ std::string samples_dx_out_name = prefix + ".count.dx";
+ std::ostream *samples_dx_os = cvm::proxy->output_stream(samples_dx_out_name, mode);
+ if (!samples_os) {
+ cvm::error("Error opening samples file " + samples_dx_out_name + " for writing");
+ return;
+ }
+ samples->write_opendx(*samples_dx_os);
+ *samples_dx_os << std::endl;
+ cvm::proxy->close_output_stream(samples_dx_out_name);
+ }
+
std::ostream *gradients_os =
cvm::proxy->output_stream(gradients_out_name, mode);
if (!gradients_os) {
cvm::error("Error opening ABF gradient file " + gradients_out_name + " for writing");
+ return;
}
gradients->write_multicol(*gradients_os);
cvm::proxy->close_output_stream(gradients_out_name);
- if (colvars.size() == 1) {
- // Do numerical integration and output a PMF
+ if (b_integrate) {
+ // Do numerical integration (to high precision) and output a PMF
+ cvm::real err;
+ pmf->integrate(integrate_initial_steps, integrate_initial_tol, err);
+ pmf->set_zero_minimum();
+
std::string pmf_out_name = prefix + ".pmf";
std::ostream *pmf_os = cvm::proxy->output_stream(pmf_out_name, mode);
if (!pmf_os) {
cvm::error("Error opening pmf file " + pmf_out_name + " for writing");
+ return;
}
- gradients->write_1D_integral(*pmf_os);
+ pmf->write_multicol(*pmf_os);
+
+ // In dimension higher than 2, dx is easier to handle and visualize
+ if (num_variables() > 2) {
+ std::string pmf_dx_out_name = prefix + ".pmf.dx";
+ std::ostream *pmf_dx_os = cvm::proxy->output_stream(pmf_dx_out_name, mode);
+ if (!pmf_dx_os) {
+ cvm::error("Error opening pmf file " + pmf_dx_out_name + " for writing");
+ return;
+ }
+ pmf->write_opendx(*pmf_dx_os);
+ *pmf_dx_os << std::endl;
+ cvm::proxy->close_output_stream(pmf_dx_out_name);
+ }
+
*pmf_os << std::endl;
cvm::proxy->close_output_stream(pmf_out_name);
}
@@ -542,6 +638,7 @@ void colvarbias_abf::write_gradients_samples(const std::string &prefix, bool app
cvm::proxy->output_stream(z_samples_out_name, mode);
if (!z_samples_os) {
cvm::error("Error opening eABF z-histogram file " + z_samples_out_name + " for writing");
+ return;
}
z_samples->write_multicol(*z_samples_os);
cvm::proxy->close_output_stream(z_samples_out_name);
@@ -553,6 +650,7 @@ void colvarbias_abf::write_gradients_samples(const std::string &prefix, bool app
cvm::proxy->output_stream(z_gradients_out_name, mode);
if (!z_gradients_os) {
cvm::error("Error opening eABF z-gradient file " + z_gradients_out_name + " for writing");
+ return;
}
z_gradients->write_multicol(*z_gradients_os);
cvm::proxy->close_output_stream(z_gradients_out_name);
@@ -563,8 +661,7 @@ void colvarbias_abf::write_gradients_samples(const std::string &prefix, bool app
czar_gradients->index_ok(ix); czar_gradients->incr(ix)) {
for (size_t n = 0; n < czar_gradients->multiplicity(); n++) {
czar_gradients->set_value(ix, z_gradients->value_output(ix, n)
- - cvm::temperature() * cvm::boltzmann() * z_samples->log_gradient_finite_diff(ix, n),
- n);
+ - cvm::temperature() * cvm::boltzmann() * z_samples->log_gradient_finite_diff(ix, n), n);
}
}
@@ -574,17 +671,39 @@ void colvarbias_abf::write_gradients_samples(const std::string &prefix, bool app
cvm::proxy->output_stream(czar_gradients_out_name, mode);
if (!czar_gradients_os) {
cvm::error("Error opening CZAR gradient file " + czar_gradients_out_name + " for writing");
+ return;
}
czar_gradients->write_multicol(*czar_gradients_os);
cvm::proxy->close_output_stream(czar_gradients_out_name);
- if (colvars.size() == 1) {
- // Do numerical integration and output a PMF
+ if (b_integrate) {
+ // Do numerical integration (to high precision) and output a PMF
+ cvm::real err;
+ czar_pmf->set_div();
+ czar_pmf->integrate(integrate_initial_steps, integrate_initial_tol, err);
+ czar_pmf->set_zero_minimum();
+
std::string czar_pmf_out_name = prefix + ".czar.pmf";
- std::ostream *czar_pmf_os =
- cvm::proxy->output_stream(czar_pmf_out_name, mode);
- if (!czar_pmf_os) cvm::error("Error opening CZAR pmf file " + czar_pmf_out_name + " for writing");
- czar_gradients->write_1D_integral(*czar_pmf_os);
+ std::ostream *czar_pmf_os = cvm::proxy->output_stream(czar_pmf_out_name, mode);
+ if (!czar_pmf_os) {
+ cvm::error("Error opening CZAR pmf file " + czar_pmf_out_name + " for writing");
+ return;
+ }
+ czar_pmf->write_multicol(*czar_pmf_os);
+
+ // In dimension higher than 2, dx is easier to handle and visualize
+ if (num_variables() > 2) {
+ std::string czar_pmf_dx_out_name = prefix + ".czar.pmf.dx";
+ std::ostream *czar_pmf_dx_os = cvm::proxy->output_stream(czar_pmf_dx_out_name, mode);
+ if (!czar_pmf_dx_os) {
+ cvm::error("Error opening CZAR pmf file " + czar_pmf_dx_out_name + " for writing");
+ return;
+ }
+ czar_pmf->write_opendx(*czar_pmf_dx_os);
+ *czar_pmf_dx_os << std::endl;
+ cvm::proxy->close_output_stream(czar_pmf_dx_out_name);
+ }
+
*czar_pmf_os << std::endl;
cvm::proxy->close_output_stream(czar_pmf_out_name);
}
@@ -708,6 +827,10 @@ std::istream & colvarbias_abf::read_state_data(std::istream& is)
if (! gradients->read_raw(is)) {
return is;
}
+ if (b_integrate) {
+ // Update divergence to account for restart data
+ pmf->set_div();
+ }
if (b_CZAR_estimator) {
diff --git a/lib/colvars/colvarbias_abf.h b/lib/colvars/colvarbias_abf.h
index 1defe72268..0260401292 100644
--- a/lib/colvars/colvarbias_abf.h
+++ b/lib/colvars/colvarbias_abf.h
@@ -40,28 +40,44 @@ private:
/// Base filename(s) for reading previous gradient data (replaces data from restart file)
std::vector input_prefix;
- bool update_bias;
- bool hide_Jacobian;
- size_t full_samples;
- size_t min_samples;
+ bool update_bias;
+ bool hide_Jacobian;
+ bool b_integrate;
+
+ size_t full_samples;
+ size_t min_samples;
/// frequency for updating output files
- int output_freq;
+ int output_freq;
/// Write combined files with a history of all output data?
- bool b_history_files;
+ bool b_history_files;
/// Write CZAR output file for stratified eABF (.zgrad)
- bool b_czar_window_file;
- size_t history_freq;
+ bool b_czar_window_file;
+ size_t history_freq;
/// Umbrella Integration estimator of free energy from eABF
UIestimator::UIestimator eabf_UI;
- // Run UI estimator?
- bool b_UI_estimator;
- // Run CZAR estimator?
- bool b_CZAR_estimator;
+ /// Run UI estimator?
+ bool b_UI_estimator;
+ /// Run CZAR estimator?
+ bool b_CZAR_estimator;
- /// Cap applied biasing force?
+ /// Frequency for updating pABF PMF (if zero, pABF is not used)
+ int pabf_freq;
+ /// Max number of CG iterations for integrating PMF at startup and for file output
+ int integrate_initial_steps;
+ /// Tolerance for integrating PMF at startup and for file output
+ cvm::real integrate_initial_tol;
+ /// Max number of CG iterations for integrating PMF at on-the-fly pABF updates
+ int integrate_steps;
+ /// Tolerance for integrating PMF at on-the-fly pABF updates
+ cvm::real integrate_tol;
+
+ /// Cap the biasing force to be applied?
bool cap_force;
std::vector max_force;
+ // Frequency for updating 2D gradients
+ int integrate_freq;
+
// Internal data and methods
std::vector bin, force_bin, z_bin;
@@ -71,12 +87,16 @@ private:
colvar_grid_gradient *gradients;
/// n-dim grid of number of samples
colvar_grid_count *samples;
+ /// n-dim grid of pmf (dimension 1 to 3)
+ integrate_potential *pmf;
/// n-dim grid: average force on "real" coordinate for eABF z-based estimator
colvar_grid_gradient *z_gradients;
/// n-dim grid of number of samples on "real" coordinate for eABF z-based estimator
colvar_grid_count *z_samples;
/// n-dim grid contining CZAR estimator of "real" free energy gradients
colvar_grid_gradient *czar_gradients;
+ /// n-dim grid of CZAR pmf (dimension 1 to 3)
+ integrate_potential *czar_pmf;
inline int update_system_force(size_t i)
{
@@ -96,9 +116,9 @@ private:
}
// shared ABF
- bool shared_on;
- size_t shared_freq;
- int shared_last_step;
+ bool shared_on;
+ size_t shared_freq;
+ int shared_last_step;
// Share between replicas -- may be called independently of update
virtual int replica_share();
@@ -114,12 +134,12 @@ private:
//// Give the count at a given bin index.
virtual int bin_count(int bin_index);
- /// Write human-readable FE gradients and sample count
- void write_gradients_samples(const std::string &prefix, bool append = false);
- void write_last_gradients_samples(const std::string &prefix, bool append = false);
+ /// Write human-readable FE gradients and sample count, and DX file in dim > 2
+ void write_gradients_samples(const std::string &prefix, bool append = false);
+ void write_last_gradients_samples(const std::string &prefix, bool append = false);
/// Read human-readable FE gradients and sample count (if not using restart)
- void read_gradients_samples();
+ void read_gradients_samples();
std::istream& read_state_data(std::istream&);
std::ostream& write_state_data(std::ostream&);
diff --git a/lib/colvars/colvarbias_alb.cpp b/lib/colvars/colvarbias_alb.cpp
index 124a15c5da..187ecc363a 100644
--- a/lib/colvars/colvarbias_alb.cpp
+++ b/lib/colvars/colvarbias_alb.cpp
@@ -7,13 +7,11 @@
// If you wish to distribute your changes, please submit them to the
// Colvars repository at GitHub.
-#include
-#include
-#include
+#include
#include "colvarmodule.h"
-#include "colvarbias_alb.h"
#include "colvarbias.h"
+#include "colvarbias_alb.h"
#ifdef _MSC_VER
#if _MSC_VER <= 1700
@@ -45,22 +43,22 @@ int colvarbias_alb::init(std::string const &conf)
size_t i;
// get the initial restraint centers
- colvar_centers.resize(colvars.size());
+ colvar_centers.resize(num_variables());
- means.resize(colvars.size());
- ssd.resize(colvars.size()); //sum of squares of differences from mean
+ means.resize(num_variables());
+ ssd.resize(num_variables()); //sum of squares of differences from mean
//setup force vectors
- max_coupling_range.resize(colvars.size());
- max_coupling_rate.resize(colvars.size());
- coupling_accum.resize(colvars.size());
- set_coupling.resize(colvars.size());
- current_coupling.resize(colvars.size());
- coupling_rate.resize(colvars.size());
+ max_coupling_range.resize(num_variables());
+ max_coupling_rate.resize(num_variables());
+ coupling_accum.resize(num_variables());
+ set_coupling.resize(num_variables());
+ current_coupling.resize(num_variables());
+ coupling_rate.resize(num_variables());
enable(f_cvb_apply_force);
- for (i = 0; i < colvars.size(); i++) {
+ for (i = 0; i < num_variables(); i++) {
colvar_centers[i].type(colvars[i]->value());
//zero moments
means[i] = ssd[i] = 0;
@@ -70,7 +68,7 @@ int colvarbias_alb::init(std::string const &conf)
}
if (get_keyval(conf, "centers", colvar_centers, colvar_centers)) {
- for (i = 0; i < colvars.size(); i++) {
+ for (i = 0; i < num_variables(); i++) {
colvar_centers[i].apply_constraints();
}
} else {
@@ -78,7 +76,7 @@ int colvarbias_alb::init(std::string const &conf)
cvm::fatal_error("Error: must define the initial centers of adaptive linear bias .\n");
}
- if (colvar_centers.size() != colvars.size())
+ if (colvar_centers.size() != num_variables())
cvm::fatal_error("Error: number of centers does not match "
"that of collective variables.\n");
@@ -100,17 +98,17 @@ int colvarbias_alb::init(std::string const &conf)
//initial guess
if (!get_keyval(conf, "forceConstant", set_coupling, set_coupling))
- for (i =0 ; i < colvars.size(); i++)
+ for (i =0 ; i < num_variables(); i++)
set_coupling[i] = 0.;
//how we're going to increase to that point
- for (i = 0; i < colvars.size(); i++)
+ for (i = 0; i < num_variables(); i++)
coupling_rate[i] = (set_coupling[i] - current_coupling[i]) / update_freq;
if (!get_keyval(conf, "forceRange", max_coupling_range, max_coupling_range)) {
//set to default
- for (i = 0; i < colvars.size(); i++) {
+ for (i = 0; i < num_variables(); i++) {
if (cvm::temperature() > 0)
max_coupling_range[i] = 3 * cvm::temperature() * cvm::boltzmann();
else
@@ -120,7 +118,7 @@ int colvarbias_alb::init(std::string const &conf)
if (!get_keyval(conf, "rateMax", max_coupling_rate, max_coupling_rate)) {
//set to default
- for (i = 0; i < colvars.size(); i++) {
+ for (i = 0; i < num_variables(); i++) {
max_coupling_rate[i] = max_coupling_range[i] / (10 * update_freq);
}
}
@@ -151,7 +149,7 @@ int colvarbias_alb::update()
// Force and energy calculation
bool finished_equil_flag = 1;
cvm::real delta;
- for (size_t i = 0; i < colvars.size(); i++) {
+ for (size_t i = 0; i < num_variables(); i++) {
colvar_forces[i] = -1.0 * restraint_force(restraint_convert_k(current_coupling[i], colvars[i]->width),
colvars[i],
colvar_centers[i]);
@@ -168,7 +166,9 @@ int colvarbias_alb::update()
} else {
//check if we've reached the setpoint
- if (coupling_rate[i] == 0 || pow(current_coupling[i] - set_coupling[i],2) < pow(coupling_rate[i],2)) {
+ cvm::real const coupling_diff = current_coupling[i] - set_coupling[i];
+ if ((coupling_rate[i] == 0) ||
+ ((coupling_diff*coupling_diff) < (coupling_rate[i]*coupling_rate[i]))) {
finished_equil_flag &= 1; //we continue equilibrating as long as we haven't reached all the set points
}
else {
@@ -209,7 +209,7 @@ int colvarbias_alb::update()
cvm::real temp;
//reset means and sum of squares of differences
- for (size_t i = 0; i < colvars.size(); i++) {
+ for (size_t i = 0; i < num_variables(); i++) {
temp = 2. * (means[i] / (static_cast (colvar_centers[i])) - 1) * ssd[i] / (update_calls - 1);
@@ -222,7 +222,7 @@ int colvarbias_alb::update()
ssd[i] = 0;
//stochastic if we do that update or not
- if (colvars.size() == 1 || rand() < RAND_MAX / ((int) colvars.size())) {
+ if (num_variables() == 1 || rand() < RAND_MAX / ((int) num_variables())) {
coupling_accum[i] += step_size * step_size;
current_coupling[i] = set_coupling[i];
set_coupling[i] += max_coupling_range[i] / sqrt(coupling_accum[i]) * step_size;
@@ -284,37 +284,37 @@ std::string const colvarbias_alb::get_state_params() const
std::ostringstream os;
os << " setCoupling ";
size_t i;
- for (i = 0; i < colvars.size(); i++) {
+ for (i = 0; i < num_variables(); i++) {
os << std::setprecision(cvm::en_prec)
<< std::setw(cvm::en_width) << set_coupling[i] << "\n";
}
os << " currentCoupling ";
- for (i = 0; i < colvars.size(); i++) {
+ for (i = 0; i < num_variables(); i++) {
os << std::setprecision(cvm::en_prec)
<< std::setw(cvm::en_width) << current_coupling[i] << "\n";
}
os << " maxCouplingRange ";
- for (i = 0; i < colvars.size(); i++) {
+ for (i = 0; i < num_variables(); i++) {
os << std::setprecision(cvm::en_prec)
<< std::setw(cvm::en_width) << max_coupling_range[i] << "\n";
}
os << " couplingRate ";
- for (i = 0; i < colvars.size(); i++) {
+ for (i = 0; i < num_variables(); i++) {
os << std::setprecision(cvm::en_prec)
<< std::setw(cvm::en_width) << coupling_rate[i] << "\n";
}
os << " couplingAccum ";
- for (i = 0; i < colvars.size(); i++) {
+ for (i = 0; i < num_variables(); i++) {
os << std::setprecision(cvm::en_prec)
<< std::setw(cvm::en_width) << coupling_accum[i] << "\n";
}
os << " mean ";
- for (i = 0; i < colvars.size(); i++) {
+ for (i = 0; i < num_variables(); i++) {
os << std::setprecision(cvm::en_prec)
<< std::setw(cvm::en_width) << means[i] << "\n";
}
os << " ssd ";
- for (i = 0; i < colvars.size(); i++) {
+ for (i = 0; i < num_variables(); i++) {
os << std::setprecision(cvm::en_prec)
<< std::setw(cvm::en_width) << ssd[i] << "\n";
}
@@ -350,7 +350,7 @@ std::ostream & colvarbias_alb::write_traj_label(std::ostream &os)
}
if (b_output_centers)
- for (size_t i = 0; i < colvars.size(); i++) {
+ for (size_t i = 0; i < num_variables(); i++) {
size_t const this_cv_width = (colvars[i]->value()).output_width(cvm::cv_width);
os << " x0_"
<< cvm::wrap_string(colvars[i]->name, this_cv_width-3);
@@ -378,7 +378,7 @@ std::ostream & colvarbias_alb::write_traj(std::ostream &os)
if (b_output_centers)
- for (size_t i = 0; i < colvars.size(); i++) {
+ for (size_t i = 0; i < num_variables(); i++) {
os << " "
<< std::setprecision(cvm::cv_prec) << std::setw(cvm::cv_width)
<< colvar_centers[i];
diff --git a/lib/colvars/colvarbias_histogram.cpp b/lib/colvars/colvarbias_histogram.cpp
index 0722e6384d..329b1d9dc0 100644
--- a/lib/colvars/colvarbias_histogram.cpp
+++ b/lib/colvars/colvarbias_histogram.cpp
@@ -8,10 +8,10 @@
// Colvars repository at GitHub.
#include "colvarmodule.h"
+#include "colvarproxy.h"
#include "colvar.h"
#include "colvarbias_histogram.h"
-/// Histogram "bias" constructor
colvarbias_histogram::colvarbias_histogram(char const *key)
: colvarbias(key),
@@ -44,7 +44,7 @@ int colvarbias_histogram::init(std::string const &conf)
get_keyval(conf, "gatherVectorColvars", colvar_array, colvar_array);
if (colvar_array) {
- for (i = 0; i < colvars.size(); i++) { // should be all vector
+ for (i = 0; i < num_variables(); i++) { // should be all vector
if (colvars[i]->value().type() != colvarvalue::type_vector) {
cvm::error("Error: used gatherVectorColvars with non-vector colvar.\n", INPUT_ERROR);
return INPUT_ERROR;
@@ -63,7 +63,7 @@ int colvarbias_histogram::init(std::string const &conf)
}
}
} else {
- for (i = 0; i < colvars.size(); i++) { // should be all scalar
+ for (i = 0; i < num_variables(); i++) { // should be all scalar
if (colvars[i]->value().type() != colvarvalue::type_scalar) {
cvm::error("Error: only scalar colvars are supported when gatherVectorColvars is off.\n", INPUT_ERROR);
return INPUT_ERROR;
@@ -77,7 +77,7 @@ int colvarbias_histogram::init(std::string const &conf)
get_keyval(conf, "weights", weights, weights);
}
- for (i = 0; i < colvars.size(); i++) {
+ for (i = 0; i < num_variables(); i++) {
colvars[i]->enable(f_cv_grid);
}
@@ -116,7 +116,7 @@ int colvarbias_histogram::update()
}
// assign a valid bin size
- bin.assign(colvars.size(), 0);
+ bin.assign(num_variables(), 0);
if (out_name.size() == 0) {
// At the first timestep, we need to assign out_name since
@@ -137,7 +137,7 @@ int colvarbias_histogram::update()
if (colvar_array_size == 0) {
// update indices for scalar values
size_t i;
- for (i = 0; i < colvars.size(); i++) {
+ for (i = 0; i < num_variables(); i++) {
bin[i] = grid->current_bin_scalar(i);
}
@@ -148,7 +148,7 @@ int colvarbias_histogram::update()
// update indices for vector/array values
size_t iv, i;
for (iv = 0; iv < colvar_array_size; iv++) {
- for (i = 0; i < colvars.size(); i++) {
+ for (i = 0; i < num_variables(); i++) {
bin[i] = grid->current_bin_scalar(i, iv);
}
diff --git a/lib/colvars/colvarbias_meta.cpp b/lib/colvars/colvarbias_meta.cpp
index b0d154dfc9..f3ae3631a0 100644
--- a/lib/colvars/colvarbias_meta.cpp
+++ b/lib/colvars/colvarbias_meta.cpp
@@ -27,7 +27,8 @@
#define PATHSEP "/"
#endif
-
+#include "colvarmodule.h"
+#include "colvarproxy.h"
#include "colvar.h"
#include "colvarbias_meta.h"
diff --git a/lib/colvars/colvarbias_restraint.cpp b/lib/colvars/colvarbias_restraint.cpp
index 23534f56eb..4ed1a95f94 100644
--- a/lib/colvars/colvarbias_restraint.cpp
+++ b/lib/colvars/colvarbias_restraint.cpp
@@ -7,7 +7,10 @@
// If you wish to distribute your changes, please submit them to the
// Colvars repository at GitHub.
+#include
+
#include "colvarmodule.h"
+#include "colvarproxy.h"
#include "colvarvalue.h"
#include "colvarbias_restraint.h"
@@ -150,13 +153,14 @@ colvarbias_restraint_k::colvarbias_restraint_k(char const *key)
: colvarbias(key), colvarbias_ti(key), colvarbias_restraint(key)
{
force_k = -1.0;
+ check_positive_k = true;
}
int colvarbias_restraint_k::init(std::string const &conf)
{
get_keyval(conf, "forceConstant", force_k, (force_k > 0.0 ? force_k : 1.0));
- if (force_k < 0.0) {
+ if (check_positive_k && (force_k < 0.0)) {
cvm::error("Error: undefined or invalid force constant.\n", INPUT_ERROR);
return INPUT_ERROR;
}
@@ -177,6 +181,7 @@ colvarbias_restraint_moving::colvarbias_restraint_moving(char const *key)
target_nstages = 0;
target_nsteps = 0;
stage = 0;
+ acc_work = 0.0;
b_chg_centers = false;
b_chg_force_k = false;
}
@@ -203,6 +208,14 @@ int colvarbias_restraint_moving::init(std::string const &conf)
cvm::error("Error: targetNumStages and lambdaSchedule are incompatible.\n", INPUT_ERROR);
return cvm::get_error();
}
+
+ get_keyval_feature(this, conf, "outputAccumulatedWork",
+ f_cvb_output_acc_work,
+ is_enabled(f_cvb_output_acc_work));
+ if (is_enabled(f_cvb_output_acc_work) && (target_nstages > 0)) {
+ return cvm::error("Error: outputAccumulatedWork and targetNumStages "
+ "are incompatible.\n", INPUT_ERROR);
+ }
}
return COLVARS_OK;
@@ -246,8 +259,6 @@ colvarbias_restraint_centers_moving::colvarbias_restraint_centers_moving(char co
{
b_chg_centers = false;
b_output_centers = false;
- b_output_acc_work = false;
- acc_work = 0.0;
}
@@ -288,9 +299,6 @@ int colvarbias_restraint_centers_moving::init(std::string const &conf)
0.5);
}
- get_keyval(conf, "outputAccumulatedWork", b_output_acc_work,
- b_output_acc_work); // TODO this conflicts with stages
-
} else {
target_centers.clear();
}
@@ -382,12 +390,14 @@ int colvarbias_restraint_centers_moving::update()
int colvarbias_restraint_centers_moving::update_acc_work()
{
- if (b_output_acc_work) {
- if ((cvm::step_relative() > 0) &&
- (cvm::step_absolute() <= target_nsteps)) {
- for (size_t i = 0; i < num_variables(); i++) {
- // project forces on the calculated increments at this step
- acc_work += colvar_forces[i] * centers_incr[i];
+ if (b_chg_centers) {
+ if (is_enabled(f_cvb_output_acc_work)) {
+ if ((cvm::step_relative() > 0) &&
+ (cvm::step_absolute() <= target_nsteps)) {
+ for (size_t i = 0; i < num_variables(); i++) {
+ // project forces on the calculated increments at this step
+ acc_work += colvar_forces[i] * centers_incr[i];
+ }
}
}
}
@@ -410,7 +420,7 @@ std::string const colvarbias_restraint_centers_moving::get_state_params() const
}
os << "\n";
- if (b_output_acc_work) {
+ if (is_enabled(f_cvb_output_acc_work)) {
os << "accumulatedWork "
<< std::setprecision(cvm::en_prec) << std::setw(cvm::en_width)
<< acc_work << "\n";
@@ -429,7 +439,7 @@ int colvarbias_restraint_centers_moving::set_state_params(std::string const &con
// cvm::log ("Reading the updated restraint centers from the restart.\n");
if (!get_keyval(conf, "centers", colvar_centers))
cvm::error("Error: restraint centers are missing from the restart.\n");
- if (b_output_acc_work) {
+ if (is_enabled(f_cvb_output_acc_work)) {
if (!get_keyval(conf, "accumulatedWork", acc_work))
cvm::error("Error: accumulatedWork is missing from the restart.\n");
}
@@ -449,7 +459,7 @@ std::ostream & colvarbias_restraint_centers_moving::write_traj_label(std::ostrea
}
}
- if (b_output_acc_work) {
+ if (b_chg_centers && is_enabled(f_cvb_output_acc_work)) {
os << " W_"
<< cvm::wrap_string(this->name, cvm::en_width-2);
}
@@ -468,7 +478,7 @@ std::ostream & colvarbias_restraint_centers_moving::write_traj(std::ostream &os)
}
}
- if (b_output_acc_work) {
+ if (b_chg_centers && is_enabled(f_cvb_output_acc_work)) {
os << " "
<< std::setprecision(cvm::en_prec) << std::setw(cvm::en_width)
<< acc_work;
@@ -488,10 +498,11 @@ colvarbias_restraint_k_moving::colvarbias_restraint_k_moving(char const *key)
{
b_chg_force_k = false;
target_equil_steps = 0;
- target_force_k = 0.0;
- starting_force_k = 0.0;
+ target_force_k = -1.0;
+ starting_force_k = -1.0;
force_k_exp = 1.0;
restraint_FE = 0.0;
+ force_k_incr = 0.0;
}
@@ -569,14 +580,13 @@ int colvarbias_restraint_k_moving::update()
if (target_equil_steps == 0 || cvm::step_absolute() % target_nsteps >= target_equil_steps) {
// Start averaging after equilibration period, if requested
- // Square distance normalized by square colvar width
- cvm::real dist_sq = 0.0;
+ // Derivative of energy with respect to force_k
+ cvm::real dU_dk = 0.0;
for (size_t i = 0; i < num_variables(); i++) {
- dist_sq += d_restraint_potential_dk(i);
+ dU_dk += d_restraint_potential_dk(i);
}
-
- restraint_FE += 0.5 * force_k_exp * std::pow(lambda, force_k_exp - 1.0)
- * (target_force_k - starting_force_k) * dist_sq;
+ restraint_FE += force_k_exp * std::pow(lambda, force_k_exp - 1.0)
+ * (target_force_k - starting_force_k) * dU_dk;
}
// Finish current stage...
@@ -607,10 +617,13 @@ int colvarbias_restraint_k_moving::update()
} else if (cvm::step_absolute() <= target_nsteps) {
+
// update force constant (slow growth)
lambda = cvm::real(cvm::step_absolute()) / cvm::real(target_nsteps);
+ cvm::real const force_k_old = force_k;
force_k = starting_force_k + (target_force_k - starting_force_k)
* std::pow(lambda, force_k_exp);
+ force_k_incr = force_k - force_k_old;
}
}
@@ -618,6 +631,23 @@ int colvarbias_restraint_k_moving::update()
}
+int colvarbias_restraint_k_moving::update_acc_work()
+{
+ if (b_chg_force_k) {
+ if (is_enabled(f_cvb_output_acc_work)) {
+ if (cvm::step_relative() > 0) {
+ cvm::real dU_dk = 0.0;
+ for (size_t i = 0; i < num_variables(); i++) {
+ dU_dk += d_restraint_potential_dk(i);
+ }
+ acc_work += dU_dk * force_k_incr;
+ }
+ }
+ }
+ return COLVARS_OK;
+}
+
+
std::string const colvarbias_restraint_k_moving::get_state_params() const
{
std::ostringstream os;
@@ -626,6 +656,12 @@ std::string const colvarbias_restraint_k_moving::get_state_params() const
os << "forceConstant "
<< std::setprecision(cvm::en_prec)
<< std::setw(cvm::en_width) << force_k << "\n";
+
+ if (is_enabled(f_cvb_output_acc_work)) {
+ os << "accumulatedWork "
+ << std::setprecision(cvm::en_prec) << std::setw(cvm::en_width)
+ << acc_work << "\n";
+ }
}
return os.str();
}
@@ -639,6 +675,10 @@ int colvarbias_restraint_k_moving::set_state_params(std::string const &conf)
// cvm::log ("Reading the updated force constant from the restart.\n");
if (!get_keyval(conf, "forceConstant", force_k, force_k))
cvm::error("Error: force constant is missing from the restart.\n");
+ if (is_enabled(f_cvb_output_acc_work)) {
+ if (!get_keyval(conf, "accumulatedWork", acc_work))
+ cvm::error("Error: accumulatedWork is missing from the restart.\n");
+ }
}
return COLVARS_OK;
@@ -647,12 +687,21 @@ int colvarbias_restraint_k_moving::set_state_params(std::string const &conf)
std::ostream & colvarbias_restraint_k_moving::write_traj_label(std::ostream &os)
{
+ if (b_chg_force_k && is_enabled(f_cvb_output_acc_work)) {
+ os << " W_"
+ << cvm::wrap_string(this->name, cvm::en_width-2);
+ }
return os;
}
std::ostream & colvarbias_restraint_k_moving::write_traj(std::ostream &os)
{
+ if (b_chg_force_k && is_enabled(f_cvb_output_acc_work)) {
+ os << " "
+ << std::setprecision(cvm::en_prec) << std::setw(cvm::en_width)
+ << acc_work;
+ }
return os;
}
@@ -765,6 +814,7 @@ int colvarbias_restraint_harmonic::update()
// update accumulated work using the current forces
error_code |= colvarbias_restraint_centers_moving::update_acc_work();
+ error_code |= colvarbias_restraint_k_moving::update_acc_work();
return error_code;
}
@@ -876,8 +926,8 @@ colvarbias_restraint_harmonic_walls::colvarbias_restraint_harmonic_walls(char co
colvarbias_restraint_moving(key),
colvarbias_restraint_k_moving(key)
{
- lower_wall_k = 0.0;
- upper_wall_k = 0.0;
+ lower_wall_k = -1.0;
+ upper_wall_k = -1.0;
}
@@ -887,26 +937,6 @@ int colvarbias_restraint_harmonic_walls::init(std::string const &conf)
colvarbias_restraint_moving::init(conf);
colvarbias_restraint_k_moving::init(conf);
- get_keyval(conf, "lowerWallConstant", lower_wall_k,
- (lower_wall_k > 0.0) ? lower_wall_k : force_k);
- get_keyval(conf, "upperWallConstant", upper_wall_k,
- (upper_wall_k > 0.0) ? upper_wall_k : force_k);
-
- if (lower_wall_k * upper_wall_k > 0.0) {
- for (size_t i = 0; i < num_variables(); i++) {
- if (variables(i)->width != 1.0)
- cvm::log("The lower and upper wall force constants for colvar \""+
- variables(i)->name+
- "\" will be rescaled to "+
- cvm::to_str(lower_wall_k /
- (variables(i)->width * variables(i)->width))+
- " and "+
- cvm::to_str(upper_wall_k /
- (variables(i)->width * variables(i)->width))+
- " according to the specified width.\n");
- }
- }
-
enable(f_cvb_scalar_variables);
size_t i;
@@ -942,16 +972,23 @@ int colvarbias_restraint_harmonic_walls::init(std::string const &conf)
}
if ((lower_walls.size() == 0) && (upper_walls.size() == 0)) {
- cvm::error("Error: no walls provided.\n", INPUT_ERROR);
- return INPUT_ERROR;
+ return cvm::error("Error: no walls provided.\n", INPUT_ERROR);
+ }
+
+ if (lower_walls.size() > 0) {
+ get_keyval(conf, "lowerWallConstant", lower_wall_k,
+ (lower_wall_k > 0.0) ? lower_wall_k : force_k);
+ }
+ if (upper_walls.size() > 0) {
+ get_keyval(conf, "upperWallConstant", upper_wall_k,
+ (upper_wall_k > 0.0) ? upper_wall_k : force_k);
}
if ((lower_walls.size() == 0) || (upper_walls.size() == 0)) {
for (i = 0; i < num_variables(); i++) {
if (variables(i)->is_enabled(f_cv_periodic)) {
- cvm::error("Error: at least one variable is periodic, "
- "both walls must be provided.\n", INPUT_ERROR);
- return INPUT_ERROR;
+ return cvm::error("Error: at least one variable is periodic, "
+ "both walls must be provided.\n", INPUT_ERROR);
}
}
}
@@ -972,19 +1009,49 @@ int colvarbias_restraint_harmonic_walls::init(std::string const &conf)
INPUT_ERROR);
return INPUT_ERROR;
}
- force_k = lower_wall_k * upper_wall_k;
- // transform the two constants to relative values
+ force_k = std::sqrt(lower_wall_k * upper_wall_k);
+ // transform the two constants to relative values using gemetric mean as ref
+ // to preserve force_k if provided as single parameter
// (allow changing both via force_k)
lower_wall_k /= force_k;
upper_wall_k /= force_k;
+ } else {
+ // If only one wall is defined, need to rescale as well
+ if (lower_walls.size() > 0) {
+ force_k = lower_wall_k;
+ lower_wall_k = 1.0;
+ }
+ if (upper_walls.size() > 0) {
+ force_k = upper_wall_k;
+ upper_wall_k = 1.0;
+ }
}
- for (i = 0; i < num_variables(); i++) {
- if (variables(i)->width != 1.0)
- cvm::log("The force constant for colvar \""+variables(i)->name+
- "\" will be rescaled to "+
- cvm::to_str(force_k / (variables(i)->width * variables(i)->width))+
- " according to the specified width.\n");
+ // Initialize starting value of the force constant (in case it's changing)
+ starting_force_k = force_k;
+
+ if (lower_walls.size() > 0) {
+ for (i = 0; i < num_variables(); i++) {
+ if (variables(i)->width != 1.0)
+ cvm::log("The lower wall force constant for colvar \""+
+ variables(i)->name+
+ "\" will be rescaled to "+
+ cvm::to_str(lower_wall_k * force_k /
+ (variables(i)->width * variables(i)->width))+
+ " according to the specified width.\n");
+ }
+ }
+
+ if (upper_walls.size() > 0) {
+ for (i = 0; i < num_variables(); i++) {
+ if (variables(i)->width != 1.0)
+ cvm::log("The upper wall force constant for colvar \""+
+ variables(i)->name+
+ "\" will be rescaled to "+
+ cvm::to_str(upper_wall_k * force_k /
+ (variables(i)->width * variables(i)->width))+
+ " according to the specified width.\n");
+ }
}
return COLVARS_OK;
@@ -1001,6 +1068,8 @@ int colvarbias_restraint_harmonic_walls::update()
error_code |= colvarbias_restraint::update();
+ error_code |= colvarbias_restraint_k_moving::update_acc_work();
+
return error_code;
}
@@ -1134,6 +1203,7 @@ colvarbias_restraint_linear::colvarbias_restraint_linear(char const *key)
colvarbias_restraint_centers_moving(key),
colvarbias_restraint_k_moving(key)
{
+ check_positive_k = false;
}
@@ -1177,6 +1247,7 @@ int colvarbias_restraint_linear::update()
// update accumulated work using the current forces
error_code |= colvarbias_restraint_centers_moving::update_acc_work();
+ error_code |= colvarbias_restraint_k_moving::update_acc_work();
return error_code;
}
diff --git a/lib/colvars/colvarbias_restraint.h b/lib/colvars/colvarbias_restraint.h
index b10649cab1..3ee999c262 100644
--- a/lib/colvars/colvarbias_restraint.h
+++ b/lib/colvars/colvarbias_restraint.h
@@ -89,8 +89,12 @@ public:
virtual int change_configuration(std::string const &conf);
protected:
+
/// \brief Restraint force constant
cvm::real force_k;
+
+ /// \brief Whether the force constant should be positive
+ bool check_positive_k;
};
@@ -129,6 +133,9 @@ protected:
/// \brief Number of steps required to reach the target force constant
/// or restraint centers
long target_nsteps;
+
+ /// \brief Accumulated work (computed when outputAccumulatedWork == true)
+ cvm::real acc_work;
};
@@ -157,8 +164,7 @@ protected:
/// \brief Initial value of the restraint centers
std::vector initial_centers;
- /// \brief Amplitude of the restraint centers' increment at each step
- /// towards the new values (calculated from target_nsteps)
+ /// \brief Increment of the restraint centers at each step
std::vector centers_incr;
/// \brief Update the centers by interpolating between initial and target
@@ -167,12 +173,6 @@ protected:
/// Whether to write the current restraint centers to the trajectory file
bool b_output_centers;
- /// Whether to write the current accumulated work to the trajectory file
- bool b_output_acc_work;
-
- /// \brief Accumulated work
- cvm::real acc_work;
-
/// Update the accumulated work
int update_acc_work();
};
@@ -212,6 +212,12 @@ protected:
/// \brief Equilibration steps for restraint FE calculation through TI
cvm::real target_equil_steps;
+
+ /// \brief Increment of the force constant at each step
+ cvm::real force_k_incr;
+
+ /// Update the accumulated work
+ int update_acc_work();
};
diff --git a/lib/colvars/colvarcomp.h b/lib/colvars/colvarcomp.h
index b94d798be9..52078a3a30 100644
--- a/lib/colvars/colvarcomp.h
+++ b/lib/colvars/colvarcomp.h
@@ -20,52 +20,48 @@
// simple_scalar_dist_functions (derived_class)
-#include
-#include
-
-
#include "colvarmodule.h"
#include "colvar.h"
#include "colvaratoms.h"
-/// \brief Colvar component (base class); most implementations of
-/// \link cvc \endlink utilize one or more \link
-/// colvarmodule::atom \endlink or \link colvarmodule::atom_group
-/// \endlink objects to access atoms.
+/// \brief Colvar component (base class for collective variables)
///
/// A \link cvc \endlink object (or an object of a
-/// cvc-derived class) specifies how to calculate a collective
-/// variable, its gradients and other related physical quantities
-/// which do not depend only on the numeric value (the \link colvar
-/// \endlink class already serves this purpose).
+/// cvc-derived class) implements the calculation of a collective
+/// variable, its gradients and any other related physical quantities
+/// that depend on microscopic degrees of freedom.
///
-/// No restriction is set to what kind of calculation a \link
-/// cvc \endlink object performs (usually calculate an
-/// analytical function of atomic coordinates). The only constraint
-/// is that the value calculated is implemented as a \link colvarvalue
-/// \endlink object. This serves to provide a unique way to calculate
-/// scalar and non-scalar collective variables, and specify if and how
-/// they can be combined together by the parent \link colvar \endlink
-/// object.
+/// No restriction is set to what kind of calculation a \link cvc \endlink
+/// object performs (usually an analytical function of atomic coordinates).
+/// The only constraints are that: \par
+///
+/// - The value is calculated by the \link calc_value() \endlink
+/// method, and is an object of \link colvarvalue \endlink class. This
+/// provides a transparent way to treat scalar and non-scalar variables
+/// alike, and allows an automatic selection of the applicable algorithms.
+///
+/// - The object provides an implementation \link apply_force() \endlink to
+/// apply forces to atoms. Typically, one or more \link cvm::atom_group
+/// \endlink objects are used, but this is not a requirement for as long as
+/// the \link cvc \endlink object communicates with the simulation program.
///
/// If you wish to implement a new collective variable component, you
/// should write your own class by inheriting directly from \link
-/// cvc \endlink, or one of its derived classes (for instance,
-/// \link distance \endlink is frequently used, because it provides
+/// colvar::cvc \endlink, or one of its derived classes (for instance,
+/// \link colvar::distance \endlink is frequently used, because it provides
/// useful data and function members for any colvar based on two
-/// atom groups). The steps are: \par
-/// 1. add the name of this class under colvar.h \par
-/// 2. add a call to the parser in colvar.C, within the function colvar::colvar() \par
-/// 3. declare the class in colvarcomp.h \par
-/// 4. implement the class in one of the files colvarcomp_*.C
+/// atom groups).
+///
+/// The steps are: \par
+/// 1. Declare the new class as a derivative of \link colvar::cvc \endlink
+/// in the file \link colvarcomp.h \endlink
+/// 2. Implement the new class in a file named colvarcomp_.cpp
+/// 3. Declare the name of the new class inside the \link colvar \endlink class
+/// in \link colvar.h \endlink (see "list of available components")
+/// 4. Add a call for the new class in colvar::init_components()
+//// (file: colvar.cpp)
///
-///
-/// The cvm::atom and cvm::atom_group classes are available to
-/// transparently communicate with the simulation program. However,
-/// they are not strictly needed, as long as all the degrees of
-/// freedom associated to the cvc are properly evolved by a simple
-/// call to e.g. apply_force().
class colvar::cvc
: public colvarparse, public colvardeps
@@ -155,7 +151,7 @@ public:
/// \brief Calculate the atomic gradients, to be reused later in
/// order to apply forces
- virtual void calc_gradients() = 0;
+ virtual void calc_gradients() {}
/// \brief Calculate the atomic fit gradients
void calc_fit_gradients();
diff --git a/lib/colvars/colvarcomp_distances.cpp b/lib/colvars/colvarcomp_distances.cpp
index ce8055843f..9911f4c87e 100644
--- a/lib/colvars/colvarcomp_distances.cpp
+++ b/lib/colvars/colvarcomp_distances.cpp
@@ -581,6 +581,12 @@ colvar::distance_inv::distance_inv(std::string const &conf)
}
}
+ if (is_enabled(f_cvc_debug_gradient)) {
+ cvm::log("Warning: debugGradients will not give correct results "
+ "for distanceInv, because its value and gradients are computed "
+ "simultaneously.\n");
+ }
+
x.type(colvarvalue::type_scalar);
}
@@ -601,11 +607,9 @@ void colvar::distance_inv::calc_value()
for (cvm::atom_iter ai2 = group2->begin(); ai2 != group2->end(); ai2++) {
cvm::rvector const dv = ai2->pos - ai1->pos;
cvm::real const d2 = dv.norm2();
- cvm::real dinv = 1.0;
- for (int ne = 0; ne < exponent/2; ne++)
- dinv *= 1.0/d2;
+ cvm::real const dinv = cvm::integer_power(d2, -1*(exponent/2));
x.real_value += dinv;
- cvm::rvector const dsumddv = -(cvm::real(exponent)) * dinv/d2 * dv;
+ cvm::rvector const dsumddv = -1.0*(exponent/2) * dinv/d2 * 2.0 * dv;
ai1->grad += -1.0 * dsumddv;
ai2->grad += dsumddv;
}
@@ -615,11 +619,9 @@ void colvar::distance_inv::calc_value()
for (cvm::atom_iter ai2 = group2->begin(); ai2 != group2->end(); ai2++) {
cvm::rvector const dv = cvm::position_distance(ai1->pos, ai2->pos);
cvm::real const d2 = dv.norm2();
- cvm::real dinv = 1.0;
- for (int ne = 0; ne < exponent/2; ne++)
- dinv *= 1.0/d2;
+ cvm::real const dinv = cvm::integer_power(d2, -1*(exponent/2));
x.real_value += dinv;
- cvm::rvector const dsumddv = -(cvm::real(exponent)) * dinv/d2 * dv;
+ cvm::rvector const dsumddv = -1.0*(exponent/2) * dinv/d2 * 2.0 * dv;
ai1->grad += -1.0 * dsumddv;
ai2->grad += dsumddv;
}
@@ -627,13 +629,11 @@ void colvar::distance_inv::calc_value()
}
x.real_value *= 1.0 / cvm::real(group1->size() * group2->size());
- x.real_value = std::pow(x.real_value, -1.0/(cvm::real(exponent)));
-}
+ x.real_value = std::pow(x.real_value, -1.0/cvm::real(exponent));
-
-void colvar::distance_inv::calc_gradients()
-{
- cvm::real const dxdsum = (-1.0/(cvm::real(exponent))) * std::pow(x.real_value, exponent+1) / cvm::real(group1->size() * group2->size());
+ cvm::real const dxdsum = (-1.0/(cvm::real(exponent))) *
+ cvm::integer_power(x.real_value, exponent+1) /
+ cvm::real(group1->size() * group2->size());
for (cvm::atom_iter ai1 = group1->begin(); ai1 != group1->end(); ai1++) {
ai1->grad *= dxdsum;
}
@@ -643,6 +643,11 @@ void colvar::distance_inv::calc_gradients()
}
+void colvar::distance_inv::calc_gradients()
+{
+}
+
+
void colvar::distance_inv::apply_force(colvarvalue const &force)
{
if (!group1->noforce)
diff --git a/lib/colvars/colvardeps.cpp b/lib/colvars/colvardeps.cpp
index ac906e7be7..a058ad55c2 100644
--- a/lib/colvars/colvardeps.cpp
+++ b/lib/colvars/colvardeps.cpp
@@ -8,10 +8,16 @@
// Colvars repository at GitHub.
+#include "colvarmodule.h"
+#include "colvarproxy.h"
#include "colvardeps.h"
+
colvardeps::colvardeps()
- : time_step_factor (1) {}
+{
+ time_step_factor = 1;
+}
+
colvardeps::~colvardeps() {
size_t i;
@@ -416,6 +422,9 @@ void colvardeps::init_cvb_requires() {
init_feature(f_cvb_get_total_force, "obtain total force", f_type_dynamic);
f_req_children(f_cvb_get_total_force, f_cv_total_force);
+ init_feature(f_cvb_output_acc_work, "output accumulated work", f_type_user);
+ f_req_self(f_cvb_output_acc_work, f_cvb_apply_force);
+
init_feature(f_cvb_history_dependent, "history-dependent", f_type_static);
init_feature(f_cvb_time_dependent, "time-dependent", f_type_static);
diff --git a/lib/colvars/colvardeps.h b/lib/colvars/colvardeps.h
index bd892fbca8..940eefb01b 100644
--- a/lib/colvars/colvardeps.h
+++ b/lib/colvars/colvardeps.h
@@ -225,6 +225,8 @@ public:
f_cvb_apply_force,
/// \brief requires total forces
f_cvb_get_total_force,
+ /// \brief whether this bias should record the accumulated work
+ f_cvb_output_acc_work,
/// \brief depends on simulation history
f_cvb_history_dependent,
/// \brief depends on time
diff --git a/lib/colvars/colvargrid.cpp b/lib/colvars/colvargrid.cpp
index 9016e2c23a..1ac4aae133 100644
--- a/lib/colvars/colvargrid.cpp
+++ b/lib/colvars/colvargrid.cpp
@@ -14,6 +14,7 @@
#include "colvarcomp.h"
#include "colvargrid.h"
+#include
colvar_grid_count::colvar_grid_count()
: colvar_grid()
@@ -22,43 +23,37 @@ colvar_grid_count::colvar_grid_count()
}
colvar_grid_count::colvar_grid_count(std::vector const &nx_i,
- size_t const &def_count)
+ size_t const &def_count)
: colvar_grid(nx_i, def_count, 1)
{}
colvar_grid_count::colvar_grid_count(std::vector &colvars,
- size_t const &def_count)
- : colvar_grid(colvars, def_count, 1)
+ size_t const &def_count,
+ bool margin)
+ : colvar_grid(colvars, def_count, 1, margin)
{}
colvar_grid_scalar::colvar_grid_scalar()
- : colvar_grid(), samples(NULL), grad(NULL)
+ : colvar_grid(), samples(NULL)
{}
colvar_grid_scalar::colvar_grid_scalar(colvar_grid_scalar const &g)
- : colvar_grid(g), samples(NULL), grad(NULL)
+ : colvar_grid(g), samples(NULL)
{
- grad = new cvm::real[nd];
}
colvar_grid_scalar::colvar_grid_scalar(std::vector const &nx_i)
- : colvar_grid(nx_i, 0.0, 1), samples(NULL), grad(NULL)
+ : colvar_grid(nx_i, 0.0, 1), samples(NULL)
{
- grad = new cvm::real[nd];
}
colvar_grid_scalar::colvar_grid_scalar(std::vector &colvars, bool margin)
- : colvar_grid(colvars, 0.0, 1, margin), samples(NULL), grad(NULL)
+ : colvar_grid(colvars, 0.0, 1, margin), samples(NULL)
{
- grad = new cvm::real[nd];
}
colvar_grid_scalar::~colvar_grid_scalar()
{
- if (grad) {
- delete [] grad;
- grad = NULL;
- }
}
cvm::real colvar_grid_scalar::maximum_value() const
@@ -143,18 +138,18 @@ void colvar_grid_gradient::write_1D_integral(std::ostream &os)
os << "# xi A(xi)\n";
- if ( cv.size() != 1 ) {
+ if (cv.size() != 1) {
cvm::error("Cannot write integral for multi-dimensional gradient grids.");
return;
}
integral = 0.0;
- int_vals.push_back( 0.0 );
+ int_vals.push_back(0.0);
min = 0.0;
// correction for periodic colvars, so that the PMF is periodic
cvm::real corr;
- if ( periodic[0] ) {
+ if (periodic[0]) {
corr = average();
} else {
corr = 0.0;
@@ -171,7 +166,7 @@ void colvar_grid_gradient::write_1D_integral(std::ostream &os)
}
if ( integral < min ) min = integral;
- int_vals.push_back( integral );
+ int_vals.push_back(integral);
}
bin = 0.0;
@@ -192,3 +187,670 @@ void colvar_grid_gradient::write_1D_integral(std::ostream &os)
+integrate_potential::integrate_potential(std::vector &colvars, colvar_grid_gradient * gradients)
+ : colvar_grid_scalar(colvars, true),
+ gradients(gradients)
+{
+ // parent class colvar_grid_scalar is constructed with margin option set to true
+ // hence PMF grid is wider than gradient grid if non-PBC
+
+ if (nd > 1) {
+ divergence.resize(nt);
+
+ // Compute inverse of Laplacian diagonal for Jacobi preconditioning
+ // For now all code related to preconditioning is commented out
+ // until a method better than Jacobi is implemented
+// cvm::log("Preparing inverse diagonal for preconditioning...");
+// inv_lap_diag.resize(nt);
+// std::vector id(nt), lap_col(nt);
+// for (int i = 0; i < nt; i++) {
+// if (i % (nt / 100) == 0)
+// cvm::log(cvm::to_str(i));
+// id[i] = 1.;
+// atimes(id, lap_col);
+// id[i] = 0.;
+// inv_lap_diag[i] = 1. / lap_col[i];
+// }
+// cvm::log("Done.");
+ }
+}
+
+
+int integrate_potential::integrate(const int itmax, const cvm::real &tol, cvm::real & err)
+{
+ int iter = 0;
+
+ if (nd == 1) {
+
+ cvm::real sum = 0.0;
+ cvm::real corr;
+ if ( periodic[0] ) {
+ corr = gradients->average(); // Enforce PBC by subtracting average gradient
+ } else {
+ corr = 0.0;
+ }
+
+ std::vector ix;
+ // Iterate over valid indices in gradient grid
+ for (ix = new_index(); gradients->index_ok(ix); incr(ix)) {
+ set_value(ix, sum);
+ sum += (gradients->value_output(ix) - corr) * widths[0];
+ }
+ if (index_ok(ix)) {
+ // This will happen if non-periodic: then PMF grid has one extra bin wrt gradient grid
+ set_value(ix, sum);
+ }
+
+ } else if (nd <= 3) {
+
+ nr_linbcg_sym(divergence, data, tol, itmax, iter, err);
+ cvm::log("Integrated in " + cvm::to_str(iter) + " steps, error: " + cvm::to_str(err));
+
+ } else {
+ cvm::error("Cannot integrate PMF in dimension > 3\n");
+ }
+
+ return iter;
+}
+
+
+void integrate_potential::set_div()
+{
+ if (nd == 1) return;
+ for (std::vector ix = new_index(); index_ok(ix); incr(ix)) {
+ update_div_local(ix);
+ }
+}
+
+
+void integrate_potential::update_div_neighbors(const std::vector &ix0)
+{
+ std::vector ix(ix0);
+ int i, j, k;
+
+ // If not periodic, expanded grid ensures that neighbors of ix0 are valid grid points
+ if (nd == 1) {
+ return;
+
+ } else if (nd == 2) {
+
+ update_div_local(ix);
+ ix[0]++; wrap(ix);
+ update_div_local(ix);
+ ix[1]++; wrap(ix);
+ update_div_local(ix);
+ ix[0]--; wrap(ix);
+ update_div_local(ix);
+
+ } else if (nd == 3) {
+
+ for (i = 0; i<2; i++) {
+ ix[1] = ix0[1];
+ for (j = 0; j<2; j++) {
+ ix[2] = ix0[2];
+ for (k = 0; k<2; k++) {
+ wrap(ix);
+ update_div_local(ix);
+ ix[2]++;
+ }
+ ix[1]++;
+ }
+ ix[0]++;
+ }
+ }
+}
+
+void integrate_potential::get_grad(cvm::real * g, std::vector &ix)
+{
+ size_t count, i;
+ bool edge = gradients->wrap_edge(ix); // Detect edge if non-PBC
+
+ if (gradients->samples) {
+ count = gradients->samples->value(ix);
+ } else {
+ count = 1;
+ }
+
+ if (!edge && count) {
+ cvm::real const *grad = &(gradients->value(ix));
+ cvm::real const fact = 1.0 / count;
+ for ( i = 0; i &ix0)
+{
+ const int linear_index = address(ix0);
+ int i, j, k;
+ std::vector ix = ix0;
+ const cvm::real * g;
+
+ if (nd == 2) {
+ // gradients at grid points surrounding the current scalar grid point
+ cvm::real g00[2], g01[2], g10[2], g11[2];
+
+ get_grad(g11, ix);
+ ix[0] = ix0[0] - 1;
+ get_grad(g01, ix);
+ ix[1] = ix0[1] - 1;
+ get_grad(g00, ix);
+ ix[0] = ix0[0];
+ get_grad(g10, ix);
+
+ divergence[linear_index] = ((g10[0]-g00[0] + g11[0]-g01[0]) / widths[0]
+ + (g01[1]-g00[1] + g11[1]-g10[1]) / widths[1]) * 0.5;
+ } else if (nd == 3) {
+ cvm::real gc[24]; // stores 3d gradients in 8 contiguous bins
+ int index = 0;
+
+ ix[0] = ix0[0] - 1;
+ for (i = 0; i<2; i++) {
+ ix[1] = ix0[1] - 1;
+ for (j = 0; j<2; j++) {
+ ix[2] = ix0[2] - 1;
+ for (k = 0; k<2; k++) {
+ get_grad(gc + index, ix);
+ index += 3;
+ ix[2]++;
+ }
+ ix[1]++;
+ }
+ ix[0]++;
+ }
+
+ divergence[linear_index] =
+ ((gc[3*4]-gc[0] + gc[3*5]-gc[3*1] + gc[3*6]-gc[3*2] + gc[3*7]-gc[3*3])
+ / widths[0]
+ + (gc[3*2+1]-gc[0+1] + gc[3*3+1]-gc[3*1+1] + gc[3*6+1]-gc[3*4+1] + gc[3*7+1]-gc[3*5+1])
+ / widths[1]
+ + (gc[3*1+2]-gc[0+2] + gc[3*3+2]-gc[3*2+2] + gc[3*5+2]-gc[3*4+2] + gc[3*7+2]-gc[3*6+2])
+ / widths[2]) * 0.25;
+ }
+}
+
+
+/// Multiplication by sparse matrix representing Laplacian
+/// NOTE: Laplacian must be symmetric for solving with CG
+void integrate_potential::atimes(const std::vector &A, std::vector &LA)
+{
+ if (nd == 2) {
+ // DIMENSION 2
+
+ size_t index, index2;
+ int i, j;
+ cvm::real fact;
+ const cvm::real ffx = 1.0 / (widths[0] * widths[0]);
+ const cvm::real ffy = 1.0 / (widths[1] * widths[1]);
+ const int h = nx[1];
+ const int w = nx[0];
+ // offsets for 4 reference points of the Laplacian stencil
+ int xm = -h;
+ int xp = h;
+ int ym = -1;
+ int yp = 1;
+
+ // NOTE on performance: this version is slightly sub-optimal because
+ // it contains two double loops on the core of the array (for x and y terms)
+ // The slightly faster version is in commit 0254cb5a2958cb2e135f268371c4b45fad34866b
+ // yet it is much uglier, and probably horrible to extend to dimension 3
+ // All terms in the matrix are assigned (=) during the x loops, then updated (+=)
+ // with the y (and z) contributions
+
+
+ // All x components except on x edges
+ index = h; // Skip first column
+
+ // Halve the term on y edges (if any) to preserve symmetry of the Laplacian matrix
+ // (Long Chen, Finite Difference Methods, UCI, 2017)
+ fact = periodic[1] ? 1.0 : 0.5;
+
+ for (i=1; i &b, std::vector &x)
+{
+ for (size_t i=0; i &b, std::vector &x, const cvm::real &tol,
+ const int itmax, int &iter, cvm::real &err)
+{
+ cvm::real ak,akden,bk,bkden,bknum,bnrm;
+ const cvm::real EPS=1.0e-14;
+ int j;
+ std::vector p(nt), r(nt), z(nt);
+
+ iter=0;
+ atimes(x,r);
+ for (j=0;j &colvars,
- size_t const &def_count = 0);
+ size_t const &def_count = 0,
+ bool margin = false);
/// Increment the counter at given position
inline void incr_count(std::vector const &ix)
@@ -1210,12 +1236,13 @@ public:
int A0, A1, A2;
std::vector ix = ix0;
+ // TODO this can be rewritten more concisely with wrap_edge()
if (periodic[n]) {
ix[n]--; wrap(ix);
- A0 = data[address(ix)];
+ A0 = value(ix);
ix = ix0;
ix[n]++; wrap(ix);
- A1 = data[address(ix)];
+ A1 = value(ix);
if (A0 * A1 == 0) {
return 0.; // can't handle empty bins
} else {
@@ -1224,10 +1251,10 @@ public:
}
} else if (ix[n] > 0 && ix[n] < nx[n]-1) { // not an edge
ix[n]--;
- A0 = data[address(ix)];
+ A0 = value(ix);
ix = ix0;
ix[n]++;
- A1 = data[address(ix)];
+ A1 = value(ix);
if (A0 * A1 == 0) {
return 0.; // can't handle empty bins
} else {
@@ -1238,9 +1265,9 @@ public:
// edge: use 2nd order derivative
int increment = (ix[n] == 0 ? 1 : -1);
// move right from left edge, or the other way around
- A0 = data[address(ix)];
- ix[n] += increment; A1 = data[address(ix)];
- ix[n] += increment; A2 = data[address(ix)];
+ A0 = value(ix);
+ ix[n] += increment; A1 = value(ix);
+ ix[n] += increment; A2 = value(ix);
if (A0 * A1 * A2 == 0) {
return 0.; // can't handle empty bins
} else {
@@ -1249,6 +1276,49 @@ public:
}
}
}
+
+ /// \brief Return the gradient of discrete count from finite differences
+ /// on the *same* grid for dimension n
+ inline cvm::real gradient_finite_diff(const std::vector &ix0,
+ int n = 0)
+ {
+ int A0, A1, A2;
+ std::vector ix = ix0;
+
+ // FIXME this can be rewritten more concisely with wrap_edge()
+ if (periodic[n]) {
+ ix[n]--; wrap(ix);
+ A0 = value(ix);
+ ix = ix0;
+ ix[n]++; wrap(ix);
+ A1 = value(ix);
+ if (A0 * A1 == 0) {
+ return 0.; // can't handle empty bins
+ } else {
+ return cvm::real(A1 - A0) / (widths[n] * 2.);
+ }
+ } else if (ix[n] > 0 && ix[n] < nx[n]-1) { // not an edge
+ ix[n]--;
+ A0 = value(ix);
+ ix = ix0;
+ ix[n]++;
+ A1 = value(ix);
+ if (A0 * A1 == 0) {
+ return 0.; // can't handle empty bins
+ } else {
+ return cvm::real(A1 - A0) / (widths[n] * 2.);
+ }
+ } else {
+ // edge: use 2nd order derivative
+ int increment = (ix[n] == 0 ? 1 : -1);
+ // move right from left edge, or the other way around
+ A0 = value(ix);
+ ix[n] += increment; A1 = value(ix);
+ ix[n] += increment; A2 = value(ix);
+ return (-1.5 * cvm::real(A0) + 2. * cvm::real(A1)
+ - 0.5 * cvm::real(A2)) * increment / widths[n];
+ }
+ }
};
@@ -1289,27 +1359,57 @@ public:
has_data = true;
}
- /// Return the gradient of the scalar field from finite differences
- inline const cvm::real * gradient_finite_diff( const std::vector &ix0 )
+ /// \brief Return the gradient of the scalar field from finite differences
+ /// Input coordinates are those of gradient grid, shifted wrt scalar grid
+ /// Should not be called on edges of scalar grid, provided the latter has margins
+ /// wrt gradient grid
+ inline void vector_gradient_finite_diff( const std::vector &ix0, std::vector &grad)
{
cvm::real A0, A1;
std::vector ix;
- if (nd != 2) {
- cvm::error("Finite differences available in dimension 2 only.");
- return grad;
- }
- for (unsigned int n = 0; n < nd; n++) {
+ size_t i, j, k, n;
+
+ if (nd == 2) {
+ for (n = 0; n < 2; n++) {
+ ix = ix0;
+ A0 = value(ix);
+ ix[n]++; wrap(ix);
+ A1 = value(ix);
+ ix[1-n]++; wrap(ix);
+ A1 += value(ix);
+ ix[n]--; wrap(ix);
+ A0 += value(ix);
+ grad[n] = 0.5 * (A1 - A0) / widths[n];
+ }
+ } else if (nd == 3) {
+
+ cvm::real p[8]; // potential values within cube, indexed in binary (4 i + 2 j + k)
ix = ix0;
- A0 = data[address(ix)];
- ix[n]++; wrap(ix);
- A1 = data[address(ix)];
- ix[1-n]++; wrap(ix);
- A1 += data[address(ix)];
- ix[n]--; wrap(ix);
- A0 += data[address(ix)];
- grad[n] = 0.5 * (A1 - A0) / widths[n];
+ int index = 0;
+ for (i = 0; i<2; i++) {
+ ix[1] = ix0[1];
+ for (j = 0; j<2; j++) {
+ ix[2] = ix0[2];
+ for (k = 0; k<2; k++) {
+ wrap(ix);
+ p[index++] = value(ix);
+ ix[2]++;
+ }
+ ix[1]++;
+ }
+ ix[0]++;
+ }
+
+ // The following would be easier to read using binary literals
+ // 100 101 110 111 000 001 010 011
+ grad[0] = 0.25 * ((p[4] + p[5] + p[6] + p[7]) - (p[0] + p[1] + p[2] + p[3])) / widths[0];
+ // 010 011 110 111 000 001 100 101
+ grad[1] = 0.25 * ((p[2] + p[3] + p[6] + p[7]) - (p[0] + p[1] + p[4] + p[5])) / widths[0];
+ // 001 011 101 111 000 010 100 110
+ grad[2] = 0.25 * ((p[1] + p[3] + p[5] + p[7]) - (p[0] + p[2] + p[4] + p[6])) / widths[0];
+ } else {
+ cvm::error("Finite differences available in dimension 2 and 3 only.");
}
- return grad;
}
/// \brief Return the value of the function at ix divided by its
@@ -1373,10 +1473,6 @@ public:
/// \brief Assuming that the map is a normalized probability density,
/// calculates the entropy (uses widths if they are defined)
cvm::real entropy() const;
-
-private:
- // gradient
- cvm::real * grad;
};
@@ -1390,6 +1486,10 @@ public:
/// should be divided
colvar_grid_count *samples;
+ /// \brief Provide the floating point weights by which each binned value
+ /// should be divided (alternate to samples, only one should be non-null)
+ colvar_grid_scalar *weights;
+
/// Default constructor
colvar_grid_gradient();
@@ -1403,6 +1503,29 @@ public:
/// Constructor from a vector of colvars
colvar_grid_gradient(std::vector &colvars);
+ /// \brief Get a vector with the binned value(s) indexed by ix, normalized if applicable
+ inline void vector_value(std::vector const &ix, std::vector &v) const
+ {
+ cvm::real const * p = &value(ix);
+ if (samples) {
+ int count = samples->value(ix);
+ if (count) {
+ cvm::real invcount = 1.0 / count;
+ for (size_t i = 0; i < mult; i++) {
+ v[i] = invcount * p[i];
+ }
+ } else {
+ for (size_t i = 0; i < mult; i++) {
+ v[i] = 0.0;
+ }
+ }
+ } else {
+ for (size_t i = 0; i < mult; i++) {
+ v[i] = p[i];
+ }
+ }
+ }
+
/// \brief Accumulate the value
inline void acc_value(std::vector const &ix, std::vector const &values) {
for (size_t imult = 0; imult < mult; imult++) {
@@ -1412,15 +1535,6 @@ public:
samples->incr_count(ix);
}
- /// \brief Accumulate the gradient
- inline void acc_grad(std::vector const &ix, cvm::real const *grads) {
- for (size_t imult = 0; imult < mult; imult++) {
- data[address(ix) + imult] += grads[imult];
- }
- if (samples)
- samples->incr_count(ix);
- }
-
/// \brief Accumulate the gradient based on the force (i.e. sums the
/// opposite of the force)
inline void acc_force(std::vector const &ix, cvm::real const *forces) {
@@ -1431,6 +1545,17 @@ public:
samples->incr_count(ix);
}
+ /// \brief Accumulate the gradient based on the force (i.e. sums the
+ /// opposite of the force) with a non-integer weight
+ inline void acc_force_weighted(std::vector const &ix,
+ cvm::real const *forces,
+ cvm::real weight) {
+ for (size_t imult = 0; imult < mult; imult++) {
+ data[address(ix) + imult] -= forces[imult] * weight;
+ }
+ weights->acc_value(ix, weight);
+ }
+
/// \brief Return the value of the function at ix divided by its
/// number of samples (if the count grid is defined)
virtual inline cvm::real value_output(std::vector const &ix,
@@ -1498,5 +1623,70 @@ public:
};
+
+/// Integrate (1D, 2D or 3D) gradients
+
+class integrate_potential : public colvar_grid_scalar
+{
+ public:
+
+ integrate_potential();
+
+ virtual ~integrate_potential()
+ {}
+
+ /// Constructor from a vector of colvars + gradient grid
+ integrate_potential (std::vector &colvars, colvar_grid_gradient * gradients);
+
+ /// \brief Calculate potential from divergence (in 2D); return number of steps
+ int integrate (const int itmax, const cvm::real & tol, cvm::real & err);
+
+ /// \brief Update matrix containing divergence and boundary conditions
+ /// based on new gradient point value, in neighboring bins
+ void update_div_neighbors(const std::vector &ix);
+
+ /// \brief Set matrix containing divergence and boundary conditions
+ /// based on complete gradient grid
+ void set_div();
+
+ /// \brief Add constant to potential so that its minimum value is zero
+ /// Useful e.g. for output
+ inline void set_zero_minimum() {
+ add_constant(-1.0 * minimum_value());
+ }
+
+ protected:
+
+ // Reference to gradient grid
+ colvar_grid_gradient *gradients;
+
+ /// Array holding divergence + boundary terms (modified Neumann) if not periodic
+ std::vector divergence;
+
+// std::vector inv_lap_diag; // Inverse of the diagonal of the Laplacian; for conditioning
+
+ /// \brief Update matrix containing divergence and boundary conditions
+ /// called by update_div_neighbors
+ void update_div_local(const std::vector &ix);
+
+ /// Obtain the gradient vector at given location ix, if available
+ /// or zero if it is on the edge of the gradient grid
+ /// ix gets wrapped in PBC
+ void get_grad(cvm::real * g, std::vector &ix);
+
+ /// \brief Solve linear system based on CG, valid for symmetric matrices only
+ void nr_linbcg_sym(const std::vector &b, std::vector &x,
+ const cvm::real &tol, const int itmax, int &iter, cvm::real &err);
+
+ /// l2 norm of a vector
+ cvm::real l2norm(const std::vector &x);
+
+ /// Multiplication by sparse matrix representing Lagrangian (or its transpose)
+ void atimes(const std::vector &x, std::vector &r);
+
+// /// Inversion of preconditioner matrix
+// void asolve(const std::vector &b, std::vector &x);
+};
+
#endif
diff --git a/lib/colvars/colvarmodule.cpp b/lib/colvars/colvarmodule.cpp
index 200c2d6848..9898e2d5e8 100644
--- a/lib/colvars/colvarmodule.cpp
+++ b/lib/colvars/colvarmodule.cpp
@@ -24,6 +24,7 @@
#include "colvaratoms.h"
#include "colvarcomp.h"
+
colvarmodule::colvarmodule(colvarproxy *proxy_in)
{
depth_s = 0;
@@ -417,10 +418,10 @@ int colvarmodule::parse_biases(std::string const &conf)
"Please ensure that their forces do not counteract each other.\n");
}
- if (biases.size() || use_scripted_forces) {
+ if (num_biases() || use_scripted_forces) {
cvm::log(cvm::line_marker);
cvm::log("Collective variables biases initialized, "+
- cvm::to_str(biases.size())+" in total.\n");
+ cvm::to_str(num_biases())+" in total.\n");
} else {
if (!use_scripted_forces) {
cvm::log("No collective variables biases were defined.\n");
@@ -431,12 +432,37 @@ int colvarmodule::parse_biases(std::string const &conf)
}
+int colvarmodule::num_variables() const
+{
+ return colvars.size();
+}
+
+
+int colvarmodule::num_variables_feature(int feature_id) const
+{
+ size_t n = 0;
+ for (std::vector::const_iterator cvi = colvars.begin();
+ cvi != colvars.end();
+ cvi++) {
+ if ((*cvi)->is_enabled(feature_id)) {
+ n++;
+ }
+ }
+ return n;
+}
+
+
+int colvarmodule::num_biases() const
+{
+ return biases.size();
+}
+
+
int colvarmodule::num_biases_feature(int feature_id) const
{
- colvarmodule *cv = cvm::main();
size_t n = 0;
- for (std::vector::iterator bi = cv->biases.begin();
- bi != cv->biases.end();
+ for (std::vector::const_iterator bi = biases.begin();
+ bi != biases.end();
bi++) {
if ((*bi)->is_enabled(feature_id)) {
n++;
@@ -448,10 +474,9 @@ int colvarmodule::num_biases_feature(int feature_id) const
int colvarmodule::num_biases_type(std::string const &type) const
{
- colvarmodule *cv = cvm::main();
size_t n = 0;
- for (std::vector::iterator bi = cv->biases.begin();
- bi != cv->biases.end();
+ for (std::vector::const_iterator bi = biases.begin();
+ bi != biases.end();
bi++) {
if ((*bi)->bias_type == type) {
n++;
@@ -465,7 +490,7 @@ std::vector const colvarmodule::time_dependent_biases() const
{
size_t i;
std::vector biases_names;
- for (i = 0; i < biases.size(); i++) {
+ for (i = 0; i < num_biases(); i++) {
if (biases[i]->is_enabled(colvardeps::f_cvb_apply_force) &&
biases[i]->is_enabled(colvardeps::f_cvb_active) &&
(biases[i]->is_enabled(colvardeps::f_cvb_history_dependent) ||
@@ -790,7 +815,7 @@ int colvarmodule::calc_biases()
{
// update the biases and communicate their forces to the collective
// variables
- if (cvm::debug() && biases.size())
+ if (cvm::debug() && num_biases())
cvm::log("Updating collective variable biases.\n");
std::vector::iterator bi;
@@ -852,7 +877,7 @@ int colvarmodule::update_colvar_forces()
std::vector::iterator bi;
// sum the forces from all biases for each collective variable
- if (cvm::debug() && biases.size())
+ if (cvm::debug() && num_biases())
cvm::log("Collecting forces from all biases.\n");
cvm::increase_depth();
for (bi = biases_active()->begin(); bi != biases_active()->end(); bi++) {
@@ -1073,8 +1098,6 @@ int colvarmodule::reset()
int colvarmodule::setup_input()
{
- if (this->size() == 0) return cvm::get_error();
-
std::string restart_in_name("");
// read the restart configuration, if available
@@ -1107,14 +1130,12 @@ int colvarmodule::setup_input()
}
}
- return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
+ return cvm::get_error();
}
int colvarmodule::setup_output()
{
- if (this->size() == 0) return cvm::get_error();
-
int error_code = COLVARS_OK;
// output state file (restart)
@@ -1123,7 +1144,8 @@ int colvarmodule::setup_output()
std::string("");
if (restart_out_name.size()) {
- cvm::log("The restart output state file will be \""+restart_out_name+"\".\n");
+ cvm::log("The restart output state file will be \""+
+ restart_out_name+"\".\n");
}
output_prefix() = proxy->output_prefix();
@@ -1154,7 +1176,7 @@ int colvarmodule::setup_output()
set_error_bits(FILE_ERROR);
}
- return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
+ return cvm::get_error();
}
@@ -1738,6 +1760,89 @@ int cvm::load_coords_xyz(char const *filename,
}
+
+// Wrappers to proxy functions: these may go in the future
+
+cvm::real cvm::unit_angstrom()
+{
+ return proxy->unit_angstrom();
+}
+
+
+cvm::real cvm::boltzmann()
+{
+ return proxy->boltzmann();
+}
+
+
+cvm::real cvm::temperature()
+{
+ return proxy->temperature();
+}
+
+
+cvm::real cvm::dt()
+{
+ return proxy->dt();
+}
+
+
+void cvm::request_total_force()
+{
+ proxy->request_total_force(true);
+}
+
+cvm::rvector cvm::position_distance(atom_pos const &pos1,
+ atom_pos const &pos2)
+{
+ return proxy->position_distance(pos1, pos2);
+}
+
+cvm::real cvm::position_dist2(cvm::atom_pos const &pos1,
+ cvm::atom_pos const &pos2)
+{
+ return proxy->position_dist2(pos1, pos2);
+}
+
+cvm::real cvm::rand_gaussian(void)
+{
+ return proxy->rand_gaussian();
+}
+
+
+
+bool cvm::replica_enabled()
+{
+ return proxy->replica_enabled();
+}
+
+int cvm::replica_index()
+{
+ return proxy->replica_index();
+}
+
+int cvm::replica_num()
+{
+ return proxy->replica_num();
+}
+
+void cvm::replica_comm_barrier()
+{
+ return proxy->replica_comm_barrier();
+}
+
+int cvm::replica_comm_recv(char* msg_data, int buf_len, int src_rep)
+{
+ return proxy->replica_comm_recv(msg_data,buf_len,src_rep);
+}
+
+int cvm::replica_comm_send(char* msg_data, int msg_len, int dest_rep)
+{
+ return proxy->replica_comm_send(msg_data,msg_len,dest_rep);
+}
+
+
+
// shared pointer to the proxy object
colvarproxy *colvarmodule::proxy = NULL;
diff --git a/lib/colvars/colvarmodule.h b/lib/colvars/colvarmodule.h
index 14e5d56701..64a98b77a0 100644
--- a/lib/colvars/colvarmodule.h
+++ b/lib/colvars/colvarmodule.h
@@ -39,16 +39,14 @@ You can browse the class hierarchy or the list of source files.
#define FILE_ERROR (1<<4)
#define MEMORY_ERROR (1<<5)
#define FATAL_ERROR (1<<6) // Should be set, or not, together with other bits
-#define DELETE_COLVARS (1<<7) // Instruct the caller to delete cvm
+//#define DELETE_COLVARS (1<<7) // Instruct the caller to delete cvm
#define COLVARS_NO_SUCH_FRAME (1<<8) // Cannot load the requested frame
#include
#include
-#include
fix_modify AtC fem create mesh
+syntax
fix_modify AtC fem create mesh <nx> <ny> <nz> <region-id> <f|p> <f|p> <f|p>- nx ny nz = number of elements in x, y, z
- region-id = id of region that is to be meshed
- f p p = perioidicity flags for x, y, z
-examples
- fix_modify AtC fem create mesh 10 1 1 feRegion p p p -description
-Creates a uniform mesh in a rectangular region-restrictions
-creates only uniform rectangular grids in a rectangular region-related
--default
-noneGenerated on Mon Aug 17 09:35:16 2009 for ATC by +
+examples
+ fix_modify AtC fem create mesh 10 1 1 feRegion p p p
+
+description
+Creates a uniform mesh in a rectangular region
++restrictions
+creates only uniform rectangular grids in a rectangular region
++related
++default
+none +Generated on Mon Aug 17 09:35:16 2009 for ATC by
1.3.9.1
diff --git a/doc/src/USER/atc/man_filter_scale.html b/doc/src/USER/atc/man_filter_scale.html
index 975f87e949..7a871f5c81 100644
--- a/doc/src/USER/atc/man_filter_scale.html
+++ b/doc/src/USER/atc/man_filter_scale.html
@@ -7,45 +7,43 @@
++ + -
-
fix_modify AtC filter scale
-syntax
+fix_modify AtC filter scale
+syntax
fix_modify AtC filter scale <scale>
- scale (real) = characteristic time scale of the filter
-examples
++examples
fix_modify AtC filter scale 10.0
-description
++description
Filters the MD dynamics to construct a more appropriate continuous field. Equilibrating first filters the time derivatives without changing the dynamics to provide a better initial condition to the filtered dynamics
--restrictions
++restrictions
only for be used with specific transfers: thermal, two_temperature
--related
++related
fix_modify AtC filter fix_modify AtC filter type
--default
++default
0.
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_filter_type.html b/doc/src/USER/atc/man_filter_type.html index 8d9dbd3d12..2711d128e9 100644 --- a/doc/src/USER/atc/man_filter_type.html +++ b/doc/src/USER/atc/man_filter_type.html @@ -7,41 +7,39 @@ +
+ + -
-
fix_modify AtC filter type
-syntax
+fix_modify AtC filter type
+syntax
fix_modify AtC filter type <exponential | step | no_filter>
-examples
++examples
fix_modify AtC filter type exponential
-description
++description
Specifies the type of time filter used.
--restrictions
++restrictions
only for be used with specific transfers: thermal, two_temperature
--related
++related
fix_modify AtC filter fix_modify AtC filter scale
--default
++default
No default.
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_fix_atc.html b/doc/src/USER/atc/man_fix_atc.html index e710c28ed2..7cc6cfea5b 100644 --- a/doc/src/USER/atc/man_fix_atc.html +++ b/doc/src/USER/atc/man_fix_atc.html @@ -7,24 +7,22 @@ +
+ + -
-
fix atc command
-syntax
+fix atc command
+syntax
fix <fixID> <group> atc <type> <parameter_file>
- fixID = name of fix @@ -38,15 +36,15 @@ syntax
- parameter_file = name of the file with material parameters.
note: Neither hardy nor field requires a parameter file
-examples
++examples
fix AtC internal atc thermal Ar_thermal.dat
fix AtC internal atc two_temperature Ar_ttm.mat
fix AtC internal atc hardy
fix AtC internal atc field
-description
++description
This fix is the beginning to creating a coupled FE/MD simulation and/or an on-the-fly estimation of continuum fields. The coupled versions of this fix do Verlet integration and the /post-processing does not. After instantiating this fix, several other fix_modify commands will be needed to set up the problem, e.g. define the finite element mesh and prescribe initial and boundary conditions.
The following coupling example is typical, but non-exhaustive:
Please refer to the standard finite element (FE) texts, e.g. T.J.R Hughes The finite element method , Dover 2003, for the basics of FE simulation.
--restrictions
++restrictions
Thermal and two_temperature (coupling) types use a Verlet time-integration algorithm. The hardy type does not contain its own time-integrator and must be used with a separate fix that does contain one, e.g. nve, nvt, etc.
Currently,
- the coupling is restricted to thermal physics
- the FE computations are done in serial on each processor.
-related
++related
fix_modify commands for setup:
-
@@ -243,8 +241,8 @@ related
- fix_modify AtC remove_molecule
Note: a set of example input files with the attendant material files are included with this package
--default
++default
none
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_fix_flux.html b/doc/src/USER/atc/man_fix_flux.html index d8369a8785..42815def6b 100644 --- a/doc/src/USER/atc/man_fix_flux.html +++ b/doc/src/USER/atc/man_fix_flux.html @@ -7,44 +7,42 @@ +
+ + -
-
fix_modify AtC fix_flux
-syntax
+fix_modify AtC fix_flux
+syntax
fix_modify AtC fix_flux <field> <face_set> <value | function>
- <field> = field name valid for type of physics, temperature | electron_temperature
- <face_set> = name of set of element faces
-examples
++examples
fix_modify atc fix_flux temperature faceSet 10.0
-description
++description
Command for fixing normal fluxes e.g. heat_flux. This command only prescribes the normal component of the physical flux, e.g. heat (energy) flux. The units are in AtC units, i.e. derived from the LAMMPS length, time, and mass scales.
--restrictions
++restrictions
Only normal fluxes (Neumann data) can be prescribed.
--related
++related
--default
++default
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_fix_nodes.html b/doc/src/USER/atc/man_fix_nodes.html index cf5c93590a..03cf86eb92 100644 --- a/doc/src/USER/atc/man_fix_nodes.html +++ b/doc/src/USER/atc/man_fix_nodes.html @@ -7,46 +7,44 @@ +
+ + -
-
fix_modify AtC fix
-syntax
+fix_modify AtC fix
+syntax
fix_modify AtC fix <field> <nodeset> <constant | function>
- <field> = field name valid for type of physics
- <nodeset> = name of set of nodes to apply boundary condition
- <constant | function> = value or name of function followed by its parameters
-examples
++examples
fix_modify AtC fix temperature groupNAME 10.
fix_modify AtC fix temperature groupNAME 0 0 0 10.0 0 0 1.0
-description
++description
Creates a constraint on the values of the specified field at specified nodes.
--restrictions
++restrictions
keyword 'all' reserved in nodeset name
--related
++related
--default
++default
none
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_hardy_computes.html b/doc/src/USER/atc/man_hardy_computes.html index c16550742b..b45b7dfb01 100644 --- a/doc/src/USER/atc/man_hardy_computes.html +++ b/doc/src/USER/atc/man_hardy_computes.html @@ -7,24 +7,22 @@ +
+ + -
-
fix_modify AtC computes
-syntax
+fix_modify AtC computes
+syntax
fix_modify AtC computes <add | delete> [per-atom compute id] <volume | number>
-
@@ -35,8 +33,8 @@ syntax
- volume | number (keyword) = field created is a per-unit-volume quantity or a per-atom quantity as weighted by kernel functions
-examples
++examples
compute virial all stress/atom
fix_modify AtC computes add virial volume
fix_modify AtC computes delete virial
@@ -44,20 +42,20 @@ examples
compute centrosymmetry all centro/atom
fix_modify AtC computes add centrosymmetry number
-description
++description
Calculates continuum fields corresponding to specified per-atom computes created by LAMMPS
-restrictions
-Must be used with the hardy/field type of AtC fix ( see fix atc command )
+
+restrictions
+Must be used with the hardy/field type of AtC fix ( see fix atc command )
Per-atom compute must be specified before corresponding continuum field can be requested
-related
++related
See manual page for compute
--default
++default
No defaults exist for this command
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_hardy_fields.html b/doc/src/USER/atc/man_hardy_fields.html index 1f55fd5e37..17903aabd0 100644 --- a/doc/src/USER/atc/man_hardy_fields.html +++ b/doc/src/USER/atc/man_hardy_fields.html @@ -7,24 +7,22 @@ +
+ + -
-
-
fix_modify AtC fields
-syntax
+fix_modify AtC fields
+syntax
fix_modify AtC fields <all | none>
fix_modify AtC fields <add | delete> <list_of_fields>
-
-examples
++examples
fix_modify AtC fields add velocity temperature
-description
++description
Allows modification of the fields calculated and output by the transfer class. The commands are cumulative, e.g.
fix_modify AtC fields none
followed by
fix_modify AtC fields add velocity temperature
will only output the velocity and temperature fields.
-restrictions
-Must be used with the hardy/field type of AtC fix, see fix atc command. Currently, the stress and heat flux formulas are only correct for central force potentials, e.g. Lennard-Jones and EAM but not Stillinger-Weber.
--related
++restrictions
+Must be used with the hardy/field type of AtC fix, see fix atc command. Currently, the stress and heat flux formulas are only correct for central force potentials, e.g. Lennard-Jones and EAM but not Stillinger-Weber.
++related
See fix_modify AtC gradients , fix_modify AtC rates and fix_modify AtC computes
--default
++default
By default, no fields are output
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_hardy_gradients.html b/doc/src/USER/atc/man_hardy_gradients.html index 708fecbca1..00935f0ae2 100644 --- a/doc/src/USER/atc/man_hardy_gradients.html +++ b/doc/src/USER/atc/man_hardy_gradients.html @@ -7,24 +7,22 @@ +
+ + -
-
fix_modify AtC gradients
-syntax
+fix_modify AtC gradients
+syntax
fix_modify AtC gradients <add | delete> <list_of_fields>
-
@@ -33,21 +31,21 @@ syntax
- fields (keyword) =
gradients can be calculated for all fields listed in fix_modify AtC fields
-examples
++examples
fix_modify AtC gradients add temperature velocity stress
fix_modify AtC gradients delete velocity
-description
++description
Requests calculation and ouput of gradients of the fields from the transfer class. These gradients will be with regard to spatial or material coordinate for eulerian or lagrangian analysis, respectively, as specified by atom_element_map (see fix_modify AtC atom_element_map )
--restrictions
-Must be used with the hardy/field type of AtC fix ( see fix atc command )
--related
--default
++restrictions
+Must be used with the hardy/field type of AtC fix ( see fix atc command )
++related
++default
No gradients are calculated by default
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_hardy_kernel.html b/doc/src/USER/atc/man_hardy_kernel.html index 3d81b367dd..f97037784c 100644 --- a/doc/src/USER/atc/man_hardy_kernel.html +++ b/doc/src/USER/atc/man_hardy_kernel.html @@ -7,24 +7,22 @@ +
+ + -
-
fix_modify AtC kernel
-syntax
+fix_modify AtC kernel
+syntax
fix_modify AtC kernel <type> <parameters>
- type (keyword) = step, cell, cubic_bar, cubic_cylinder, cubic_sphere, quartic_bar, quartic_cylinder, quartic_sphere
@@ -40,22 +38,22 @@ syntax quartic_sphere = radius (double)
-examples
++examples
fix_modify AtC kernel cell 1.0 1.0 1.0
fix_modify AtC kernel quartic_sphere 10.0
-description
--restrictions
++description
++restrictions
Must be used with the hardy AtC fix
For bar kernel types, half-width oriented along x-direction
For cylinder kernel types, cylindrical axis is assumed to be in z-direction
- ( see fix atc command )
-related
--default
+ ( see fix atc command ) ++related
++default
No default
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_hardy_on_the_fly.html b/doc/src/USER/atc/man_hardy_on_the_fly.html index d140cf6840..79c1006c97 100644 --- a/doc/src/USER/atc/man_hardy_on_the_fly.html +++ b/doc/src/USER/atc/man_hardy_on_the_fly.html @@ -7,24 +7,22 @@ +
+ + -
-on | off (keyword) = activate or discontinue on-the-fly mode
-
diff --git a/doc/src/USER/atc/man_hardy_rates.html b/doc/src/USER/atc/man_hardy_rates.html
index ab0315cb65..e51cbc9873 100644
--- a/doc/src/USER/atc/man_hardy_rates.html
+++ b/doc/src/USER/atc/man_hardy_rates.html
@@ -7,24 +7,22 @@
+fix_modify AtC on_the_fly
-syntax
+fix_modify AtC on_the_fly
+syntax
fix_modify AtC on_the_fly <bond | kernel> <optional on | off>
- bond | kernel (keyword) = specifies on-the-fly calculation of bond or kernel matrix elements
-examples
++examples
fix_modify AtC on_the_fly bond on
fix_modify AtC on_the_fly kernel
fix_modify AtC on_the_fly kernel off
-description
++description
Overrides normal mode of pre-calculating and storing bond pair-to-node a nd kernel atom-to-node matrices. If activated, will calculate elements of t hese matrices during repeated calls of field computations (i.e. "on-the-fly") and not store them for future use.
on flag is optional - if omitted, on_the_fly will be activated for the s pecified matrix. Can be deactivated using off flag.
-restrictions
-Must be used with the hardy/field type of AtC fix ( see fix atc command )
--related
--default
++restrictions
+Must be used with the hardy/field type of AtC fix ( see fix atc command )
++related
++default
By default, on-the-fly calculation is not active (i.e. off). However, code does a memory allocation check to determine if it can store all needed bond and kernel matrix ele ments. If this allocation fails, on-the-fly is activated.
+ + -
-
fix_modify AtC rates
-syntax
+fix_modify AtC rates
+syntax
fix_modify AtC rates <add | delete> <list_of_fields>
-
@@ -33,22 +31,22 @@ syntax
- fields (keyword) =
rates can be calculated for all fields listed in fix_modify AtC fields
-examples
++examples
fix_modify AtC rates add temperature velocity stress
fix_modify AtC rates delete stress
-description
++description
Requests calculation and ouput of rates (time derivatives) of the fields from the transfer class. For eulerian analysis (see fix_modify AtC atom_element_map ), these rates are the partial time derivatives of the nodal fields, not the full (material) time derivatives.
-restrictions
-Must be used with the hardy/field type of AtC fix ( see fix atc command )
--related
--default
++restrictions
+Must be used with the hardy/field type of AtC fix ( see fix atc command )
++related
++default
No rates are calculated by default
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_initial.html b/doc/src/USER/atc/man_initial.html index c0a0be3852..41ae06eb8c 100644 --- a/doc/src/USER/atc/man_initial.html +++ b/doc/src/USER/atc/man_initial.html @@ -7,41 +7,39 @@ +
+ + -
-
fix_modify AtC initial
-syntax
+fix_modify AtC initial
+syntax
fix_modify AtC initial <field> <nodeset> <constant | function>
- <field> = field name valid for type of physics, temperature | electron_temperature
- <nodeset> = name of set of nodes to apply initial condition
- <constant | function> = value or name of function followed by its parameters
-examples
++examples
fix_modify atc initial temperature groupNAME 10.
-description
++description
Sets the initial values for the specified field at the specified nodes.
--restrictions
++restrictions
keyword 'all' reserved in nodeset name
--default
++default
none
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_internal_atom_integrate.html b/doc/src/USER/atc/man_internal_atom_integrate.html index b15bf71aad..dfa19474e5 100644 --- a/doc/src/USER/atc/man_internal_atom_integrate.html +++ b/doc/src/USER/atc/man_internal_atom_integrate.html @@ -7,30 +7,28 @@ +
+ + -
-
fix_modify AtC internal_atom_integrate
-syntax
+fix_modify AtC internal_atom_integrate
+syntax
fix_modify AtC internal_atom_integrate <on | off> fix_modify AtC internal_atom_integrate on
-description
++description
Has AtC perform time integration for the atoms in the group on which it operates. This does not include boundary atoms.
--default
++default
on for coupling methods, off for post-processors off
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_internal_element_set.html b/doc/src/USER/atc/man_internal_element_set.html index 31bee57860..849e8f0671 100644 --- a/doc/src/USER/atc/man_internal_element_set.html +++ b/doc/src/USER/atc/man_internal_element_set.html @@ -7,42 +7,40 @@ +
+ + -
-
fix_modify AtC internal_element_set
-syntax
+fix_modify AtC internal_element_set
+syntax
fix_modify AtC internal_element_set <element-set-name>
- <element-set-name> = name of element set defining internal region, or off
-examples
++examples
fix_modify AtC internal_element_set myElementSet fix_modify AtC internal_element_set off
-description
++description
Enables AtC to base the region for internal atoms to be an element set. If no ghost atoms are used, all the AtC atoms must be constrained to remain in this element set by the user, e.g., with walls. If boundary atoms are used in conjunction with Eulerian atom maps AtC will partition all atoms of a boundary or internal type to be of type internal if they are in the internal region or to be of type boundary otherwise.
--restrictions
++restrictions
If boundary atoms are used in conjunction with Eulerian atom maps, the Eulerian reset frequency must be an integer multiple of the Lammps reneighbor frequency
--related
++related
see atom_element_map_type and boundary
--default
++default
off
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_internal_quadrature.html b/doc/src/USER/atc/man_internal_quadrature.html index 172187c298..7f10e17076 100644 --- a/doc/src/USER/atc/man_internal_quadrature.html +++ b/doc/src/USER/atc/man_internal_quadrature.html @@ -7,40 +7,38 @@ +
+ + -
-
fix_modify AtC internal_quadrature
-syntax
+fix_modify AtC internal_quadrature
+syntax
fix_modify atc internal_quadrature <on | off> [region]
--examples
++examples
fix_modify atc internal_quadrature off
-description
++description
Command to use or not use atomic quadrature on internal elements fully filled with atoms. By turning the internal quadrature off these elements do not contribute to the governing PDE and the fields at the internal nodes follow the weighted averages of the atomic data.
--optional
++optional
Optional region tag specifies which finite element nodes will be treated as being within the MD region. This option is only valid with internal_quadrature off.
--restrictions
--related
--default
++restrictions
++related
++default
on
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_kernel_function.html b/doc/src/USER/atc/man_kernel_function.html index 08ec827dec..92db590198 100644 --- a/doc/src/USER/atc/man_kernel_function.html +++ b/doc/src/USER/atc/man_kernel_function.html @@ -7,24 +7,22 @@ +
+ + -
-
fix_modify AtC kernel
-syntax
+fix_modify AtC kernel
+syntax
fix_modify AtC kernel <type> <parameters>
- type (keyword) = step, cell, cubic_bar, cubic_cylinder, cubic_sphere, quartic_bar, quartic_cylinder, quartic_sphere
@@ -40,21 +38,21 @@ syntax quartic_sphere = radius (double)
-examples
++examples
fix_modify AtC kernel cell 1.0 1.0 1.0 fix_modify AtC kernel quartic_sphere 10.0
--description
--restrictions
++description
++restrictions
Must be used with the hardy AtC fix
For bar kernel types, half-width oriented along x-direction
For cylinder kernel types, cylindrical axis is assumed to be in z-direction
- ( see fix atc command )
-related
--default
+ ( see fix atc command ) ++related
++default
No default
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_localized_lambda.html b/doc/src/USER/atc/man_localized_lambda.html index 5dadb9d730..fd845d0a71 100644 --- a/doc/src/USER/atc/man_localized_lambda.html +++ b/doc/src/USER/atc/man_localized_lambda.html @@ -7,38 +7,36 @@ +
+ + -
-
fix_modify AtC control localized_lambda
-syntax
+fix_modify AtC control localized_lambda
+syntax
fix_modify AtC control localized_lambda <on|off>
--examples
++examples
fix_modify atc control localized_lambda on
-description
++description
Turns on localization algorithms for control algorithms to restrict the influence of FE coupling or boundary conditions to a region near the boundary of the MD region. Control algorithms will not affect atoms in elements not possessing faces on the boundary of the region. Flux-based control is localized via row-sum lumping while quantity control is done by solving a truncated matrix equation.
--restrictions
--related
--default
++restrictions
++related
++default
Default is off.
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_lumped_lambda_solve.html b/doc/src/USER/atc/man_lumped_lambda_solve.html index bb3f8cfde8..ade780ddee 100644 --- a/doc/src/USER/atc/man_lumped_lambda_solve.html +++ b/doc/src/USER/atc/man_lumped_lambda_solve.html @@ -7,38 +7,36 @@ +
+ + -
-
fix_modify AtC control lumped_lambda_solve
-syntax
+fix_modify AtC control lumped_lambda_solve
+syntax
fix_modify AtC control lumped_lambda_solve <on|off>
--examples
++examples
fix_modify atc control lumped_lambda_solve on
-description
++description
Command to use or not use lumped matrix for lambda solve
--restrictions
--related
--default
++restrictions
++related
++default
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_mask_direction.html b/doc/src/USER/atc/man_mask_direction.html index 01ca9d192b..31c18b4f1f 100644 --- a/doc/src/USER/atc/man_mask_direction.html +++ b/doc/src/USER/atc/man_mask_direction.html @@ -7,38 +7,36 @@ +
+ + -
-
fix_modify AtC control mask_direction
-syntax
+fix_modify AtC control mask_direction
+syntax
fix_modify AtC control mask_direction <direction> <on|off>
--examples
++examples
fix_modify atc control mask_direction 0 on
-description
++description
Command to mask out certain dimensions from the atomic regulator
--restrictions
--related
--default
++restrictions
++related
++default
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_mass_matrix.html b/doc/src/USER/atc/man_mass_matrix.html index 5f543fc20c..140b745f09 100644 --- a/doc/src/USER/atc/man_mass_matrix.html +++ b/doc/src/USER/atc/man_mass_matrix.html @@ -7,41 +7,39 @@ +
+ + -
-
fix_modify AtC mass_matrix
-syntax
+fix_modify AtC mass_matrix
+syntax
fix_modify AtC mass_matrix <fe | md_fe>
- <fe | md_fe> = activiate/deactiviate using the FE mass matrix in the MD region
-examples
++examples
fix_modify atc mass_matrix fe
-description
++description
Determines whether AtC uses the FE mass matrix based on Gaussian quadrature or based on atomic quadrature in the MD region. This is useful for fully overlapping simulations to improve efficiency.
--restrictions
++restrictions
Should not be used unless the FE region is contained within the MD region, otherwise the method will be unstable and inaccurate
--related
--default
++related
++default
Default is off
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_material.html b/doc/src/USER/atc/man_material.html index 9867e90f77..c31ab4938d 100644 --- a/doc/src/USER/atc/man_material.html +++ b/doc/src/USER/atc/man_material.html @@ -7,39 +7,37 @@ +
+ + -
-
fix_modify AtC material
-syntax
+fix_modify AtC material
+syntax
fix_modify AtC material [elementset_name] [material_id]
-examples
++examples
fix_modify AtC material gap_region 2
-description
++description
Sets the material model in elementset_name to be of type material_id.
--restrictions
++restrictions
The element set must already be created and the material must be specified in the material file given the the atc fix on construction
--related
--default
++related
++default
All elements default to the first material in the material file.
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_mesh_add_to_nodeset.html b/doc/src/USER/atc/man_mesh_add_to_nodeset.html index cf5ad52f60..25a5c2cdae 100644 --- a/doc/src/USER/atc/man_mesh_add_to_nodeset.html +++ b/doc/src/USER/atc/man_mesh_add_to_nodeset.html @@ -7,41 +7,39 @@ +
+ + -
-
fix_modify AtC mesh add_to_nodeset
-syntax
+fix_modify AtC mesh add_to_nodeset
+syntax
fix_modify AtC mesh add_to_nodeset <id> <xmin> <xmax> <ymin> <ymax> <zmin> <zmax>
- <id> = id of FE nodeset to be added to
- <xmin> <xmax> <ymin> <ymax> <zmin> <zmax> = coordinates of the bounding box that contains the desired nodes to be added
-examples
++examples
fix_modify AtC mesh add_to_nodeset lbc -11.9 -11 -12 12 -12 12
-description
++description
Command to add nodes to an already existing FE nodeset.
--restrictions
--related
--default
++restrictions
++related
++default
Coordinates are assumed to be in lattice units.
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_mesh_create.html b/doc/src/USER/atc/man_mesh_create.html index efaf7f4307..a7ee112614 100644 --- a/doc/src/USER/atc/man_mesh_create.html +++ b/doc/src/USER/atc/man_mesh_create.html @@ -7,24 +7,22 @@ +
+ + -
-
fix_modify AtC mesh create
-syntax
+fix_modify AtC mesh create
+syntax
fix_modify AtC mesh create <nx> <ny> <nz> <region-id> <f|p> <f|p> <f|p>
-
@@ -32,21 +30,21 @@ syntax
- region-id = id of region that is to be meshed
- f p p = periodicity flags for x, y, z
-examples
++examples
fix_modify AtC mesh create 10 1 1 feRegion p p p
-description
++description
Creates a uniform mesh in a rectangular region
--restrictions
++restrictions
Creates only uniform rectangular grids in a rectangular region
--related
++related
fix_modify AtC mesh quadrature
--default
++default
When created, mesh defaults to gauss2 (2-point Gaussian) quadrature. Use "mesh quadrature" command to change quadrature style.
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_mesh_create_elementset.html b/doc/src/USER/atc/man_mesh_create_elementset.html index 51bdae4faa..2ac383a974 100644 --- a/doc/src/USER/atc/man_mesh_create_elementset.html +++ b/doc/src/USER/atc/man_mesh_create_elementset.html @@ -7,42 +7,40 @@ +
+ + -
-
fix_modify AtC mesh create_elementset
-syntax
+fix_modify AtC mesh create_elementset
+syntax
fix_modify AtC create_elementset <id> <xmin> <xmax> <ymin> <ymax> <zmin> <zmax>
- <id> = id to assign to the collection of FE element
- <xmin> <xmax> <ymin> <ymax> <zmin> <zmax> = coordinates of the bounding box that contains only the desired elements
-examples
++examples
fix_modify AtC mesh create_elementset middle -4.1 4.1 -100 100 -100 1100
-description
++description
Command to assign an id to a set of FE elements to be used subsequently in defining material and mesh-based operations.
--restrictions
++restrictions
Only viable for rectangular grids.
--related
--default
++related
++default
Coordinates are assumed to be in lattice units.
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_mesh_create_faceset_box.html b/doc/src/USER/atc/man_mesh_create_faceset_box.html index 163a6b442c..e62a827a78 100644 --- a/doc/src/USER/atc/man_mesh_create_faceset_box.html +++ b/doc/src/USER/atc/man_mesh_create_faceset_box.html @@ -7,24 +7,22 @@ +
+ + -
-
fix_modify AtC mesh create_faceset box
-syntax
+fix_modify AtC mesh create_faceset box
+syntax
fix_modify AtC mesh create_faceset <id> box <xmin> <xmax> <ymin> <ymax> <zmin> <zmax> <in|out> [units]
- <id> = id to assign to the collection of FE faces @@ -32,19 +30,19 @@ syntax
- <in|out> = "in" gives inner faces to the box, "out" gives the outer faces to the box
- units = option to specify real as opposed to lattice units
-examples
++examples
fix_modify AtC mesh create_faceset obndy box -4.0 4.0 -12 12 -12 12 out
-description
++description
Command to assign an id to a set of FE faces.
--restrictions
++restrictions
Only viable for rectangular grids.
--related
--default
++related
++default
The default options are units = lattice and the use of outer faces
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_mesh_create_faceset_plane.html b/doc/src/USER/atc/man_mesh_create_faceset_plane.html index 3ca1108d1a..b1969cb79d 100644 --- a/doc/src/USER/atc/man_mesh_create_faceset_plane.html +++ b/doc/src/USER/atc/man_mesh_create_faceset_plane.html @@ -7,24 +7,22 @@ +
+ + -
-
fix_modify AtC mesh create_faceset plane
-syntax
+fix_modify AtC mesh create_faceset plane
+syntax
fix_modify AtC mesh create_faceset <id> plane <x|y|z> <val1> <x|y|z> <lval2> <uval2> [units]
- <id> = id to assign to the collection of FE faces @@ -32,19 +30,19 @@ syntax
- <val1>,<lval2>,<uval2> = plane is specified as the x|y|z=val1 plane bounded by the segments x|y|z = [lval2,uval2]
- units = option to specify real as opposed to lattice units
-examples
++examples
fix_modify AtC mesh create_faceset xyplane plane y 0 x -4 0
-description
++description
Command to assign an id to a set of FE faces.
--restrictions
++restrictions
Only viable for rectangular grids.
--related
--default
++related
++default
The default option is units = lattice.
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_mesh_create_nodeset.html b/doc/src/USER/atc/man_mesh_create_nodeset.html index 9d5d155654..39bfffd119 100644 --- a/doc/src/USER/atc/man_mesh_create_nodeset.html +++ b/doc/src/USER/atc/man_mesh_create_nodeset.html @@ -7,41 +7,39 @@ +
+ + -
-
fix_modify AtC mesh create_nodeset
-syntax
+fix_modify AtC mesh create_nodeset
+syntax
fix_modify AtC mesh create_nodeset <id> <xmin> <xmax> <ymin> <ymax> <zmin> <zmax>
- <id> = id to assign to the collection of FE nodes
- <xmin> <xmax> <ymin> <ymax> <zmin> <zmax> = coordinates of the bounding box that contains only the desired nodes
-examples
++examples
fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -12 12 -12 12
-description
++description
Command to assign an id to a set of FE nodes to be used subsequently in defining boundary conditions.
--restrictions
--related
--default
++restrictions
++related
++default
Coordinates are assumed to be in lattice units.
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_mesh_delete_elements.html b/doc/src/USER/atc/man_mesh_delete_elements.html index cc269c8e65..60a2fe59a1 100644 --- a/doc/src/USER/atc/man_mesh_delete_elements.html +++ b/doc/src/USER/atc/man_mesh_delete_elements.html @@ -7,40 +7,38 @@ +
+ + -
-
fix_modify AtC mesh delete_elements
-syntax
+fix_modify AtC mesh delete_elements
+syntax
fix_modify AtC mesh delete_elements <element_set>
- <element_set> = name of an element set
-examples
++examples
fix_modify AtC delete_elements gap
-description
++description
Deletes a group of elements from the mesh.
--restrictions
--related
--default
++restrictions
++related
++default
none
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_mesh_nodeset_to_elementset.html b/doc/src/USER/atc/man_mesh_nodeset_to_elementset.html index 45d03fc986..d05429ebab 100644 --- a/doc/src/USER/atc/man_mesh_nodeset_to_elementset.html +++ b/doc/src/USER/atc/man_mesh_nodeset_to_elementset.html @@ -7,43 +7,41 @@ +
+ + -
-
fix_modify AtC mesh nodeset_to_elementset
-syntax
+fix_modify AtC mesh nodeset_to_elementset
+syntax
fix_modify AtC nodeset_to_elementset <nodeset_id> <elementset_id> <max/min>
- <nodeset_id> = id of desired nodeset from which to create elementset
- <elementset_id> = id to assign to the collection of FE element
- <max/min> = flag to choose either the maximal or minimal elementset
-examples
++examples
fix_modify AtC mesh nodeset_to_elementset myNodeset myElementset min
-description
++description
Command to create an elementset from an existing nodeset. Either the minimal element set of elements with all nodes in the set, or maximal element set with all elements with at least one node in the set, can be created
--restrictions
++restrictions
None.
--related
--default
++related
++default
Unless specified, the maximal element set is created
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_mesh_output.html b/doc/src/USER/atc/man_mesh_output.html index be1b4c194f..f768a29c41 100644 --- a/doc/src/USER/atc/man_mesh_output.html +++ b/doc/src/USER/atc/man_mesh_output.html @@ -7,39 +7,37 @@ +
+ + -
-
fix_modify AtC mesh output
-syntax
+fix_modify AtC mesh output
+syntax
fix_modify AtC mesh output <file_prefix>
--examples
++examples
fix_modify AtC mesh output meshData
-description
++description
Command to output mesh and associated data: nodesets, facesets, and elementsets. This data is only output once upon initialization since currently the mesh is static. Creates (binary, "gold" format) Ensight output of mesh data.
--restrictions
++restrictions
none
--related
--default
++related
++default
none
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_mesh_quadrature.html b/doc/src/USER/atc/man_mesh_quadrature.html index d5291d99db..46487fdce7 100644 --- a/doc/src/USER/atc/man_mesh_quadrature.html +++ b/doc/src/USER/atc/man_mesh_quadrature.html @@ -7,41 +7,39 @@ +
+ + -
-
fix_modify AtC mesh quadrature
-syntax
+fix_modify AtC mesh quadrature
+syntax
fix_modify AtC mesh quadrature <quad>
- quad = one of <nodal|gauss1|gauss2|gauss3|face> --- when a mesh is created it defaults to gauss2, use this call to change it after the fact
-examples
++examples
fix_modify AtC mesh quadrature face
-description
++description
(Re-)assigns the quadrature style for the existing mesh.
--restrictions
--related
++restrictions
++related
--default
++default
none
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+ + -
-
fix_modify AtC mesh read
-syntax
+fix_modify AtC mesh read
+syntax
fix_modify AtC mesh read <filename> <f|p> <f|p> <f|p>
- filename = name of file containing mesh to be read
- f p p = periodicity flags for x, y, z
-examples
++examples
fix_modify AtC mesh read myComponent.mesh p p p
fix_modify AtC mesh read myOtherComponent.exo
-description
++description
Reads a mesh from a text or exodus file, and assigns periodic boundary conditions if needed.
--restrictions
--related
--default
++restrictions
++related
++default
periodicity flags are false by default
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_mesh_write.html b/doc/src/USER/atc/man_mesh_write.html index 21754a1e68..756cf49922 100644 --- a/doc/src/USER/atc/man_mesh_write.html +++ b/doc/src/USER/atc/man_mesh_write.html @@ -7,41 +7,39 @@ +
+ + -
-
fix_modify AtC mesh write
-syntax
+fix_modify AtC mesh write
+syntax
fix_modify AtC mesh write <filename>
- filename = name of file to write mesh
-examples
++examples
fix_modify AtC mesh write myMesh.mesh
-description
++description
Writes a mesh to a text file.
--restrictions
--related
--default
++restrictions
++related
++default
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_momentum_time_integration.html b/doc/src/USER/atc/man_momentum_time_integration.html index 3b987f70ef..60fbfcd888 100644 --- a/doc/src/USER/atc/man_momentum_time_integration.html +++ b/doc/src/USER/atc/man_momentum_time_integration.html @@ -7,24 +7,22 @@ +
+ + -
-
fix_modify AtC time_integration (momentum)
-syntax
+fix_modify AtC time_integration (momentum)
+syntax
fix_modify AtC time_integration <descriptor>
-
@@ -33,24 +31,24 @@ syntax
various time integration methods for the finite elements
-description
++description
verlet - atomic velocity update with 2nd order Verlet, nodal temperature update with 2nd order Verlet, kinetostats based on controlling force
fractional_step - atomic velocity update with 2nd order Verlet, mixed nodal momentum update, 2nd order Verlet for continuum and exact 2nd order Verlet for atomic contributions, kinetostats based on controlling discrete momentum changes
gear - atomic velocity update with 2nd order Verlet, nodal temperature update with 3rd or 4th order Gear, kinetostats based on controlling power
-examples
++examples
fix_modify atc time_integration verlet
fix_modify atc time_integration fractional_step
-description
--related
-see fix atc command
--default
++description
++related
+see fix atc command
++default
none
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_output.html b/doc/src/USER/atc/man_output.html index 3129ff30c9..aec1d5d55a 100644 --- a/doc/src/USER/atc/man_output.html +++ b/doc/src/USER/atc/man_output.html @@ -7,24 +7,22 @@ +
+ + -
-
fix_modify AtC output
-syntax
+fix_modify AtC output
+syntax
fix_modify AtC output <filename_prefix> <frequency> [text | full_text | binary | vector_components | tensor_components ] fix_modify AtC output index [step | time ]
- filename_prefix (string) = prefix for data files @@ -37,23 +35,23 @@ syntax tensor_components = outputs tensor as scalar components (use this for Paraview)
-examples
++examples
fix_modify AtC output heatFE 100
fix_modify AtC output hardyFE 1 text tensor_components
fix_modify AtC output hardyFE 10 text binary tensor_components
fix_modify AtC output index step
-description
++description
Creates text and/or binary (Ensight, "gold" format) output of nodal/mesh data which is transfer/physics specific. Output indexed by step or time is possible.
--restrictions
--related
-see fix atc command
--default
++restrictions
++related
+see fix atc command
++default
no default format output indexed by time
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_output_elementset.html b/doc/src/USER/atc/man_output_elementset.html index be259388ba..54079027c5 100644 --- a/doc/src/USER/atc/man_output_elementset.html +++ b/doc/src/USER/atc/man_output_elementset.html @@ -7,44 +7,42 @@ +
+ + -
-
fix_modify AtC output elementset
-syntax
+fix_modify AtC output elementset
+syntax
fix_modify AtC output volume_integral <eset_name> <field> {`
- set_name (string) = name of elementset to be integrated over
- fieldname (string) = name of field to integrate csum = creates nodal sum over nodes in specified nodeset
-examples
++examples
fix_modify AtC output eset1 mass_density
-description
++description
Performs volume integration of specified field over elementset and outputs resulting variable values to GLOBALS file.
--restrictions
--related
-see fix atc command
--default
++restrictions
++related
+see fix atc command
++default
none
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_output_nodeset.html b/doc/src/USER/atc/man_output_nodeset.html index db76c8008e..2fc6e02681 100644 --- a/doc/src/USER/atc/man_output_nodeset.html +++ b/doc/src/USER/atc/man_output_nodeset.html @@ -7,24 +7,22 @@ +
+ + -
-
fix_modify AtC output nodeset
-syntax
+fix_modify AtC output nodeset
+syntax
fix_modify AtC output nodeset <nodeset_name> <operation>
- nodeset_name (string) = name of nodeset to be operated on @@ -32,20 +30,20 @@ syntax sum = creates nodal sum over nodes in specified nodeset
-examples
++examples
fix_modify AtC output nodeset nset1 sum
-description
++description
Performs operation over the nodes belonging to specified nodeset and outputs resulting variable values to GLOBALS file.
--restrictions
--related
-see fix atc command
--default
++restrictions
++related
+see fix atc command
++default
none
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_pair_interactions.html b/doc/src/USER/atc/man_pair_interactions.html index d46dcb1234..2cb2cb6113 100644 --- a/doc/src/USER/atc/man_pair_interactions.html +++ b/doc/src/USER/atc/man_pair_interactions.html @@ -7,40 +7,38 @@ +
+ + -
-
fix_modify AtC pair_interactions/bond_interactions
-syntax
+fix_modify AtC pair_interactions/bond_interactions
+syntax
fix_modify AtC pair_interactions <on|off>
fix_modify AtC bond_interactions <on|off>
-examples
++examples
fix_modify AtC bond_interactions on
-description
++description
include bonds and/or pairs in the stress and heat flux computations
--restrictions
--related
--default
++restrictions
++related
++default
pair interactions: on, bond interactions: off
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_poisson_solver.html b/doc/src/USER/atc/man_poisson_solver.html index d69d74db1a..b6fabbb27c 100644 --- a/doc/src/USER/atc/man_poisson_solver.html +++ b/doc/src/USER/atc/man_poisson_solver.html @@ -7,43 +7,41 @@ +
+ + -
-
fix_modify AtC poisson_solver
-syntax
+fix_modify AtC poisson_solver
+syntax
fix_modify AtC poisson_solver mesh create <nx> <ny> <nz> <region-id> <f|p> <f|p> <f|p>
- nx ny nz = number of elements in x, y, z
- region-id = id of region that is to be meshed
- f p p = perioidicity flags for x, y, z
-examples
++examples
fix_modify AtC poisson_solver mesh create 10 1 1 feRegion p p p
-description
++description
Creates a uniform mesh in a rectangular region
--restrictions
++restrictions
creates only uniform rectangular grids in a rectangular region
--related
--default
++related
++default
none
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_read_restart.html b/doc/src/USER/atc/man_read_restart.html index 96168fccc7..5fc21282f6 100644 --- a/doc/src/USER/atc/man_read_restart.html +++ b/doc/src/USER/atc/man_read_restart.html @@ -7,41 +7,39 @@ +
+ + -
-
fix_modify AtC read_restart
-syntax
+fix_modify AtC read_restart
+syntax
fix_modify AtC read_restart [file_name]
-examples
++examples
fix_modify AtC read_restart ATC_state
-description
++description
Reads the current state of the fields from a named text-based restart file.
--restrictions
++restrictions
The restart file only contains fields and their time derivatives. The reference positions of the atoms and the commands that initialize the fix are not saved e.g. an identical mesh containing the same atoms will have to be recreated.
--related
++related
see write_restart fix_modify AtC write_restart
--default
++default
none
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_remove_molecule.html b/doc/src/USER/atc/man_remove_molecule.html index 054291efda..e6ad418de6 100644 --- a/doc/src/USER/atc/man_remove_molecule.html +++ b/doc/src/USER/atc/man_remove_molecule.html @@ -7,44 +7,42 @@ +
+ + -
-
fix_modify AtC remove_molecule
-syntax
+fix_modify AtC remove_molecule
+syntax
fix_modify_AtC remove_molecule <TAG>
- <TAG> = tag for tracking a molecule type
-examples
++examples
fix_modify AtC remove_molecule water
-description
++description
Removes tag designated for tracking a specified set of molecules.
-restrictions
--related
--default
++restrictions
++related
++default
No defaults for this command.
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_remove_source.html b/doc/src/USER/atc/man_remove_source.html index d1d249eb76..acea7a5607 100644 --- a/doc/src/USER/atc/man_remove_source.html +++ b/doc/src/USER/atc/man_remove_source.html @@ -7,43 +7,41 @@ +
+ + -
-
fix_modify AtC remove_source
-syntax
+fix_modify AtC remove_source
+syntax
fix_modify AtC remove_source <field> <element_set>
- <field> = field name valid for type of physics
- <element_set> = name of set of elements
-examples
++examples
fix_modify atc remove_source temperature groupNAME
-description
++description
Remove a domain source.
--restrictions
++restrictions
keyword 'all' reserved in element_set name
--related
++related
--default
++default
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_remove_species.html b/doc/src/USER/atc/man_remove_species.html index ba94a52658..561364518f 100644 --- a/doc/src/USER/atc/man_remove_species.html +++ b/doc/src/USER/atc/man_remove_species.html @@ -7,44 +7,42 @@ +
+ + -
-
fix_modify AtC remove_species
-syntax
+fix_modify AtC remove_species
+syntax
fix_modify_AtC delete_species <TAG>
- <TAG> = tag for tracking a species
-examples
++examples
fix_modify AtC remove_species gold
-description
++description
Removes tag designated for tracking a specified species.
-restrictions
--related
--default
++restrictions
++related
++default
No defaults for this command.
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_reset_atomic_reference_positions.html b/doc/src/USER/atc/man_reset_atomic_reference_positions.html index cb82f61bbb..88e6748001 100644 --- a/doc/src/USER/atc/man_reset_atomic_reference_positions.html +++ b/doc/src/USER/atc/man_reset_atomic_reference_positions.html @@ -7,39 +7,37 @@ +
+ + -
-
fix_modify AtC reset_atomic_reference_positions
-syntax
+fix_modify AtC reset_atomic_reference_positions
+syntax
fix_modify AtC reset_atomic_reference_positions
--examples
++examples
fix_modify atc reset_atomic_reference_positions
-description
++description
Resets the atomic positions ATC uses to perform point to field operations. In can be used to use perfect lattice sites in ATC but a thermalized or deformed lattice in LAMMPS.
-restrictions
++restrictions
-related
++related
-default
++default
Default is off
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_reset_time.html b/doc/src/USER/atc/man_reset_time.html index 35d75ccb97..a6429bf6d6 100644 --- a/doc/src/USER/atc/man_reset_time.html +++ b/doc/src/USER/atc/man_reset_time.html @@ -7,55 +7,53 @@ +
+ + -
-
fix_modify AtC reset_time
-syntax
+fix_modify AtC reset_time
+syntax
fix_modify AtC reset_time
--examples
++examples
fix_modify atc reset_time 0.0
-description
++description
Resets the simulation time counter.
--restrictions
--related
--default
--syntax
++restrictions
++related
++default
++syntax
fix_modify AtC kernel_bandwidth
--examples
++examples
fix_modify atc reset_time 8
-description
++description
Sets a maximum parallel bandwidth for the kernel functions during parallel communication. If the command is not issued, the default will be to assume the bandwidth of the kernel matrix corresponds to the number of sampling locations.
--restrictions
++restrictions
Only is used if kernel functions are being used.
--related
--default
++related
++default
Number of sample locations.
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_sample_frequency.html b/doc/src/USER/atc/man_sample_frequency.html index 13f468b222..4e48c4bb29 100644 --- a/doc/src/USER/atc/man_sample_frequency.html +++ b/doc/src/USER/atc/man_sample_frequency.html @@ -7,42 +7,40 @@ +
+ + -
-
fix_modify AtC sample_frequency
-syntax
+fix_modify AtC sample_frequency
+syntax
fix_modify AtC sample_frequency [freq]
- freq (int) : frequency to sample field in number of steps
-examples
++examples
fix_modify AtC sample_frequency 10
-description
++description
Specifies a frequency at which fields are computed for the case where time filters are being applied.
-restrictions
- Must be used with the hardy/field AtC fix ( see fix atc command ) and is only relevant when time filters are being used.
-related
++restrictions
+ Must be used with the hardy/field AtC fix ( see fix atc command ) and is only relevant when time filters are being used.
+related
-default
++default
none
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_set.html b/doc/src/USER/atc/man_set.html index d104e535b6..cf775c9b36 100644 --- a/doc/src/USER/atc/man_set.html +++ b/doc/src/USER/atc/man_set.html @@ -7,46 +7,44 @@ +
+ + -
-
fix_modify AtC set
-syntax
+fix_modify AtC set
+syntax
fix_modify AtC set reference_potential_energy <value_or_filename(optional)>
- value (double) : optional user specified zero point for PE in native LAMMPS energy units
- filename (string) : optional user specified string for file of nodal PE values to be read-in
-examples
++examples
fix_modify AtC set reference_potential_energy
fix_modify AtC set reference_potential_energy -0.05
fix_modify AtC set reference_potential_energy myPEvalues
-description
++description
Used to set various quantities for the post-processing algorithms. It sets the zero point for the potential energy density using the value provided for all nodes, or from the current configuration of the lattice if no value is provided, or values provided within the specified filename.
--restrictions
-Must be used with the hardy/field type of AtC fix ( see fix atc command )
--related
--default
++restrictions
+Must be used with the hardy/field type of AtC fix ( see fix atc command )
++related
++default
Defaults to lammps zero point i.e. isolated atoms
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_source.html b/doc/src/USER/atc/man_source.html index 833b2a866f..c7239f2c41 100644 --- a/doc/src/USER/atc/man_source.html +++ b/doc/src/USER/atc/man_source.html @@ -7,43 +7,41 @@ +
+ + -
-
fix_modify AtC source
-syntax
+fix_modify AtC source
+syntax
fix_modify AtC source <field> <element_set> <value | function>
- <field> = field name valid for type of physics
- <element_set> = name of set of elements
-examples
++examples
fix_modify atc source temperature middle temporal_ramp 10. 0.
-description
++description
Add domain sources to the mesh. The units are consistent with LAMMPS's units for mass, length and time and are defined by the PDE being solved, e.g. for thermal transfer the balance equation is for energy and source is energy per time.
--restrictions
++restrictions
keyword 'all' reserved in element_set name
--related
++related
see fix_modify AtC remove_source
--default
++default
none
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+ + -
-
fix_modify AtC source_integration
-syntax
+fix_modify AtC source_integration
+syntax
fix_modify AtC source_integration < fe | atom>
--examples
++examples
fix_modify atc source_integration atom
-description
--restrictions
--related
--default
++description
++restrictions
++related
++default
Default is fe
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_temperature_definition.html b/doc/src/USER/atc/man_temperature_definition.html index f4fb21471c..a07ba29cab 100644 --- a/doc/src/USER/atc/man_temperature_definition.html +++ b/doc/src/USER/atc/man_temperature_definition.html @@ -7,37 +7,35 @@ +
+ + -
-
fix_modify AtC temperature_definition
-syntax
+fix_modify AtC temperature_definition
+syntax
fix_modify AtC temperature_definition <kinetic|total>
--examples
++examples
fix_modify atc temperature_definition kinetic
-description
++description
Change the definition for the atomic temperature used to create the finite element temperature. The kinetic option is based only on the kinetic energy of the atoms while the total option uses the total energy (kinetic + potential) of an atom.
--restrictions
++restrictions
This command is only valid when using thermal coupling. Also, while not a formal restriction, the user should ensure that associating a potential energy with each atom makes physical sense for the total option to be meaningful.
--default
++default
kinetic
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+ + -
-
fix_modify AtC time_integration (thermal)
-syntax
+fix_modify AtC time_integration (thermal)
+syntax
fix_modify AtC time_integration <descriptor>
-
@@ -33,23 +31,23 @@ syntax
various time integration methods for the finite elements
-description
++description
gear - atomic velocity update with 2nd order Verlet, nodal temperature update with 3rd or 4th order Gear, thermostats based on controlling power
fractional_step - atomic velocity update with 2nd order Verlet, mixed nodal temperature update, 3/4 Gear for continuum and 2 Verlet for atomic contributions, thermostats based on controlling discrete energy changes
-examples
++examples
fix_modify atc time_integration gear
fix_modify atc time_integration fractional_step
-description
--related
-see fix atc command
--default
++description
++related
+see fix atc command
++default
none
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+ + -
-
fix_modify AtC filter
-syntax
+fix_modify AtC filter
+syntax
fix_modify AtC filter <on | off | equilibrate>
-
@@ -32,22 +30,22 @@ syntax
- equilibrate = runs dynamics without filtering but initializes filtered quantities
-examples
++examples
fix_modify atc transfer filter on
-description
++description
Filters the MD dynamics to construct a more appropriate continuous field. Equilibrating first filters the time derivatives without changing the dynamics to provide a better initial condition to the filtered dynamics
--restrictions
++restrictions
only for be used with specific transfers: thermal, two_temperature
--related
++related
fix_modify AtC filter scale
fix_modify AtC equilibrium_start
-default
++default
off
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+ + -
-
fix_modify AtC track_displacement
-syntax
+fix_modify AtC track_displacement
+syntax
fix_modify AtC track_displacement <on/off>
-examples
++examples
fix_modify atc track_displacement on
-description
++description
Determines whether displacement is tracked or not. For solids problems this is a useful quantity, but for fluids it is not relevant.
--restrictions
++restrictions
Some constitutive models require the displacement field
--default
++default
on
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+ + -
-
fix_modify AtC unfix_flux
-syntax
+fix_modify AtC unfix_flux
+syntax
fix_modify AtC fix_flux <field> <face_set> <value | function>
- <field> = field name valid for type of physics, temperature | electron_temperature
- <face_set> = name of set of element faces
-examples
++examples
fix_modify atc unfix_flux temperature faceSet
-description
++description
Command for removing prescribed normal fluxes e.g. heat_flux, stress.
--restrictions
--related
++restrictions
++related
--default
++default
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+ + -
-
fix_modify AtC unfix
-syntax
+fix_modify AtC unfix
+syntax
fix_modify AtC unfix <field> <nodeset>
- <field> = field name valid for type of physics
- <nodeset> = name of set of nodes
-examples
++examples
fix_modify AtC unfix temperature groupNAME
-description
++description
Removes constraint on field values for specified nodes.
--restrictions
++restrictions
keyword 'all' reserved in nodeset name
--related
++related
--default
++default
none
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+ + -
-
fix_modify AtC write_atom_weights
-syntax
+fix_modify AtC write_atom_weights
+syntax
fix_modify AtC write_atom_weights <filename> <frequency>
- <filename> = name of file that atomic weights are written to
@@ -32,19 +30,19 @@ syntax - <frequency> = how often writes will occur
-examples
++examples
fix_modify atc write_atom_weights atm_wt_file.txt 10
-description
++description
Command for writing the values of atomic weights to a specified file.
--restrictions
--related
--default
++restrictions
++related
++default
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+ + -
-
fix_modify AtC write_restart
-syntax
+fix_modify AtC write_restart
+syntax
fix_modify AtC write_restart [file_name]
-examples
++examples
fix_modify AtC write_restart restart.mydata
-description
++description
Dumps the current state of the fields to a named text-based restart file. This done when the command is invoked and not repeated, unlike the similar lammps command.
--restrictions
++restrictions
The restart file only contains fields and their time derivatives. The reference positions of the atoms and the commands that initialize the fix are not saved e.g. an identical mesh containing the same atoms will have to be recreated.
--related
++related
see read_restart fix_modify AtC read_restart
--default
++default
none
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/body.txt b/doc/src/body.txt index 54ec157c74..344e5b1d65 100644 --- a/doc/src/body.txt +++ b/doc/src/body.txt @@ -6,7 +6,7 @@ :line -Body particles :h3 +Body particles :h1 [Overview:] diff --git a/doc/src/fix_atc.txt b/doc/src/fix_atc.txt index 75a82f063a..49014f0591 100644 --- a/doc/src/fix_atc.txt +++ b/doc/src/fix_atc.txt @@ -90,13 +90,11 @@ likewise for this post-processing example: run 1000 :pre the mesh's linear interpolation functions can be used as the localization function - by using the field option: +by using the field option: fix AtC internal atc field - fix_modify AtC mesh create 1 1 1 box p p p - - ... + ... :pre Note coupling and post-processing can be combined in the same simulations using separate fixes. @@ -108,11 +106,10 @@ No information about this fix is written to "binary restart files"_restart.html. [Restrictions:] -Thermal and two_temperature (coupling) types use a Verlet time-integration algorithm. The hardy type does not contain its own time-integrator and must be used with a separate fix that does contain one, e.g. nve, nvt, etc. +Thermal and two_temperature (coupling) types use a Verlet time-integration algorithm. The hardy type does not contain its own time-integrator and must be used with a separate fix that does contain one, e.g. nve, nvt, etc. In addition, currently: -Currently, -- the coupling is restricted to thermal physics -- the FE computations are done in serial on each processor. :ul +the coupling is restricted to thermal physics :ulb,l +the FE computations are done in serial on each processor. :l,ule [Related commands:] diff --git a/doc/src/fix_gcmc.txt b/doc/src/fix_gcmc.txt index c78142a999..38f0fb95ce 100644 --- a/doc/src/fix_gcmc.txt +++ b/doc/src/fix_gcmc.txt @@ -95,8 +95,8 @@ which will result in roughly one MC move per atom or molecule per MC cycle. All inserted particles are always added to two groups: the default -group "all" and the fix group specified in the fix command (which can -also be "all"). In addition, particles are also added to any groups +group "all" and the fix group specified in the fix command. +In addition, particles are also added to any groups specified by the {group} and {grouptype} keywords. If inserted particles are individual atoms, they are assigned the atom type given by the type argument. If they are molecules, the type argument has no @@ -104,6 +104,12 @@ effect and must be set to zero. Instead, the type of each atom in the inserted molecule is specified in the file read by the "molecule"_molecule.html command. +NOTE: Care should be taken to apply fix gcmc only to +a group that contains only those atoms and molecules +that you wish to manipulate using Monte Carlo. +Hence it is generally not a good idea to specify +the default group "all" in the fix command, although it is allowed. + This fix cannot be used to perform GCMC insertions of gas atoms or molecules other than the exchanged type, but GCMC deletions, and MC translations, and rotations can be performed on any atom/molecule in diff --git a/doc/src/group.txt b/doc/src/group.txt index afa218c5a3..dddb0459e3 100644 --- a/doc/src/group.txt +++ b/doc/src/group.txt @@ -13,11 +13,13 @@ group command :h3 group ID style args :pre ID = user-defined name of the group :ulb,l -style = {delete} or {region} or {type} or {id} or {molecule} or {variable} or \ +style = {delete} or {clear} or {empty} or {region} or \ + {type} or {id} or {molecule} or {variable} or \ {include} or {subtract} or {union} or {intersect} or \ {dynamic} or {static} :l {delete} = no args {clear} = no args + {empty} = no args {region} args = region-ID {type} or {id} or {molecule} args = list of one or more atom types, atom IDs, or molecule IDs @@ -41,6 +43,7 @@ style = {delete} or {region} or {type} or {id} or {molecule} or {variable} or \ keyword = {region} or {var} or {every} {region} value = region-ID {var} value = name of variable + {property} value = name of per-atom property {every} value = N = update group every this many timesteps {static} = no args :pre :ule @@ -99,6 +102,10 @@ e.g. using the "run every"_run.html command if a fix or compute or other operation expects the atoms in the group to remain constant, but LAMMPS does not check for this. +The {empty} style creates an empty group, which is useful for commands +like "fix gcmc"_fix_gcmc.html or with complex scripts that add atoms +to a group. + The {region} style puts all atoms in the region volume into the group. Note that this is a static one-time assignment. The atoms remain assigned (or not assigned) to the group even in they later move out of @@ -215,7 +222,11 @@ conditions are applied. If the {region} keyword is used, atoms not in the specified region are removed from the dynamic group. If the {var} keyword is used, the variable name must be an atom-style or atomfile-style variable. The variable is evaluated and atoms whose -per-atom values are 0.0, are removed from the dynamic group. +per-atom values are 0.0, are removed from the dynamic group. If the {property} +keyword is used, the per-atom property name must be a previously defined +per-atom property. The per-atom property is evaluated and atoms whose +values are 0.0 are removed from the dynamic group, otherwise they +are added to the group. The assignment of atoms to a dynamic group is done at the beginning of each run and on every timestep that is a multiple of {N}, which is the diff --git a/doc/src/lammps.book b/doc/src/lammps.book index d4e73453b0..878e4ad355 100644 --- a/doc/src/lammps.book +++ b/doc/src/lammps.book @@ -20,6 +20,7 @@ Section_python.html Section_errors.html Section_history.html +lammps_tutorials.html tutorial_bash_on_windows.html tutorial_drude.html tutorial_github.html @@ -28,6 +29,7 @@ tutorial_pylammps.html body.html manifolds.html +lammps_commands.html angle_coeff.html angle_style.html atom_modify.html @@ -138,7 +140,6 @@ fix_adapt_fep.html fix_addforce.html fix_addtorque.html fix_append_atoms.html -fix_atc.html fix_atom_swap.html fix_ave_atom.html fix_ave_chunk.html @@ -276,6 +277,7 @@ fix_spring_self.html fix_srd.html fix_store_force.html fix_store_state.html +fix_surface_global.html fix_temp_berendsen.html fix_temp_csvr.html fix_temp_rescale.html @@ -422,11 +424,13 @@ pair_airebo.html pair_awpmd.html pair_beck.html pair_body.html +pair_body_rounded_polygon.html pair_bop.html pair_born.html pair_brownian.html pair_buck.html pair_buck_long.html +pair_buck6d_coul_gauss.html pair_charmm.html pair_class2.html pair_colloid.html @@ -538,6 +542,7 @@ bond_zero.html angle_charmm.html angle_class2.html angle_cosine.html +angle_cosine_buck6d.html angle_cosine_delta.html angle_cosine_periodic.html angle_cosine_shift.html @@ -577,11 +582,13 @@ improper_distance.html improper_fourier.html improper_harmonic.html improper_hybrid.html +improper_inversion_harmonic.html improper_none.html improper_ring.html improper_umbrella.html improper_zero.html +fix_atc.html USER/atc/man_add_molecule.html USER/atc/man_add_species.html USER/atc/man_atom_element_map.html diff --git a/doc/src/lammps_commands.txt b/doc/src/lammps_commands.txt new file mode 100644 index 0000000000..f9c2e7366a --- /dev/null +++ b/doc/src/lammps_commands.txt @@ -0,0 +1,10 @@ + +LAMMPS Commands :h1 + +The following pages contain the detailed documentation of all +LAMMPS commands included in this version of LAMMPS. Generic +commands are listed first (in alphabetical order) followed by +command categories like compute styles or pair styles and so on. + +The documentation for the USER-ATC package fix_modify commands +follow at the very end of this manual. diff --git a/doc/src/lammps_tutorials.txt b/doc/src/lammps_tutorials.txt new file mode 100644 index 0000000000..5ceda65b60 --- /dev/null +++ b/doc/src/lammps_tutorials.txt @@ -0,0 +1,6 @@ + +Tutorials :h2 + +The following pages contain some in-depth tutorials for +selected topics, that did not fit into any other place +in the manual. diff --git a/doc/src/manifolds.txt b/doc/src/manifolds.txt index c9bb1ce57f..36c6caacb7 100644 --- a/doc/src/manifolds.txt +++ b/doc/src/manifolds.txt @@ -6,7 +6,7 @@ :line -Manifolds (surfaces) :h3 +Manifolds (surfaces) :h1 [Overview:] diff --git a/doc/src/pair_lj.txt b/doc/src/pair_lj.txt index 058d54fb59..e297d479bc 100644 --- a/doc/src/pair_lj.txt +++ b/doc/src/pair_lj.txt @@ -32,6 +32,8 @@ pair_style lj/cut/coul/long/omp command :h3 pair_style lj/cut/coul/msm command :h3 pair_style lj/cut/coul/msm/gpu command :h3 pair_style lj/cut/coul/msm/omp command :h3 +pair_style lj/cut/coul/wolf command :h3 +pair_style lj/cut/coul/wolf/omp command :h3 pair_style lj/cut/tip4p/cut command :h3 pair_style lj/cut/tip4p/cut/omp command :h3 pair_style lj/cut/tip4p/long command :h3 @@ -63,6 +65,10 @@ args = list of arguments for a particular style :ul {lj/cut/coul/msm} args = cutoff (cutoff2) cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units) cutoff2 = global cutoff for Coulombic (optional) (distance units) + {lj/cut/coul/wolf} args = alpha cutoff (cutoff2) + alpha = damping parameter (inverse distance units) + cutoff = global cutoff for LJ (and Coulombic if only 2 arg) (distance units) + cutoff2 = global cutoff for Coulombic (optional) (distance units) {lj/cut/tip4p/cut} args = otype htype btype atype qdist cutoff (cutoff2) otype,htype = atom types for TIP4P O and H btype,atype = bond and angle types for TIP4P waters @@ -115,6 +121,10 @@ pair_style lj/cut/tip4p/cut 1 2 7 8 0.15 12.0 10.0 pair_coeff * * 100.0 3.0 pair_coeff 1 1 100.0 3.5 9.0 :pre +pair_style lj/cut/coul/wolf 0.2 5. 10.0 +pair_coeff * * 1.0 1.0 +pair_coeff 1 1 1.0 1.0 2.5 :pre + pair_style lj/cut/tip4p/long 1 2 7 8 0.15 12.0 pair_style lj/cut/tip4p/long 1 2 7 8 0.15 12.0 10.0 pair_coeff * * 100.0 3.0 @@ -179,6 +189,24 @@ that a term is added for the "core/shell model"_Section_howto.html#howto_25 to allow charges on core and shell particles to be separated by r = 0.0. +Style {coul/wolf} adds a Coulombic pairwise interaction via the Wolf +summation method, described in "Wolf"_#Wolf1, given by: + +:c,image(Eqs/pair_coul_wolf.jpg) + +where {alpha} is the damping parameter, and erfc() is the +complementary error-function terms. This potential +is essentially a short-range, spherically-truncated, +charge-neutralized, shifted, pairwise {1/r} summation. With a +manipulation of adding and subtracting a self term (for i = j) to the +first and second term on the right-hand-side, respectively, and a +small enough {alpha} damping parameter, the second term shrinks and +the potential becomes a rapidly-converging real-space summation. With +a long enough cutoff and small enough alpha parameter, the energy and +forces calculated by the Wolf summation method approach those of the +Ewald sum. So it is a means of getting effective long-range +interactions with a short-range potential. + Styles {lj/cut/tip4p/cut} and {lj/cut/tip4p/long} implement the TIP4P water model of "(Jorgensen)"_#Jorgensen2, which introduces a massless site located a short distance away from the oxygen atom along the diff --git a/doc/src/read_data.txt b/doc/src/read_data.txt index 8c9aa02e22..fd297e36c1 100644 --- a/doc/src/read_data.txt +++ b/doc/src/read_data.txt @@ -15,10 +15,11 @@ read_data file keyword args ... :pre file = name of data file to read in :ulb,l zero or more keyword/arg pairs may be appended :l keyword = {add} or {offset} or {shift} or {extra/atom/types} or {extra/bond/types} or {extra/angle/types} or {extra/dihedral/types} or {extra/improper/types} or {extra/bond/per/atom} or {extra/angle/per/atom} or {extra/dihedral/per/atom} or {extra/improper/per/atom} or {group} or {nocoeff} or {fix} :l - {add} arg = {append} or {Nstart} or {merge} - append = add new atoms with IDs appended to current IDs - Nstart = add new atoms with IDs starting with Nstart - merge = add new atoms with their IDs unchanged + {add} arg = {append} or {IDoffset} or {IDoffset MOLoffset} or {merge} + append = add new atoms with atom IDs appended to current IDs + IDoffset = add new atoms with atom IDs having IDoffset added + MOLoffset = add new atoms with molecule IDs having MOLoffset added (only when molecule IDs are enabled) + merge = add new atoms with their atom IDs (and molecule IDs) unchanged {offset} args = toff boff aoff doff ioff toff = offset to add to atom types boff = offset to add to bond types @@ -120,20 +121,26 @@ boundary, then the atoms may become far apart if the box size grows. This will separate the atoms in the bond, which can lead to "lost" bond atoms or bad dynamics. -The three choices for the {add} argument affect how the IDs of atoms -in the data file are treated. If {append} is specified, atoms in the -data file are added to the current system, with their atom IDs reset -so that an atomID = M in the data file becomes atomID = N+M, where N -is the largest atom ID in the current system. This rule is applied to -all occurrences of atom IDs in the data file, e.g. in the Velocity or -Bonds section. If {Nstart} is specified, then {Nstart} is a numeric -value is given, e.g. 1000, so that an atomID = M in the data file -becomes atomID = 1000+M. If {merge} is specified, the data file atoms +The three choices for the {add} argument affect how the atom IDs and +molecule IDs of atoms in the data file are treated. If {append} is +specified, atoms in the data file are added to the current system, +with their atom IDs reset so that an atomID = M in the data file +becomes atomID = N+M, where N is the largest atom ID in the current +system. This rule is applied to all occurrences of atom IDs in the +data file, e.g. in the Velocity or Bonds section. This is also done +for molecule IDs, if the atom style does support molecule IDs or +they are enabled via fix property/atom. If {IDoffset} is specified, +then {IDoffset} is a numeric value is given, e.g. 1000, so that an +atomID = M in the data file becomes atomID = 1000+M. For systems +with enabled molecule IDs, another numerical argument {MOLoffset} +is required representing the equivalent offset for molecule IDs. +If {merge} is specified, the data file atoms are added to the current system without changing their IDs. They are assumed to merge (without duplication) with the currently defined atoms. It is up to you to insure there are no multiply defined atom IDs, as LAMMPS only performs an incomplete check that this is the case -by insuring the resulting max atomID >= the number of atoms. +by insuring the resulting max atomID >= the number of atoms. For +molecule IDs, there is no check done at all. The {offset} and {shift} keywords can only be used if the {add} keyword is also specified. @@ -547,7 +554,7 @@ charge: atom-ID atom-type q x y z dipole: atom-ID atom-type q x y z mux muy muz dpd: atom-ID atom-type theta x y z edpd: atom-ID atom-type edpd_temp edpd_cv x y z -mdpd: atom-ID atom-type x y z +mdpd: atom-ID atom-type rho x y z tdpd: atom-ID atom-type x y z cc1 cc2 ... ccNspecies electron: atom-ID atom-type q spin eradius x y z ellipsoid: atom-ID atom-type ellipsoidflag density x y z diff --git a/doc/src/tutorial_pylammps.txt b/doc/src/tutorial_pylammps.txt index 52eb6415db..11cddb3cbf 100644 --- a/doc/src/tutorial_pylammps.txt +++ b/doc/src/tutorial_pylammps.txt @@ -6,14 +6,14 @@ :line -PyLammps Tutorial :h1 +PyLammps Tutorial :h3 -Overview :h2 +Overview :h4 PyLammps is a Python wrapper class which can be created on its own or use an existing lammps Python object. It creates a simpler, Python-like interface to @@ -23,16 +23,16 @@ C++ code implementation. Finally, the IPyLammps wrapper builds on top of PyLammps and adds some additional features for IPython integration into IPython notebooks, e.g. for embedded visualization output from dump/image. -Comparison of lammps and PyLammps interfaces :h3 +Comparison of lammps and PyLammps interfaces :h5 -lammps.lammps :h4 +lammps.lammps :h6 uses C-Types direct memory access to native C++ data provides functions to send and receive data to LAMMPS requires knowledge of how LAMMPS internally works (C pointers, etc) :ul -lammps.PyLammps :h4 +lammps.PyLammps :h6 higher-level abstraction built on top of original C-Types interface manipulation of Python objects @@ -41,11 +41,11 @@ shorter, more concise Python better IPython integration, designed for quick prototyping :ul -Quick Start :h2 +Quick Start :h4 -System-wide Installation :h3 +System-wide Installation :h5 -Step 1: Building LAMMPS as a shared library :h4 +Step 1: Building LAMMPS as a shared library :h6 To use LAMMPS inside of Python it has to be compiled as shared library. This library is then loaded by the Python interface. In this example we enable the @@ -60,7 +60,7 @@ make yes-MOLECULE :pre # compile shared library using Makefile make mpi mode=shlib LMP_INC="-DLAMMPS_PNG -DLAMMPS_JPEG -DLAMMPS_FFMPEG -DLAMMPS_EXCEPTIONS" JPG_LIB="-lpng -ljpeg" :pre -Step 2: Installing the LAMMPS Python package :h4 +Step 2: Installing the LAMMPS Python package :h6 PyLammps is part of the lammps Python package. To install it simply install that package into your current Python installation. @@ -71,12 +71,12 @@ python install.py :pre NOTE: Recompiling the shared library requires reinstalling the Python package -Installation inside of a virtualenv :h3 +Installation inside of a virtualenv :h5 You can use virtualenv to create a custom Python environment specifically tuned for your workflow. -Benefits of using a virtualenv :h4 +Benefits of using a virtualenv :h6 isolation of your system Python installation from your development installation installation can happen in your user directory without root access (useful for HPC clusters) @@ -87,7 +87,7 @@ you can even install specific old versions of a package if necessary :ul apt-get install python-virtualenv :pre -Creating a virtualenv with lammps installed :h4 +Creating a virtualenv with lammps installed :h6 # create virtualenv name 'testing' :pre @@ -107,7 +107,7 @@ source testing/bin/activate :pre (testing) deactivate :pre -Creating a new instance of PyLammps :h2 +Creating a new instance of PyLammps :h4 To create a PyLammps object you need to first import the class from the lammps module. By using the default constructor, a new {lammps} instance is created. @@ -121,7 +121,7 @@ from lammps import lammps, PyLammps lmp = lammps() L = PyLammps(ptr=lmp) :pre -Commands :h2 +Commands :h4 Sending a LAMMPS command with the existing library interfaces is done using the command method of the lammps object instance. @@ -155,7 +155,7 @@ them automatically to a final command string. L.region("box block", xlo, xhi, ylo, yhi, zlo, zhi) :pre -System state :h2 +System state :h4 In addition to dispatching commands directly through the PyLammps object, it also provides several properties which allow you to query the system state. @@ -208,7 +208,7 @@ List of groups present in the current system :dd :dle -Working with LAMMPS variables :h2 +Working with LAMMPS variables :h4 LAMMPS variables can be both defined and accessed via the PyLammps interface. @@ -229,7 +229,7 @@ property of this object. print(a.value) a.value = 4 :pre -Retrieving the value of an arbitrary LAMMPS expressions :h2 +Retrieving the value of an arbitrary LAMMPS expressions :h4 LAMMPS expressions can be immediately evaluated by using the eval method. The passed string parameter can be any expression containing global thermo values, @@ -240,7 +240,7 @@ result = L.eval("pe") # potential energy :pre result = L.eval("v_t/2.0") :pre -Accessing atom data :h2 +Accessing atom data :h4 All atoms in the current simulation can be accessed by using the L.atoms list. Each element of this list is an object which exposes its properties (id, type, @@ -263,7 +263,7 @@ L.atoms\[0\].position = (1.0, 0.0) :pre # set position in 3D simulation L.atoms\[0\].position = (1.0, 0.0, 1.) :pre -Evaluating thermo data :h2 +Evaluating thermo data :h4 Each simulation run usually produces thermo output based on system state, computes, fixes or variables. The trajectories of these values can be queried @@ -291,7 +291,7 @@ steps = L.runs\[0\].step ke = L.runs\[0\].ke plt.plot(steps, ke) :pre -Error handling with PyLammps :h2 +Error handling with PyLammps :h4 Compiling the shared library with C++ exception support provides a better error handling experience. Without exceptions the LAMMPS code will terminate the @@ -304,7 +304,7 @@ current LAMMPS process is in an illegal state and must be terminated. It is advised to save your data and terminate the Python instance as quickly as possible. -Using PyLammps in IPython notebooks and Jupyter :h2 +Using PyLammps in IPython notebooks and Jupyter :h4 If the LAMMPS Python package is installed for the same Python interpreter as IPython, you can use PyLammps directly inside of an IPython notebook inside of @@ -320,7 +320,7 @@ Python environment (this assumes you followed the Quick Start instructions): jupyter notebook :pre -IPyLammps Examples :h2 +IPyLammps Examples :h4 Examples of IPython notebooks can be found in the python/examples/pylammps subdirectory. To open these notebooks launch {jupyter notebook} inside this @@ -328,7 +328,7 @@ directory and navigate to one of them. If you compiled and installed a LAMMPS shared library with exceptions, PNG, JPEG and FFMPEG support you should be able to rerun all of these notebooks. -Validating a dihedral potential :h3 +Validating a dihedral potential :h5 This example showcases how an IPython Notebook can be used to compare a simple LAMMPS simulation of a harmonic dihedral potential to its analytical solution. @@ -353,7 +353,7 @@ plot inside the IPython notebook. :c,image(JPG/pylammps_dihedral.jpg) -Running a Monte Carlo relaxation :h3 +Running a Monte Carlo relaxation :h5 This second example shows how to use PyLammps to create a 2D Monte Carlo Relaxation simulation, computing and plotting energy terms and even embedding video output. @@ -424,7 +424,7 @@ The energies of each iteration are collected in a Python list and finally plotte The IPython notebook also shows how to use dump commands and embed video files inside of the IPython notebook. -Using PyLammps and mpi4py (Experimental) :h2 +Using PyLammps and mpi4py (Experimental) :h4 PyLammps can be run in parallel using mpi4py. This python package can be installed using @@ -451,7 +451,7 @@ mpirun -np 4 python melt.py :pre IMPORTANT NOTE: Any command must be executed by all MPI processes. However, evaluations and querying the system state is only available on rank 0. -Feedback and Contributing :h2 +Feedback and Contributing :h4 If you find this Python interface useful, please feel free to provide feedback and ideas on how to improve it to Richard Berger (richard.berger@temple.edu). We also diff --git a/doc/src/variable.txt b/doc/src/variable.txt index e3b7c5de0d..c0851464c3 100644 --- a/doc/src/variable.txt +++ b/doc/src/variable.txt @@ -689,7 +689,7 @@ increase in increments of z, starting at x, until a is reached. At that point the timestep increases in increments of c, from a to b, then after b, increments by z are resumed until y is reached. For any current timestep, the next timestep in the sequence is returned. Thus -if stride(1000,2000,100,1350,1360,1) is used in a variable by the +if stride2(1000,2000,100,1350,1360,1) is used in a variable by the "dump_modify every"_dump_modify.html command, it will generate the sequence of output timesteps: diff --git a/examples/USER/meso/edpd/in.edpd b/examples/USER/meso/edpd/in.edpd index 316099bce3..af1a79d73d 100644 --- a/examples/USER/meso/edpd/in.edpd +++ b/examples/USER/meso/edpd/in.edpd @@ -1,54 +1,54 @@ -######################################################################## -### Heat conduction analog of periodic Poiseuille flow problem ### -### using energy-conserving DPD (eDPD) simulation ### -### ### -### Created : Zhen Li (zhen_li@brown.edu) ### -### Division of Applied Mathematics, Brown University. ### -### ### -### mDPD system setup follows Fig.12 in the publication: ### -### Z. Li, Y.-H. Tang, H. Lei, B. Caswell and G.E. Karniadakis. ### -### "Energy-conserving dissipative particle dynamics with ### -### temperature-dependent properties". J. Comput. Phys., ### -### 2014, 265: 113-127. DOI: 10.1016/j.jcp.2014.02.003 ### -######################################################################## -units lj -dimension 3 -boundary p p p -neighbor 0.2 bin -neigh_modify every 1 delay 0 check yes - -atom_style edpd - -region edpd block -10 10 -10 10 -5 5 units box -create_box 1 edpd -create_atoms 1 random 16000 276438 NULL -mass 1 1.0 -set atom * edpd/temp 1.0 -set atom * edpd/cv 1.0E5 - -pair_style edpd 1.58 9872598 -#pair_coeff 1 1 18.75 4.5 0.41 1.58 1.45E-5 2.0 1.58 -pair_coeff 1 1 18.75 4.5 0.41 1.58 1.41E-5 2.0 1.58 & - power 10.54 -3.66 3.44 -4.10 & - kappa -0.44 -3.21 5.04 0.00 - -compute mythermo all temp -thermo 100 -thermo_modify temp mythermo -thermo_modify flush yes - -velocity all create 1.0 432982 loop local dist gaussian - -fix mvv all mvv/edpd 0.5 -fix upper all edpd/source cuboid 0.0 5.0 0.0 20.0 10.0 10.0 0.01 -fix lower all edpd/source cuboid 0.0 -5.0 0.0 20.0 10.0 10.0 -0.01 - -timestep 0.01 -run 500 -reset_timestep 0 - -compute temp all edpd/temp/atom -compute ccT all chunk/atom bin/1d y 0.0 1.0 -fix stat all ave/chunk 1 500 500 ccT c_temp density/number norm sample file temp.profile - -run 500 +######################################################################## +### Heat conduction analog of periodic Poiseuille flow problem ### +### using energy-conserving DPD (eDPD) simulation ### +### ### +### Created : Zhen Li (zhen_li@brown.edu) ### +### Division of Applied Mathematics, Brown University. ### +### ### +### mDPD system setup follows Fig.12 in the publication: ### +### Z. Li, Y.-H. Tang, H. Lei, B. Caswell and G.E. Karniadakis. ### +### "Energy-conserving dissipative particle dynamics with ### +### temperature-dependent properties". J. Comput. Phys., ### +### 2014, 265: 113-127. DOI: 10.1016/j.jcp.2014.02.003 ### +######################################################################## +units lj +dimension 3 +boundary p p p +neighbor 0.2 bin +neigh_modify every 1 delay 0 check yes + +atom_style edpd + +region edpd block -10 10 -10 10 -5 5 units box +create_box 1 edpd +create_atoms 1 random 16000 276438 NULL +mass 1 1.0 +set atom * edpd/temp 1.0 +set atom * edpd/cv 1.0E5 + +pair_style edpd 1.58 9872598 +#pair_coeff 1 1 18.75 4.5 0.41 1.58 1.45E-5 2.0 1.58 +pair_coeff 1 1 18.75 4.5 0.41 1.58 1.41E-5 2.0 1.58 & + power 10.54 -3.66 3.44 -4.10 & + kappa -0.44 -3.21 5.04 0.00 + +compute mythermo all temp +thermo 100 +thermo_modify temp mythermo +thermo_modify flush yes + +velocity all create 1.0 432982 loop local dist gaussian + +fix mvv all mvv/edpd 0.5 +fix upper all edpd/source cuboid 0.0 5.0 0.0 20.0 10.0 10.0 0.01 +fix lower all edpd/source cuboid 0.0 -5.0 0.0 20.0 10.0 10.0 -0.01 + +timestep 0.01 +run 500 +reset_timestep 0 + +compute temp all edpd/temp/atom +compute ccT all chunk/atom bin/1d y 0.0 1.0 +fix stat all ave/chunk 1 500 500 ccT c_temp density/number norm sample file temp.profile + +run 500 diff --git a/examples/USER/meso/mdpd/in.mdpd b/examples/USER/meso/mdpd/in.mdpd index 201b4a340e..b0740c8227 100644 --- a/examples/USER/meso/mdpd/in.mdpd +++ b/examples/USER/meso/mdpd/in.mdpd @@ -1,52 +1,52 @@ -######################################################################## -#### 3D droplet oscilation using many-body DPD simulation ### -#### ### -#### Created : Zhen Li (zhen_li@brown.edu) ### -#### Division of Applied Mathematics, Brown University. ### -#### ### -#### mDPD parameters follow the choice of the publication: ### -#### Z. Li et al. "Three dimensional flow structures in a moving ### -#### droplet on substrate: a dissipative particle dynamics study" ### -#### Physics of Fluids, 2013, 25: 072103. DOI: 10.1063/1.4812366 ### -######################################################################## -units lj -dimension 3 -boundary p p p -neighbor 0.3 bin -neigh_modify every 1 delay 0 check yes - -atom_style mdpd - -region mdpd block -25 25 -10 10 -10 10 units box -create_box 1 mdpd - -lattice fcc 6 -region film block -20 20 -7.5 7.5 -2.0 2.0 units box -create_atoms 1 region film - -pair_style hybrid/overlay mdpd/rhosum mdpd 1.0 1.0 9872598 -pair_coeff 1 1 mdpd/rhosum 0.75 -pair_coeff 1 1 mdpd -40 25 18.0 1.0 0.75 -mass 1 1.0 - -compute mythermo all temp -thermo 100 -thermo_modify temp mythermo -thermo_modify flush yes - -velocity all create 1.0 38497 loop local dist gaussian - -fix mvv all mvv/dpd - -#dump mydump all atom 100 atom.lammpstrj - -#dump jpg all image 200 image.*.jpg type type zoom 5 adiam 0.5 & -# view 90 90 box no 0 size 600 200 -#dump_modify jpg pad 4 - -#dump avi all movie 200 movie.avi type type zoom 5 adiam 0.5 & -# view 90 90 box no 0 size 600 200 -#dump_modify avi pad 4 - -timestep 0.01 -run 4000 +######################################################################## +#### 3D droplet oscilation using many-body DPD simulation ### +#### ### +#### Created : Zhen Li (zhen_li@brown.edu) ### +#### Division of Applied Mathematics, Brown University. ### +#### ### +#### mDPD parameters follow the choice of the publication: ### +#### Z. Li et al. "Three dimensional flow structures in a moving ### +#### droplet on substrate: a dissipative particle dynamics study" ### +#### Physics of Fluids, 2013, 25: 072103. DOI: 10.1063/1.4812366 ### +######################################################################## +units lj +dimension 3 +boundary p p p +neighbor 0.3 bin +neigh_modify every 1 delay 0 check yes + +atom_style mdpd + +region mdpd block -25 25 -10 10 -10 10 units box +create_box 1 mdpd + +lattice fcc 6 +region film block -20 20 -7.5 7.5 -2.0 2.0 units box +create_atoms 1 region film + +pair_style hybrid/overlay mdpd/rhosum mdpd 1.0 1.0 9872598 +pair_coeff 1 1 mdpd/rhosum 0.75 +pair_coeff 1 1 mdpd -40 25 18.0 1.0 0.75 +mass 1 1.0 + +compute mythermo all temp +thermo 100 +thermo_modify temp mythermo +thermo_modify flush yes + +velocity all create 1.0 38497 loop local dist gaussian + +fix mvv all mvv/dpd + +#dump mydump all atom 100 atom.lammpstrj + +#dump jpg all image 200 image.*.jpg type type zoom 5 adiam 0.5 & +# view 90 90 box no 0 size 600 200 +#dump_modify jpg pad 4 + +#dump avi all movie 200 movie.avi type type zoom 5 adiam 0.5 & +# view 90 90 box no 0 size 600 200 +#dump_modify avi pad 4 + +timestep 0.01 +run 4000 diff --git a/examples/USER/meso/tdpd/in.tdpd b/examples/USER/meso/tdpd/in.tdpd index 748a4f5077..5107e7a454 100644 --- a/examples/USER/meso/tdpd/in.tdpd +++ b/examples/USER/meso/tdpd/in.tdpd @@ -1,54 +1,54 @@ -######################################################################## -### Pure diffusion with a reaction source term analog of a periodic ### -### Poiseuille flow problem using transport DPD (tDPD) simulation ### -### ### -### Created : Zhen Li (zhen_li@brown.edu) ### -### Division of Applied Mathematics, Brown University. ### -### ### -### tDPD system setup follows Fig.1 in the publication: ### -### Z. Li, A. Yazdani, A. Tartakovsky and G.E. Karniadakis. ### -### "Transport dissipative particle dynamics model for mesoscopic ### -### advection-diffusion-reaction problems. J. Chem. Phys., ### -### 2015, 143: 014101. DOI: 10.1063/1.4923254 ### -######################################################################## -units lj -dimension 3 -boundary p p p -neighbor 0.2 bin -neigh_modify every 1 delay 0 check yes - -atom_style tdpd 2 - -region tdpd block -10 10 -10 10 -5 5 units box -create_box 1 tdpd -create_atoms 1 random 16000 276438 NULL -mass 1 1.0 -set atom * cc 1 1.0 -set atom * cc 2 1.0 - -pair_style tdpd 1.0 1.58 9872598 -pair_coeff 1 1 18.75 4.5 0.41 1.58 1.58 1.0 1.0E-5 2.0 3.0 1.0E-5 2.0 - -compute mythermo all temp -thermo 50 -thermo_modify temp mythermo -thermo_modify flush yes - -velocity all create 1.0 432982 loop local dist gaussian - -fix mvv all mvv/tdpd 0.5 -fix upper1 all tdpd/source 1 cuboid 0.0 5.0 0.0 20.0 10.0 10.0 0.01 -fix lower1 all tdpd/source 1 cuboid 0.0 -5.0 0.0 20.0 10.0 10.0 -0.01 -fix upper2 all tdpd/source 2 cuboid 0.0 5.0 0.0 20.0 10.0 10.0 -0.01 -fix lower2 all tdpd/source 2 cuboid 0.0 -5.0 0.0 20.0 10.0 10.0 0.01 - -timestep 0.01 -run 500 -reset_timestep 0 - -compute cc1 all tdpd/cc/atom 1 -compute cc2 all tdpd/cc/atom 2 -compute bin all chunk/atom bin/1d y 0.0 1.0 -fix stat all ave/chunk 1 100 100 bin c_cc1 c_cc2 norm sample file cc.profile - -run 100 +######################################################################## +### Pure diffusion with a reaction source term analog of a periodic ### +### Poiseuille flow problem using transport DPD (tDPD) simulation ### +### ### +### Created : Zhen Li (zhen_li@brown.edu) ### +### Division of Applied Mathematics, Brown University. ### +### ### +### tDPD system setup follows Fig.1 in the publication: ### +### Z. Li, A. Yazdani, A. Tartakovsky and G.E. Karniadakis. ### +### "Transport dissipative particle dynamics model for mesoscopic ### +### advection-diffusion-reaction problems. J. Chem. Phys., ### +### 2015, 143: 014101. DOI: 10.1063/1.4923254 ### +######################################################################## +units lj +dimension 3 +boundary p p p +neighbor 0.2 bin +neigh_modify every 1 delay 0 check yes + +atom_style tdpd 2 + +region tdpd block -10 10 -10 10 -5 5 units box +create_box 1 tdpd +create_atoms 1 random 16000 276438 NULL +mass 1 1.0 +set atom * cc 1 1.0 +set atom * cc 2 1.0 + +pair_style tdpd 1.0 1.58 9872598 +pair_coeff 1 1 18.75 4.5 0.41 1.58 1.58 1.0 1.0E-5 2.0 3.0 1.0E-5 2.0 + +compute mythermo all temp +thermo 50 +thermo_modify temp mythermo +thermo_modify flush yes + +velocity all create 1.0 432982 loop local dist gaussian + +fix mvv all mvv/tdpd 0.5 +fix upper1 all tdpd/source 1 cuboid 0.0 5.0 0.0 20.0 10.0 10.0 0.01 +fix lower1 all tdpd/source 1 cuboid 0.0 -5.0 0.0 20.0 10.0 10.0 -0.01 +fix upper2 all tdpd/source 2 cuboid 0.0 5.0 0.0 20.0 10.0 10.0 -0.01 +fix lower2 all tdpd/source 2 cuboid 0.0 -5.0 0.0 20.0 10.0 10.0 0.01 + +timestep 0.01 +run 500 +reset_timestep 0 + +compute cc1 all tdpd/cc/atom 1 +compute cc2 all tdpd/cc/atom 2 +compute bin all chunk/atom bin/1d y 0.0 1.0 +fix stat all ave/chunk 1 100 100 bin c_cc1 c_cc2 norm sample file cc.profile + +run 100 diff --git a/examples/USER/mgpt/log.lammps b/examples/USER/mgpt/log.lammps deleted file mode 100644 index 9485c36e47..0000000000 --- a/examples/USER/mgpt/log.lammps +++ /dev/null @@ -1,78 +0,0 @@ -LAMMPS (23 Oct 2015) -# script for mgpt t=0 eos with relaxed vacancy in bcc structure: -# input for relaxed vacancy formation energy at constant pressure - -echo screen -Lattice spacing in x,y,z = 6.23812 6.23812 6.23812 -Created orthogonal box = (0 0 0) to (31.1906 31.1906 31.1906) - 1 by 1 by 1 MPI processor grid -Created 250 atoms -Deleted 1 atoms, new total = 249 -Reading potential file Ta6.8x.mgpt.potin with DATE: 2015-07-30 -Neighbor list info ... - 2 neighbor list requests - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 13.1712 - ghost atom cutoff = 13.1712 - binsize = 6.58562 -> bins = 5 5 5 -Memory usage per processor = 4.66978 Mbytes -Step Volume Temp PotEng TotEng Press - 0 30343.887 0 -73.994511 -73.994511 -1.0504398e+09 - 10 30343.887 0 -74.002332 -74.002332 -1.107516e+09 - 20 30343.887 0 -74.00485 -74.00485 -1.1316373e+09 - 30 30343.887 0 -74.005762 -74.005762 -1.143304e+09 - 40 30343.887 0 -74.006116 -74.006116 -1.149395e+09 - 50 30343.887 0 -74.006262 -74.006262 -1.1527914e+09 - 60 30343.887 0 -74.006323 -74.006323 -1.1547677e+09 - 70 30343.887 0 -74.00635 -74.00635 -1.1559529e+09 - 80 30343.887 0 -74.006361 -74.006361 -1.1566763e+09 - 90 30343.887 0 -74.006366 -74.006366 -1.1571256e+09 - 100 30343.887 0 -74.006369 -74.006369 -1.1574093e+09 - 110 30343.887 0 -74.00637 -74.00637 -1.1575908e+09 - 120 30343.887 0 -74.00637 -74.00637 -1.1577083e+09 - 130 30343.887 0 -74.00637 -74.00637 -1.1577849e+09 - 139 30343.887 0 -74.006371 -74.006371 -1.1578311e+09 -Loop time of 4.33109 on 1 procs for 139 steps with 249 atoms - -92.4% CPU use with 1 MPI tasks x no OpenMP threads - -Minimization stats: - Stopping criterion = energy tolerance - Energy initial, next-to-last, final = - -73.9945109564 -74.0063705487 -74.0063705557 - Force two-norm initial, final = 0.0366227 8.09081e-05 - Force max component initial, final = 0.00730948 8.05242e-06 - Final line search alpha, max atom move = 1 8.05242e-06 - Iterations, force evaluations = 139 139 - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 4.3064 | 4.3064 | 4.3064 | 0.0 | 99.43 -Neigh | 0.019113 | 0.019113 | 0.019113 | 0.0 | 0.44 -Comm | 0.0017624 | 0.0017624 | 0.0017624 | 0.0 | 0.04 -Output | 0.00084376 | 0.00084376 | 0.00084376 | 0.0 | 0.02 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0.00297 | | | 0.07 - -Nlocal: 249 ave 249 max 249 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 1479 ave 1479 max 1479 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 7936 ave 7936 max 7936 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 15872 ave 15872 max 15872 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 15872 -Ave neighs/atom = 63.743 -Neighbor list builds = 4 -Dangerous builds = 0 -number of atoms = 249 -atomic volume (a.u.) = 121.863 -total energy (ry/atom) = -0.594428679162064 -pressure (gpa) = -1.15783109519801 -249 121.863 -148.012741111354 -1.15783109519801 -121.863 -0.594428679162064 -1.15783109519801 -Total wall time: 0:00:04 diff --git a/examples/gcmc/in.gcmc.co2 b/examples/gcmc/in.gcmc.co2 index 128f05b489..bb6916fc48 100644 --- a/examples/gcmc/in.gcmc.co2 +++ b/examples/gcmc/in.gcmc.co2 @@ -58,21 +58,21 @@ timestep 1.0 # rigid constraints with thermostat -fix myrigidnvt all rigid/nvt/small molecule temp ${temp} ${temp} 100 mol co2mol +fix myrigidnvt co2 rigid/nvt/small molecule temp ${temp} ${temp} 100 mol co2mol fix_modify myrigidnvt dynamic/dof no # gcmc variable tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans) -fix mygcmc all gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol & +fix mygcmc co2 gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol & co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt # atom counts variable carbon atom "type==1" variable oxygen atom "type==2" -group carbon dynamic all var carbon -group oxygen dynamic all var oxygen +group carbon dynamic co2 var carbon +group oxygen dynamic co2 var oxygen variable nC equal count(carbon) variable nO equal count(oxygen) diff --git a/examples/gcmc/in.gcmc.lj b/examples/gcmc/in.gcmc.lj index 3fe78efb25..a1c7c6eb10 100644 --- a/examples/gcmc/in.gcmc.lj +++ b/examples/gcmc/in.gcmc.lj @@ -29,14 +29,18 @@ create_box 1 box pair_coeff * * 1.0 1.0 mass * 1.0 +# we recommend setting up a dedicated group for gcmc + +group gcmcgroup type 1 + # gcmc -fix mygcmc all gcmc 1 100 100 1 29494 ${temp} ${mu} ${disp} +fix mygcmc gcmcgroup gcmc 1 100 100 1 29494 ${temp} ${mu} ${disp} # atom count variable type1 atom "type==1" -group type1 dynamic all var type1 +group type1 dynamic gcmcgroup var type1 variable n1 equal count(type1) # averaging diff --git a/examples/latte/latte.in b/examples/latte/latte.in index 7df354a742..b8b214b78b 100644 --- a/examples/latte/latte.in +++ b/examples/latte/latte.in @@ -12,7 +12,7 @@ CONTROL{ xControl= 1 BASISTYPE= NONORTHO COORDSFILE= "./coords.dat" - PARAMPATH= "/home/user/LATTE/TBparam" + PARAMPATH= "./TBparam" KBT= 0.0 ENTROPYKIND= 1 PPOTON= 1 diff --git a/lib/colvars/colvar.cpp b/lib/colvars/colvar.cpp index ce76b3b9eb..5a4e8b617a 100644 --- a/lib/colvars/colvar.cpp +++ b/lib/colvars/colvar.cpp @@ -195,7 +195,7 @@ int colvar::init(std::string const &conf) // - it is homogeneous // - all cvcs are periodic // - all cvcs have the same period - if (cvcs[0]->b_periodic) { // TODO make this a CVC feature + if (is_enabled(f_cv_homogeneous) && cvcs[0]->b_periodic) { // TODO make this a CVC feature bool b_periodic = true; period = cvcs[0]->period; for (i = 1; i < cvcs.size(); i++) { diff --git a/lib/colvars/colvar.h b/lib/colvars/colvar.h index 20dad2771b..32c329460d 100644 --- a/lib/colvars/colvar.h +++ b/lib/colvars/colvar.h @@ -11,8 +11,6 @@ #define COLVAR_H #include