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Configuration files

In exaStamp, multiple configuration files are located in the data/config folder. The master configuration file is the main-config.msp file which controls the entire simulation graph and defines both simulation, includes and configuration blocks. The content of main-config.msp and all other configuration files are displayed below.

Tip

The main-config.msp file is included by default by your input file when launching exaStamp. You can redefine its content to define new simulation scenarios at your own risk.

main-config.msp

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print_logo_banner:
  profiling: false
  body:
    - message: |

       ███████╗██╗  ██╗ █████╗ ███████╗████████╗ █████╗ ███╗   ███╗██████╗     ██╗   ██╗██████╗
       ██╔════╝╚██╗██╔╝██╔══██╗██╔════╝╚══██╔══╝██╔══██╗████╗ ████║██╔══██╗    ██║   ██║╚════██╗
       █████╗   ╚███╔╝ ███████║███████╗   ██║   ███████║██╔████╔██║██████╔╝    ██║   ██║ █████╔╝
       ██╔══╝   ██╔██╗ ██╔══██║╚════██║   ██║   ██╔══██║██║╚██╔╝██║██╔═══╝     ╚██╗ ██╔╝ ╚═══██╗
       ███████╗██╔╝ ██╗██║  ██║███████║   ██║   ██║  ██║██║ ╚═╝ ██║██║          ╚████╔╝ ██████╔╝
       ╚══════╝╚═╝  ╚═╝╚═╝  ╚═╝╚══════╝   ╚═╝   ╚═╝  ╚═╝╚═╝     ╚═╝╚═╝           ╚═══╝  ╚═════╝
    - version_info

# --------------- Default Includes --------------- #

includes:
  - config_defaults.msp
  - config_debug.msp
  - config_move_particles.msp
  - config_numerical_schemes.msp
  - config_globals.msp
  - config_iteration_log.msp
  - config_iteration_dump.msp
  - config_end_iteration.msp
  - config_init_temperature.msp
  - config_input.msp

# ------------------------------------------------ #

# -------- Simulation Program Description -------- #

simulation:
  name: sim
  body:
    - print_logo_banner
    - hw_device_init   # provide MPI_COMM_WORLD as a default communicator
    - make_empty_grid
    - grid_flavor
    - global
    - init_parameters
    - generate_default_species
    - particle_regions
    - preinit_rcut_max
    - domain
    - init_prolog
    - input_data
    - species: { verbose: false , fail_if_empty: true }
    - grid_post_processing
    - reduce_species_after_read
    - init_rcut_max
    - print_domain
    - performance_adviser: { verbose: true }
    - initialize_temperature
    - init_epilog
    - species: { verbose: true , fail_if_empty: true }
    - first_iteration
    - compute_loop
    - simulation_epilog
    - hw_device_finalize

# ------------------------------------------------ #

# ----------------- Compute Loop ----------------- #

# First iteration
first_iteration:
  - init_particles
  - compute_all_forces_energy
  - default_thermodynamic_state
  - default_print_thermodynamic_state: { lb_flag: false , move_flag: false , print_header: true }
  - default_dump_thermodynamic_state
  - next_time_step

# Loop structure
compute_loop:
  loop: true
  name: loop
  condition: compute_loop_continue
  body:
    - compute_loop_prolog
    - begin_iteration
    - numerical_scheme
    - end_iteration
    - compute_loop_epilog
    - next_time_step
    - compute_loop_stop

# Stop condition
compute_loop_stop:
  profiling: false
  rebind: { end_at: simulation_end_iteration , result: compute_loop_continue }
  body:
    - sim_continue

# Prolog and epilog
compute_loop_prolog: nop
compute_loop_epilog: nop

# ------------------------------------------------ #

# ------ Hardware Device + Simulation Epilog ----- #

hw_device_init:
  - mpi_comm_world
  - init_cuda

hw_device_finalize:
  - finalize_cuda

# This enables user to use this command line to disable cuda
# --set-init_cuda-enable_cuda false 
init_cuda:
  enable_cuda: true

simulation_epilog:
  - default_thermodynamic_state
  - final_dump

# ------------------------------------------------ #

# ---------- Initialization Functions ------------ #

init_prolog: nop
init_epilog: nop
init_parameters: nop

# Executed once whitout verbosity first to
# enable automatic cell_size calculation
preinit_rcut_max:
  profiling: false
  rebind: { grid: null_grid, chunk_neighbors: null_neighbors, domain: empty_domain }
  body:
    - domain:
        cell_size: 0.0 ang
        grid_dims: [ 0 , 0 , 0 ]
        periodic: [ true , true , true ]
    - compute_force
    - nbh_dist

# Executing potential sub nodes initializes rcut_max which
# won't actually compute anything since grid is empty at this time
init_rcut_max:
  profiling: false
  rebind: { grid: null_grid, chunk_neighbors: null_neighbors }
  body:
    - compute_force
    - nbh_dist: 
        verbose: true

# ------------------------------------------------ #

# -------------- Some Default Values ------------- #

memory_stats: { graph_res_mem: false }

# Usually outputs ParticleSpecies type to a slot named species
# in case the data reader doesn't provide species description
reduce_species_after_read: nop

# By default, species use the default definition of species
# operator to generate initial species
species: { species: [ ] , verbose: false }
generate_default_species: species

# ------------------------------------------------ #

config_defaults.msp

The config_defaults.msp file contains the configuration YAML block that allows the user to parametrize different things:

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configuration:
  physics:                        
    units:
      length: angstrom
      mass: Dalton
      time: picosecond
      charge: elementary_charge
      temperature: kelvin
      amount: particle
      luminosity: candela
      angle: radian
      energy: joule
  logging:
    parallel: false
    debug: false
    profiling: false
  profiling:
    exectime: false
    summary: false
  debug:
    plugins: false
    config: false
    graph: false
    graph_lod: 0
    filter: []
  mpimt: true
  pinethreads: false
  num_threads: {}
  omp_max_nesting: 2

config_globals.msp

The config_globals.msp file contains the default definitiong of global block as well as some values related to the grid, domain and regions.

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# Default global values
global:
  dt: 1.0e-3 ps
  rcut_inc: 1.0 ang   # additional distance so that we d'ont have to rebuild neighbor list each time step
  compute_loop_continue: true
  simulation_end_iteration: 10000
  simulation_log_frequency: 10
  simulation_load_balance_frequency: 100
  simulation_dump_frequency: 1000         # 0 means no dump at all
  simulation_dump_thermo_frequency: 10
  analysis_dump_frequency: 0
  trigger_thermo_state: true
  timestep: 0
  physical_time: 0.
  init_temperature: -1.0
  scale_temperature: -1.0
  enable_load_balance: true
  enable_task_graph: false
  enable_grid_compact: true
  trigger_cost_model_fitting: false
  cost_model_coefs: [ 0.0 , 0.0 , 1.0 , 0.0 ]
  log_mode: mechanical # set to chemistry or default

# Default grid variant
grid_flavor: grid_flavor_full

# Generate empty grid
make_empty_grid:
  rebind: { grid: null_grid }
  body:
    - grid_flavor

# Default domain
domain:
  grid_dims: [ 0 , 0 , 0 ] # deduced from cell_size
  cell_size: 0.0 ang # deduced from max rcut (a.k.a. output slot ghost_dist from nbh_dist node)

# Default empty regions
particle_regions: []

config_input.msp

The config_input.msp file contains the default definition of the input_data block. By default, it tries to read the lastLegacyDump file with StampV3 format. If the read fails,

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# StampV3 Reader, domain bounds are determined from file
read_stamp_v3:
  filename: lastLegacyDump
  bounds_mode: FILE

# Returns true if file `lastLegacyDump`exists
has_legacy_dump_file:
  rebind: { result: has_dump_file }
  body: [ file_exists: { filename: lastLegacyDump } ]

# Default `input_data` block
input_data:
  # Tests if file exists and read file if so
  - has_legacy_dump_file
  - read_lastLegacyDump:
      condition: has_dump_file
      body: [ read_stamp_v3 ]
  # If file doesn't exist, create fake species
  - reset_input_data:
      condition: not has_dump_file
      body:
        - message: "No input data"
        - grid_flavor
        - species:
            verbose: false
            species:
              - XX: { mass: 1.0 Da , z: 1 , charge: 0.0 e- }

config_init_temperature.msp

The config_init_temperature.msp contains a block that allows to initialize the system's temperature. The init_temperature and scale_temperature can be defined in the global block.

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initialize_temperature:
  - block1:
      rebind: { value: init_temperature , result: enable_init_temperature }
      body:
        - greater_than: { threshold: 0.0 K }
  - block2:
      rebind: { value: scale_temperature , result: enable_scale_temperature }
      body:
        - greater_than: { threshold: 0.0 K }
  - block3:
      condition: enable_init_temperature
      rebind: { temperature: init_temperature }
      body:
        - gaussian_noise_v
        - init_temperature
  - block4:
      condition: enable_scale_temperature
      rebind: { temperature: scale_temperature }
      body:
        - init_temperature

config_move_particles.msp

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########### Generic particle update block ################

includes:
  - config_load_balance.msp

# define a test node which outputs a boolean value 'trigger_move_particles'
# which tells when to move particles across cells and update neighbor lists
trigger_move_particles:
  rebind: { threshold: max_displ , result: trigger_move_particles }
  body:
    - particle_displ_over


################### AMR ############################
rebuild_amr:
  sub_grid_density: 6.5
  amr_z_curve: false
  enforced_ordering: 1
####################################################


############ default ghost update parameters #######
ghost_update_r: &ghost_update_parms
  gpu_buffer_pack: true
  async_buffer_pack: true
  staging_buffer: true
  serialize_pack_send: true
  wait_all: false

ghost_update_rq: *ghost_update_parms

update_force_energy_from_ghost: *ghost_update_parms

ghost_update_all_no_fv: *ghost_update_parms
####################################################



################### Neighbor list update ############################
chunk_neighbors:
  config:
    free_scratch_memory: false
    build_particle_offset: true
    subcell_compaction: true
    scratch_mem_per_cell: 1048576
    stream_prealloc_factor: 1.05 # standard value to avoid most of dynamic allocations
    chunk_size: 1

chunk_neighbors_impl: chunk_neighbors

update_particle_neighbors:
  - amr_grid_pairs
  - chunk_neighbors_impl
  - resize_particle_locks
####################################################################

grid_post_processing: grid_memory_compact

profile_ghost_comm_scheme: nop
#profile_ghost_comm_scheme: print_ghost_comm_stats # exchange volume stats
#profile_ghost_comm_scheme: print_ghost_comm_scheme # full print

ghost_update_all_impl: ghost_update_all_no_fv

ghost_full_update:
  - ghost_comm_scheme
  - profile_ghost_comm_scheme
  - ghost_update_all_impl


################### parallel particle migration ############################
parallel_update_particles:
  - migrate_cell_particles
  - rebuild_amr
  - backup_r
  - ghost_full_update
  - grid_post_processing
  - update_particle_neighbors

# define actions to initialize particles at startup, just after file read
init_particles:
  - move_particles
  - extend_domain
  - load_balance
  - parallel_update_particles
###########################################################################


update_particles_full_body:
  - move_particles
  - trigger_load_balance
  - load_balancing_if_triggered
  - parallel_update_particles

update_particles_full:
  condition: trigger_move_particles
  body:
    - update_particles_full_body

update_particles_fast_body:
    - ghost_update_r

update_particles_fast:
  condition: not trigger_move_particles
  body:
    - update_particles_fast_body

check_and_update_particles:
  - trigger_move_particles
  - update_particles_full
  - update_particles_fast
  - loadbalance_log_helper:
      rebind: { lb_flag: trigger_load_balance , move_flag: trigger_move_particles }
      body: [ lb_event_counter ]

config_numerical_schemes.msp

The config_numerical_schemes.msp file contains the default numerical scheme used in exaStamp as well as additional ones.

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thermostat: nop

compute_force_prolog: zero_force_energy
compute_force: nop
compute_force_epilog: force_to_accel

compute_all_forces_energy:
  - compute_force_prolog
  - compute_force
  - compute_force_epilog

verlet_first_half:
  - push_f_v_r: { dt_scale: 1.0 , xform_mode: INV_XFORM }
  - push_f_v: { dt_scale: 0.5  , xform_mode: IDENTITY }

verlet_second_half:
  - push_f_v: { dt_scale: 0.5 , xform_mode: IDENTITY }

# define the verlet numerical scheme
numerical_scheme_verlet:
  name: scheme
  body:
    - verlet_first_half
    - check_and_update_particles
    - load_balance_auto_tune_start
    - compute_all_forces_energy
    - verlet_second_half
    - thermostat
    - load_balance_auto_tune_end

# define the verlet numerical scheme
numerical_scheme_basic:
  - compute_all_forces_energy
  - push_f_v: { xform_mode: IDENTITY }
  - push_v_r: { xform_mode: INV_XFORM }
  - check_and_update_particles

numerical_scheme_overdamped:
  - compute_all_forces_energy
  - push_f_r: { xform_mode: INV_XFORM }
  - check_and_update_particles

numerical_scheme: numerical_scheme_verlet

config_iteration_log.msp

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default_print_thermodynamic_state: print_thermodynamic_state

# Defines when `print_thermo` must be called
trigger_print_log:
  rebind: { freq: simulation_log_frequency , result: trigger_print_log , lb_flag: trigger_load_balance , move_flag: trigger_move_particles }
  body:
    - nth_timestep: { first: true }

# Conditional `print_thermo`
print_log_if_triggered:
  condition: trigger_print_log
  body:
    - default_print_thermodynamic_state: { print_header: false }

config_iteration_dump.msp

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default_dump_thermodynamic_state: dump_thermodynamic_state

# Defines when `dump_data` must be done
trigger_dump_data:
  rebind: { freq: simulation_dump_frequency , result: trigger_dump_data }
  body:
    - nth_timestep: { first: false }

# Defines when `dump_analysis` must be done
trigger_dump_analysis:
  rebind: { freq: analysis_dump_frequency , result: trigger_dump_analysis }
  body:
    - nth_timestep: { first: false }

# Defines when `dump_thermo` must be done
trigger_dump_thermo:
  rebind: { freq: simulation_dump_thermo_frequency , result: trigger_dump_thermo }
  body:
    - nth_timestep: { first: false }

# Conditional `dump_data`
dump_data_if_triggered:
  condition: trigger_dump_data
  body:
    - dump_data

# Conditional `dump_analysis`
dump_analysis_if_triggered:
  condition: trigger_dump_analysis
  body:
    - dump_analysis

# Conditional `dump_thermo` 
dump_thermo_if_triggered:
  condition: trigger_dump_thermo
  body:
    - default_dump_thermodynamic_state: { print_header: false }

dump_data_exastamp_v4:
  rebind: { thermodynamic_state: thermodynamic_state_4_dump }
  body:
    - timestep_file: "ExaStampV4prot_%09d.MpiIO"
    - message: { mesg: "Write dump " , endl: false }
    - print_dump_file:
        rebind: { mesg: filename }
        body:
          - message: { endl: true }
    - simulation_thermodynamic_state
    - write_exastamp_v4

dump_data_stamp_v4:
  rebind: { thermodynamic_state: thermodynamic_state_4_dump }
  body:
    - timestep_file: "StampV4prot_%09d.MpiIO"
    - message: { mesg: "Write dump " , endl: false }
    - print_dump_file:
        rebind: { mesg: filename }
        body:
          - message: { endl: true }
    - simulation_thermodynamic_state
    - write_stamp_v4

dump_data_stamp_v3:
  - timestep_file: "StampV3prot_%09d.MpiIO"
  - message: { mesg: "Write dump " , endl: false }
  - print_dump_file:
      rebind: { mesg: filename }
      body:
        - message: { endl: true }
  - write_stamp_v3

# Native ExaNB dump format for single atoms
dump_data_atoms:
  - timestep_file: "atoms_%09d.MpiIO"
  - write_dump_atoms

# Native ExaNB dump format for rigid molecules
dump_data_rigidmol:
  - timestep_file: "rigidmol_%09d.MpiIO"
  - write_dump_rigidmol

dump_data_vtklegacy:
  - timestep_file: "output_%09d.vtk"
  - message: { mesg: "Write vtk-legacy " , endl: false }
  - print_dump_file:
      rebind: { mesg: filename }
      body:
        - message: { endl: true }
  - write_vtklegacy: { ghost: false }

dump_data_vtk:
  - timestep_file: "output_%09d"
  - message: { mesg: "Write vtk " , endl: false }
  - print_dump_file:
      rebind: { mesg: filename }
      body:
        - message: { endl: true }
  - write_vtk

dump_data_paraview:
  - timestep_file: "paraview/output_%09d"
  - message: { mesg: "Write " , endl: false }
  - print_dump_file:
      rebind: { mesg: filename }
      body:
        - message: { endl: true }
  - write_paraview

dump_data_grid_vtklegacy:
  - grid_flavor
  - resize_grid_cell_values
  - atom_cell_projection
  - timestep_file: "grid_%09d.vtk"
  - write_grid_vtklegacy

dump_data_grid_vtk:
  - grid_flavor
  - resize_grid_cell_values
  - atom_cell_projection
  - timestep_file: "grid_%09d"
  - write_grid_vtk

#dump_data: dump_data_stamp_v3
dump_data: dump_data_atoms

dump_data_CCL:
  - grid_flavor
  - resize_grid_cell_values
  - atom_cell_projection
  - cc_label
  - timestep_file: "cc_%09d"
  - write_grid_vtk
  - write_cc_table

dump_data_xyz:
  - timestep_file: "exaStamp_%09d.xyz"
  - message: { mesg: "Write xyz " , endl: false }
  - print_dump_file:
      rebind: { mesg: filename }
      body:
        - message: { endl: true }
  - write_xyz_file

dump_data_lmp:
  - timestep_file: "exaStamp_%09d.lmp"
  - message: { mesg: "Write xyz " , endl: false }
  - print_dump_file:
      rebind: { mesg: filename }
      body:
        - message: { endl: true }
  - write_lmp_file

dump_analysis: dump_data_grid_vtk

# usefull to cleanly place particles in corresponding cells
# and/or extend domain, just before a dump
cleanup_before_dump: init_particles

final_dump:
    - dump_data

config_end_iteration.msp

The config_end_iteration.msp file contains operators that allow to decide what to do at the end of an iteration. 

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# Defines when thermo state must be called
trigger_thermo_state:
  - combine1:
      rebind: { in1: trigger_dump_data , in2: trigger_print_log , result: output1 }
      body:
        - boolean_or
  - combine2:
      rebind: { in1: output1 , in2: trigger_dump_thermo , result: trigger_thermo_state }
      body:
        - boolean_or

default_thermodynamic_state: simulation_thermodynamic_state

thermo_state_if_triggered:
  condition: trigger_thermo_state
  body:
    - default_thermodynamic_state

# Trigger functions at iteration start
begin_iteration:
  - trigger_thermo_state
  - trigger_print_log
  - trigger_dump_data
  - trigger_dump_analysis
  - trigger_dump_thermo

# Dump/print functions at iteration end 
end_iteration:
  - thermo_state_if_triggered
  - print_log_if_triggered
  - dump_data_if_triggered
  - dump_analysis_if_triggered
  - dump_thermo_if_triggered