RMPCDMD: Data Fields - Variables

RMPCDMD

- a -

a : cell_system::cell_system_t

- b -

bc : cell_system::cell_system_t
bind_product : common::enzyme_kinetics_t
bind_substrate : common::enzyme_kinetics_t
block_length : correlator::correlator_t
block_size : common::alist_t
box : particle_system_io::particle_system_io_t

- c -

cell_count : cell_system::cell_system_t
cell_count_tmp : cell_system::cell_system_t
cell_start : cell_system::cell_system_t
center_of_mass_velocity : particle_system_io::thermo_t
correlation : correlator::correlator_t
count : common::profile_t , correlator::correlator_t , planar_fields::planar_fields_t , polar_fields::polar_fields_t
current_idx : common::alist_t , common::timer_list_t
cut : interaction::lj_params_t
cut_energy : interaction::lj_params_t
cut_sq : interaction::lj_params_t

- d -

data : common::alist_t , common::histogram_t , common::profile_t
dim : correlator::correlator_t
dr : polar_fields::polar_fields_t
dtheta : polar_fields::polar_fields_t
dx : common::histogram_t , common::profile_t , planar_fields::planar_fields_t
dy : planar_fields::planar_fields_t

- e -

edges : cell_system::cell_system_t
epsilon : interaction::lj_params_t
error : particle_system_io::particle_system_io_t

- f -

flags : particle_system::particle_system_t
flags1 : particle_system::particle_system_t
flags2 : particle_system::particle_system_t
flags_old : particle_system::particle_system_t
force : md::rigid_body_t , particle_system::particle_system_t , particle_system_io::particle_system_io_t
force1 : particle_system::particle_system_t
force2 : particle_system::particle_system_t
force3 : particle_system::particle_system_t
force4 : particle_system::particle_system_t
force_info : particle_system_io::particle_system_io_t
force_old : particle_system::particle_system_t
force_old_store : particle_system::particle_system_t
force_pointer : particle_system::particle_system_t
force_store : particle_system::particle_system_t

- g -

group : particle_system_io::particle_system_io_t

- h -

has_walls : cell_system::cell_system_t

- i -

i_body : md::rigid_body_t
i_start : md::rigid_body_t
i_stop : md::rigid_body_t
id : particle_system::particle_system_t , particle_system_io::particle_system_io_t
id1 : particle_system::particle_system_t
id2 : particle_system::particle_system_t
id_info : particle_system_io::particle_system_io_t
id_old : particle_system::particle_system_t
id_pointer : particle_system::particle_system_t
id_to_idx : particle_system::particle_system_t
idx : particle_system_io::thermo_t
image : particle_system::particle_system_t , particle_system_io::particle_system_io_t
image1 : particle_system::particle_system_t
image2 : particle_system::particle_system_t
image_info : particle_system_io::particle_system_io_t
image_old : particle_system::particle_system_t
image_pointer : particle_system::particle_system_t
input_file : common::args_t
internal_energy : particle_system_io::thermo_t
is_md : cell_system::cell_system_t
is_reac : cell_system::cell_system_t

- k -

kinetic_energy : particle_system_io::thermo_t

- l -

l : cell_system::cell_system_t , md::rigid_body_t
list : neighbor_list::neighbor_list_t

- m -

m : cell_system::cell_system_t
mass : md::rigid_body_t , particle_system::particle_system_t
max_v : cell_system::cell_system_t
mode : particle_system_io::particle_system_io_info_t
msd : correlator::axial_correlator_t

- n -

n : cell_system::cell_system_t , common::histogram_t , common::profile_t , correlator::correlator_t , neighbor_list::neighbor_list_t
n1 : interaction::lj_params_t
n2 : interaction::lj_params_t
n_blocks : correlator::correlator_t
n_buffer : particle_system_io::thermo_t
n_species : common::histogram_t , particle_system::particle_system_t
name : common::timer_t
nmax : neighbor_list::neighbor_list_t , particle_system::particle_system_t , particle_system_io::particle_system_io_t
npoints : neighbor_list::neighbor_list_t

- o -

- p -

p : common::timer_pointer_t
parallel_vacf : correlator::axial_correlator_t
pos : md::rigid_body_t , particle_system::particle_system_t
pos1 : particle_system::particle_system_t
pos2 : particle_system::particle_system_t
pos_body : md::rigid_body_t
pos_old : particle_system::particle_system_t
pos_pointer : particle_system::particle_system_t
pos_rattle : particle_system::particle_system_t
position : particle_system_io::particle_system_io_t
position_info : particle_system_io::particle_system_io_t
potential_energy : particle_system_io::thermo_t

- q -

q : md::rigid_body_t

- r -

r_max : polar_fields::polar_fields_t
r_min : polar_fields::polar_fields_t
release_product : common::enzyme_kinetics_t
release_substrate : common::enzyme_kinetics_t

- s -

seed : common::args_t
shift : interaction::lj_params_t
sigma : interaction::lj_params_t
sigma_sq : interaction::lj_params_t
species : particle_system::particle_system_t , particle_system_io::particle_system_io_t
species1 : particle_system::particle_system_t
species2 : particle_system::particle_system_t
species_info : particle_system_io::particle_system_io_t
species_old : particle_system::particle_system_t
species_pointer : particle_system::particle_system_t
stencil : neighbor_list::neighbor_list_t
step : particle_system_io::particle_system_io_info_t
step_offset : particle_system_io::particle_system_io_info_t
store : particle_system_io::particle_system_io_info_t

- t -

temperature : particle_system_io::thermo_t
thickness : planar_fields::planar_fields_t
tic_time : common::timer_t
time : particle_system_io::particle_system_io_info_t
time_apply_pbc : particle_system::particle_system_t
time_count : particle_system::particle_system_t
time_ct : particle_system::particle_system_t
time_elastic : particle_system::particle_system_t
time_force : neighbor_list::neighbor_list_t
time_max_disp : particle_system::particle_system_t
time_md_pos : particle_system::particle_system_t
time_md_vel : particle_system::particle_system_t
time_offset : particle_system_io::particle_system_io_info_t
time_polar_update : polar_fields::polar_fields_t
time_rattle_pos : particle_system::particle_system_t
time_rattle_vel : particle_system::particle_system_t
time_self_force : particle_system::particle_system_t
time_sort : particle_system::particle_system_t
time_step : particle_system::particle_system_t
time_stream : particle_system::particle_system_t
time_update : neighbor_list::neighbor_list_t
timer : planar_fields::planar_fields_t
timers : common::timer_list_t
torque : md::rigid_body_t
total : common::timer_t
transverse_vacf : correlator::axial_correlator_t

- v -

v : planar_fields::planar_fields_t , polar_fields::polar_fields_t
vacf : correlator::axial_correlator_t
value : correlator::correlator_t
vel : md::rigid_body_t , particle_system::particle_system_t
vel1 : particle_system::particle_system_t
vel2 : particle_system::particle_system_t
vel_old : particle_system::particle_system_t
vel_pointer : particle_system::particle_system_t
velocity : particle_system_io::particle_system_io_t
velocity_info : particle_system_io::particle_system_io_t

- x -

x_min : planar_fields::planar_fields_t
xmin : common::histogram_t , common::profile_t

- y -

y_min : planar_fields::planar_fields_t