[Mechanics_OG] Add method from agent away from agent

[joseestraguesbsc]

this function is unnecessary - again, it is not responsibility of agent_data to fill it with reasonable values, its responsibility is just to allocate data

Originally posted by @asmelko in #75 (comment)

[joseestraguesbsc]

void mechanical_agent_data::add(index_t new_id, index_t cell_type, mechanical_parameters& parameters, bool is_2D)
{
assert(new_id == base_data.agents_count);

base_data.add();
add();

assert(new_id < agents_count);

const index_t dim_offset = new_id * base_data.dims;
std::fill_n(&velocity[dim_offset], base_data.dims, 0.0);
std::fill_n(&previous_velocity[dim_offset], base_data.dims, 0.0);
std::fill_n(&motility_data.migration_bias_direction[dim_offset], base_data.dims, 0.0);
std::fill_n(&motility_data.motility_vector[dim_offset], base_data.dims, 0.0);
std::fill_n(&state_data.orientation[dim_offset], base_data.dims, 0.0);

radius[new_id] = 0.0;

state_data.agent_type_index[new_id] = cell_type;

// Directly assign scalar values from mechanical_parameters
mechanics_data.cell_cell_adhesion_strength[new_id] = parameters.cell_cell_adhesion_strength;
mechanics_data.cell_BM_adhesion_strength[new_id] = parameters.cell_BM_adhesion_strength;
mechanics_data.cell_cell_repulsion_strength[new_id] = parameters.cell_cell_repulsion_strength;
mechanics_data.cell_BM_repulsion_strength[new_id] = parameters.cell_BM_repulsion_strength;

// Copy cell_adhesion_affinities vector directly
const index_t affinity_offset = new_id * agent_types_count;
index_t other = 0;
for (; other < agent_types_count && other < static_cast<index_t>(parameters.cell_adhesion_affinity.size()); ++other)
{
	mechanics_data.cell_adhesion_affinities[affinity_offset + other] = parameters.cell_adhesion_affinity[other];
}
for (; other < agent_types_count; ++other)
{
	mechanics_data.cell_adhesion_affinities[affinity_offset + other] = 0.0;
}

mechanics_data.relative_maximum_adhesion_distance[new_id] = parameters.relative_maximum_adhesion_distance;
mechanics_data.maximum_number_of_attachments[new_id] = parameters.maximum_number_of_attachments;
mechanics_data.attachment_elastic_constant[new_id] = parameters.attachment_elastic_coefficient;
mechanics_data.attachment_rate[new_id] = parameters.attachment_rate;
mechanics_data.detachment_rate[new_id] = parameters.detachment_rate;

motility_data.is_motile[new_id] = static_cast<std::uint8_t>(parameters.is_movable);
state_data.is_movable[new_id] = static_cast<std::uint8_t>(parameters.is_movable);
motility_data.persistence_time[new_id] = parameters.motility_persistence_time;
motility_data.migration_speed[new_id] = parameters.motility_speed;
motility_data.migration_bias[new_id] = parameters.motility_bias;
motility_data.restrict_to_2d[new_id] = static_cast<std::uint8_t>(is_2D);

index_t chosen_substrate = 0;
bool found_substrate = false;

for (index_t s = 0; s < substrates_count; ++s)
{
	const bool enabled = s < parameters.chemotaxis_enabled.size() ? parameters.chemotaxis_enabled[s] : false;
	const real_t sensitivity =
		enabled && s < parameters.chemotaxis_sensitivity.size() ? parameters.chemotaxis_sensitivity[s] : 0.0;

	motility_data.chemotactic_sensitivities[new_id * substrates_count + s] = sensitivity;

	if (!found_substrate && enabled)
	{
		chosen_substrate = s;
		found_substrate = true;
	}
}

motility_data.chemotaxis_index[new_id] = found_substrate ? chosen_substrate : 0;
motility_data.chemotaxis_direction[new_id] = found_substrate ? 1 : 0;

state_data.neighbors[new_id].clear();
state_data.springs[new_id].clear();
state_data.attached_cells[new_id].clear();

state_data.simple_pressure[new_id] = 0.0;

}