From b377e442a67c13bd4c647ac3e462b989d758e8fd Mon Sep 17 00:00:00 2001 From: TApplencourt Date: Tue, 1 Nov 2016 16:20:26 -0500 Subject: [PATCH] Add mising readme --- plugins/Full_CI_ZMQ/README.rst | 461 +++++++++++++++++++++++++++++++++ src/Davidson/README.rst | 322 +++++++++++++++++++++++ 2 files changed, 783 insertions(+) create mode 100644 plugins/Full_CI_ZMQ/README.rst create mode 100644 src/Davidson/README.rst diff --git a/plugins/Full_CI_ZMQ/README.rst b/plugins/Full_CI_ZMQ/README.rst new file mode 100644 index 00000000..d1677a7d --- /dev/null +++ b/plugins/Full_CI_ZMQ/README.rst @@ -0,0 +1,461 @@ +Needed Modules +============== +.. Do not edit this section It was auto-generated +.. by the `update_README.py` script. + + +.. image:: tree_dependency.png + +* `Perturbation `_ +* `Selectors_full `_ +* `Generators_full `_ +* `ZMQ `_ +* `Full_CI `_ + +Documentation +============= +.. Do not edit this section It was auto-generated +.. by the `update_README.py` script. + + +`add_task_to_taskserver `_ + Get a task from the task server + + +`add_to_selection_buffer `_ + Undocumented + + +`assert `_ + Undocumented + + +`connect_to_taskserver `_ + Connect to the task server and obtain the worker ID + + +`create_selection_buffer `_ + Undocumented + + +`disconnect_from_taskserver `_ + Disconnect from the task server + + +`end_parallel_job `_ + End a new parallel job with name 'name'. The slave tasks execute subroutine 'slave' + + +`end_zmq_pair_socket `_ + Terminate socket on which the results are sent. + + +`end_zmq_pull_socket `_ + Terminate socket on which the results are sent. + + +`end_zmq_push_socket `_ + Terminate socket on which the results are sent. + + +`end_zmq_sub_socket `_ + Terminate socket on which the results are sent. + + +`end_zmq_to_qp_run_socket `_ + Terminate the socket from the application to qp_run + + +`fci_zmq `_ + Undocumented + + +`fill_buffer_double `_ + Undocumented + + +`fill_buffer_single `_ + Undocumented + + +`full_ci `_ + Undocumented + + +`get_d0 `_ + Undocumented + + +`get_d1 `_ + Undocumented + + +`get_d2 `_ + Undocumented + + +`get_m0 `_ + Undocumented + + +`get_m1 `_ + Undocumented + + +`get_m2 `_ + Undocumented + + +`get_mask_phase `_ + Undocumented + + +`get_phase_bi `_ + Undocumented + + +`get_task_from_taskserver `_ + Get a task from the task server + + +h_apply_fci + Calls H_apply on the HF determinant and selects all connected single and double + excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script. + + +h_apply_fci_diexc + Undocumented + + +h_apply_fci_diexcorg + Generate all double excitations of key_in using the bit masks of holes and + particles. + Assume N_int is already provided. + + +h_apply_fci_diexcp + Undocumented + + +h_apply_fci_mono + Calls H_apply on the HF determinant and selects all connected single and double + excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script. + + +h_apply_fci_mono_diexc + Undocumented + + +h_apply_fci_mono_diexcorg + Generate all double excitations of key_in using the bit masks of holes and + particles. + Assume N_int is already provided. + + +h_apply_fci_mono_diexcp + Undocumented + + +h_apply_fci_mono_monoexc + Generate all single excitations of key_in using the bit masks of holes and + particles. + Assume N_int is already provided. + + +h_apply_fci_monoexc + Generate all single excitations of key_in using the bit masks of holes and + particles. + Assume N_int is already provided. + + +h_apply_fci_no_selection + Calls H_apply on the HF determinant and selects all connected single and double + excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script. + + +h_apply_fci_no_selection_diexc + Undocumented + + +h_apply_fci_no_selection_diexcorg + Generate all double excitations of key_in using the bit masks of holes and + particles. + Assume N_int is already provided. + + +h_apply_fci_no_selection_diexcp + Undocumented + + +h_apply_fci_no_selection_monoexc + Generate all single excitations of key_in using the bit masks of holes and + particles. + Assume N_int is already provided. + + +h_apply_fci_no_skip + Calls H_apply on the HF determinant and selects all connected single and double + excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script. + + +h_apply_fci_no_skip_diexc + Undocumented + + +h_apply_fci_no_skip_diexcorg + Generate all double excitations of key_in using the bit masks of holes and + particles. + Assume N_int is already provided. + + +h_apply_fci_no_skip_diexcp + Undocumented + + +h_apply_fci_no_skip_monoexc + Generate all single excitations of key_in using the bit masks of holes and + particles. + Assume N_int is already provided. + + +h_apply_fci_pt2 + Calls H_apply on the HF determinant and selects all connected single and double + excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script. + + +h_apply_fci_pt2_collector + Collects results from the selection in an array of generators + + +h_apply_fci_pt2_diexc + Undocumented + + +h_apply_fci_pt2_diexcorg + Generate all double excitations of key_in using the bit masks of holes and + particles. + Assume N_int is already provided. + + +h_apply_fci_pt2_diexcp + Undocumented + + +h_apply_fci_pt2_monoexc + Generate all single excitations of key_in using the bit masks of holes and + particles. + Assume N_int is already provided. + + +h_apply_fci_pt2_slave + Calls H_apply on the HF determinant and selects all connected single and double + excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script. + + +h_apply_fci_pt2_slave_inproc + Computes a buffer using threads + + +h_apply_fci_pt2_slave_tcp + Computes a buffer over the network + + +`integral8 `_ + Undocumented + + +`new_parallel_job `_ + Start a new parallel job with name 'name'. The slave tasks execute subroutine 'slave' + + +`new_zmq_pair_socket `_ + Socket on which the collector and the main communicate + + +`new_zmq_pull_socket `_ + Socket on which the results are sent. If thread is 1, use inproc + + +`new_zmq_push_socket `_ + Socket on which the results are sent. If thread is 1, use inproc + + +`new_zmq_sub_socket `_ + Socket to read the state published by the Task server + + +`new_zmq_to_qp_run_socket `_ + Socket on which the qp_run process replies + + +`past_d1 `_ + Undocumented + + +`past_d2 `_ + Undocumented + + +`provide_everything `_ + Undocumented + + +`psi_phasemask `_ + Undocumented + + +`pull_selection_results `_ + Undocumented + + +`push_selection_results `_ + Undocumented + + +`qp_run_address `_ + Address of the qp_run socket + Example : tcp://130.120.229.139:12345 + + +`reset_zmq_addresses `_ + Socket which pulls the results (2) + + +`run_selection_slave `_ + Undocumented + + +`run_wf `_ + Undocumented + + +`select_connected `_ + Undocumented + + +`select_doubles `_ + Undocumented + + +`select_singles `_ + Select determinants connected to i_det by H + + +`selection_collector `_ + Undocumented + + +`selection_slave `_ + Helper program to compute the PT2 in distributed mode. + + +`selection_slave_inproc `_ + Undocumented + + +`selection_slave_tcp `_ + Undocumented + + +`sort_selection_buffer `_ + Undocumented + + +`splash_p `_ + Undocumented + + +`splash_pq `_ + Undocumented + + +`spot_hasbeen `_ + Undocumented + + +`spot_isinwf `_ + Undocumented + + +`switch_qp_run_to_master `_ + Address of the master qp_run socket + Example : tcp://130.120.229.139:12345 + + +`task_done_to_taskserver `_ + Get a task from the task server + + +`update_energy `_ + Update energy when it is received from ZMQ + + +`var_pt2_ratio_run `_ + Undocumented + + +`wait_for_next_state `_ + Undocumented + + +`wait_for_state `_ + Wait for the ZMQ state to be ready + + +`wait_for_states `_ + Wait for the ZMQ state to be ready + + +`zmq_context `_ + Context for the ZeroMQ library + + +`zmq_delete_task `_ + When a task is done, it has to be removed from the list of tasks on the qp_run + queue. This guarantees that the results have been received in the pull. + + +`zmq_port `_ + Return the value of the ZMQ port from the corresponding integer + + +`zmq_port_start `_ + Address of the qp_run socket + Example : tcp://130.120.229.139:12345 + + +`zmq_selection `_ + Undocumented + + +`zmq_set_running `_ + Set the job to Running in QP-run + + +`zmq_socket_pair_inproc_address `_ + Socket which pulls the results (2) + + +`zmq_socket_pull_inproc_address `_ + Socket which pulls the results (2) + + +`zmq_socket_pull_tcp_address `_ + Socket which pulls the results (2) + + +`zmq_socket_push_inproc_address `_ + Socket which pulls the results (2) + + +`zmq_socket_push_tcp_address `_ + Socket which pulls the results (2) + + +`zmq_socket_sub_tcp_address `_ + Socket which pulls the results (2) + + +`zmq_state `_ + Threads executing work through the ZeroMQ interface + diff --git a/src/Davidson/README.rst b/src/Davidson/README.rst new file mode 100644 index 00000000..15e9b46a --- /dev/null +++ b/src/Davidson/README.rst @@ -0,0 +1,322 @@ +Needed Modules +============== +.. Do not edit this section It was auto-generated +.. by the `update_README.py` script. + + +.. image:: tree_dependency.png + +* `Determinants `_ + +Documentation +============= +.. Do not edit this section It was auto-generated +.. by the `update_README.py` script. + + +`ci_eigenvectors `_ + Eigenvectors/values of the CI matrix + + +`ci_eigenvectors_mono `_ + Eigenvectors/values of the CI matrix + + +`ci_eigenvectors_s2 `_ + Eigenvectors/values of the CI matrix + + +`ci_eigenvectors_s2_mono `_ + Eigenvectors/values of the CI matrix + + +`ci_electronic_energy `_ + Eigenvectors/values of the CI matrix + + +`ci_electronic_energy_mono `_ + Eigenvectors/values of the CI matrix + + +`ci_energy `_ + N_states lowest eigenvalues of the CI matrix + + +`dav_det `_ + Temporary arrays for parallel davidson + .br + Touched in davidson_miniserver_get + + +`dav_size `_ + Size of the arrays for Davidson + .br + Touched in davidson_miniserver_get + + +`dav_ut `_ + Temporary arrays for parallel davidson + .br + Touched in davidson_miniserver_get + + +`davidson_add_task `_ + Undocumented + + +`davidson_collect `_ + Undocumented + + +`davidson_collector `_ + Undocumented + + +`davidson_converged `_ + True if the Davidson algorithm is converged + + +`davidson_criterion `_ + Can be : [ energy | residual | both | wall_time | cpu_time | iterations ] + + +`davidson_diag `_ + Davidson diagonalization. + .br + dets_in : bitmasks corresponding to determinants + .br + u_in : guess coefficients on the various states. Overwritten + on exit + .br + dim_in : leftmost dimension of u_in + .br + sze : Number of determinants + .br + N_st : Number of eigenstates + .br + iunit : Unit number for the I/O + .br + Initial guess vectors are not necessarily orthonormal + + +`davidson_diag_hjj `_ + Davidson diagonalization with specific diagonal elements of the H matrix + .br + H_jj : specific diagonal H matrix elements to diagonalize de Davidson + .br + dets_in : bitmasks corresponding to determinants + .br + u_in : guess coefficients on the various states. Overwritten + on exit + .br + dim_in : leftmost dimension of u_in + .br + sze : Number of determinants + .br + N_st : Number of eigenstates + .br + N_st_diag : Number of states in which H is diagonalized + .br + iunit : Unit for the I/O + .br + Initial guess vectors are not necessarily orthonormal + + +`davidson_diag_hjj_sjj `_ + Davidson diagonalization with specific diagonal elements of the H matrix + .br + H_jj : specific diagonal H matrix elements to diagonalize de Davidson + .br + S2_jj : specific diagonal S^2 matrix elements + .br + dets_in : bitmasks corresponding to determinants + .br + u_in : guess coefficients on the various states. Overwritten + on exit + .br + dim_in : leftmost dimension of u_in + .br + sze : Number of determinants + .br + N_st : Number of eigenstates + .br + N_st_diag : Number of states in which H is diagonalized. Assumed > sze + .br + iunit : Unit for the I/O + .br + Initial guess vectors are not necessarily orthonormal + + +`davidson_diag_hs2 `_ + Davidson diagonalization. + .br + dets_in : bitmasks corresponding to determinants + .br + u_in : guess coefficients on the various states. Overwritten + on exit + .br + dim_in : leftmost dimension of u_in + .br + sze : Number of determinants + .br + N_st : Number of eigenstates + .br + iunit : Unit number for the I/O + .br + Initial guess vectors are not necessarily orthonormal + + +`davidson_init `_ + Undocumented + + +`davidson_iter_max `_ + Max number of Davidson iterations + + +`davidson_miniserver_end `_ + Undocumented + + +`davidson_miniserver_get `_ + Undocumented + + +`davidson_miniserver_run `_ + Undocumented + + +`davidson_process `_ + Undocumented + + +`davidson_pull_results `_ + Undocumented + + +`davidson_push_results `_ + Undocumented + + +`davidson_run `_ + Undocumented + + +`davidson_run_slave `_ + Undocumented + + +`davidson_slave `_ + Undocumented + + +`davidson_slave_inproc `_ + Undocumented + + +`davidson_slave_tcp `_ + Undocumented + + +`davidson_slave_work `_ + Undocumented + + +`davidson_sze_max `_ + Max number of Davidson sizes + + +`det_inf `_ + Ordering function for determinants + + +`diagonalize_ci `_ + Replace the coefficients of the CI states by the coefficients of the + eigenstates of the CI matrix + + +`diagonalize_ci_mono `_ + Replace the coefficients of the CI states by the coefficients of the + eigenstates of the CI matrix + + +`first_guess `_ + Select all the determinants with the lowest energy as a starting point. + + +`h_s2_u_0_nstates `_ + Computes v_0 = H|u_0> and s_0 = S^2 |u_0> + .br + n : number of determinants + .br + H_jj : array of + .br + S2_jj : array of + + +`h_u_0_nstates `_ + Computes v_0 = H|u_0> + .br + n : number of determinants + .br + H_jj : array of + + +`max_blocksize `_ + Undocumented + + +`n_states_diag `_ + n_states_diag + + +`provide_everything `_ + Undocumented + + +`psi_energy `_ + Energy of the current wave function + + +`shortcut_ `_ + Undocumented + + +`sort_dets_ab `_ + Uncodumented : TODO + + +`sort_dets_ab_v `_ + Uncodumented : TODO + + +`sort_dets_ba_v `_ + Uncodumented : TODO + + +`sort_idx_ `_ + Undocumented + + +`sorted_ `_ + Undocumented + + +`tamiser `_ + Uncodumented : TODO + + +`threshold_davidson `_ + Thresholds of Davidson's algorithm + + +`u_0_h_u_0 `_ + Computes e_0 = / + .br + n : number of determinants + .br + + +`version_ `_ + Undocumented +