From 0d0c47ede381b1d7e163a13175e3d1c2b91e38e4 Mon Sep 17 00:00:00 2001
From: Will Handley <wh260@cam.ac.uk>
Date: Tue, 9 Jan 2024 12:41:56 +0000
Subject: [PATCH] Remove GenerateFromSeed functionality (#112)

* Removed GenerateFromSeed functionality

* Removed more_points_needed and request_point

* Removed generate_from_seed from settings

* Bumped version number
---
 README.rst                        |   2 +-
 pypolychord/__init__.py           |   2 +-
 src/polychord/feedback.f90        |   4 +-
 src/polychord/generate.F90        | 255 +-----------------------------
 src/polychord/ini.f90             |   2 -
 src/polychord/mpi_utils.F90       |  64 +-------
 src/polychord/nested_sampling.F90 |   8 +-
 src/polychord/settings.f90        |   1 -
 8 files changed, 10 insertions(+), 328 deletions(-)

diff --git a/README.rst b/README.rst
index 156ca1c2..8105303c 100644
--- a/README.rst
+++ b/README.rst
@@ -5,7 +5,7 @@
    :target: https://arxiv.org/abs/1506.00171
    :alt: Open-access paper
 
-PolyChord v 1.21.0
+PolyChord v 1.21.1
 
 Will Handley, Mike Hobson & Anthony Lasenby
 
diff --git a/pypolychord/__init__.py b/pypolychord/__init__.py
index 7c6e3ddb..cfbdea33 100644
--- a/pypolychord/__init__.py
+++ b/pypolychord/__init__.py
@@ -1,3 +1,3 @@
-__version__ = "1.21.0"
+__version__ = "1.21.1"
 from pypolychord.settings import PolyChordSettings
 from pypolychord.polychord import run_polychord
diff --git a/src/polychord/feedback.f90 b/src/polychord/feedback.f90
index 8c8e4596..c27e93bf 100644
--- a/src/polychord/feedback.f90
+++ b/src/polychord/feedback.f90
@@ -28,8 +28,8 @@ subroutine write_opening_statement(settings)
             write(stdout_unit,'("")')
             write(stdout_unit,'("PolyChord: Next Generation Nested Sampling")')
             write(stdout_unit,'("copyright: Will Handley, Mike Hobson & Anthony Lasenby")')
-            write(stdout_unit,'("  version: 1.21.0")')
-            write(stdout_unit,'("  release: 1st June 2021")')
+            write(stdout_unit,'("  version: 1.21.1")')
+            write(stdout_unit,'("  release: 9th Jan 2024")')
             write(stdout_unit,'("    email: wh260@mrao.cam.ac.uk")')
             write(stdout_unit,'("")')
         end if
diff --git a/src/polychord/generate.F90 b/src/polychord/generate.F90
index 3bc0decc..fc8e3a25 100644
--- a/src/polychord/generate.F90
+++ b/src/polychord/generate.F90
@@ -69,7 +69,7 @@ subroutine GenerateLivePoints(loglikelihood,prior,settings,RTI,mpi_information)
         use array_module,     only: add_point
         use abort_module
 #ifdef MPI
-        use mpi_module, only: mpi_bundle,is_root,linear_mode,throw_point,catch_point,more_points_needed,sum_integers,sum_doubles,request_point,no_more_points,request_live_point,live_point_needed
+        use mpi_module, only: mpi_bundle,is_root,linear_mode,throw_point,catch_point,sum_integers,sum_doubles,no_more_points,request_live_point,live_point_needed
 #else
         use mpi_module, only: mpi_bundle,is_root,linear_mode
 #endif
@@ -454,257 +454,4 @@ function prior(cube) result(theta)
 
     end subroutine time_speeds
 
-
-    subroutine GenerateLivePointsFromSeed(loglikelihood,prior,settings,RTI,mpi_information)
-        use settings_module,  only: program_settings
-        use utils_module,    only: write_phys_unit,DB_FMT,fmt_len,minpos,time,stdout_unit
-        use calculate_module, only: calculate_point
-        use read_write_module, only: phys_live_file
-        use feedback_module,  only: write_started_generating,write_finished_generating,write_generating_live_points
-        use run_time_module,   only: run_time_info,initialise_run_time_info, find_min_loglikelihoods
-        use array_module,     only: add_point
-        use abort_module
-        use chordal_module, only: slice_sample
-#ifdef MPI
-        use mpi_module, only: mpi_bundle,is_root,linear_mode,throw_point,catch_point,more_points_needed,sum_integers,sum_doubles,request_point,no_more_points
-#else
-        use mpi_module, only: mpi_bundle,is_root,linear_mode
-#endif
-
-        implicit none
-
-        interface
-            function loglikelihood(theta,phi)
-                import :: dp
-                real(dp), intent(in), dimension(:)  :: theta
-                real(dp), intent(out), dimension(:) :: phi
-                real(dp) :: loglikelihood
-            end function
-        end interface
-        interface
-            function prior(cube) result(theta)
-                import :: dp
-                real(dp), intent(in), dimension(:) :: cube
-                real(dp), dimension(size(cube))    :: theta
-            end function
-        end interface
-
-
-        !> Program settings
-        type(program_settings), intent(in) :: settings
-
-        ! The run time info (very important, see src/run_time_info.f90)
-        type(run_time_info) :: RTI
-
-        type(mpi_bundle),intent(in) :: mpi_information
-#ifdef MPI
-        integer             :: active_workers    !  Number of currently working workers
-        integer             :: worker_id         !  Worker identifier to signal who to throw back to
-#endif
-
-        real(dp), dimension(settings%nTotal) :: live_point ! Temporary live point array
-
-
-        character(len=fmt_len) :: fmt_dbl ! writing format variable
-
-        integer :: nprior
-
-        real(dp) :: time0,time1
-        real(dp),dimension(size(settings%grade_dims)) :: speed
-        real(dp),dimension(size(settings%grade_dims)) :: times
-        integer, dimension(size(settings%grade_dims)) :: nlikes
-
-        integer :: i_dim,i_repeat,i_grade
-        integer, dimension(settings%nDims) :: grade
-        real(dp), dimension(settings%nDims) :: nhat
-
-        do i_grade = size(settings%grade_dims),1,-1
-            grade(:sum(settings%grade_dims(:i_grade))) = i_grade
-        end do
-        nlikes = 0
-        times = 0d0
-
-        if(is_root(mpi_information)) then
-            ! ---------------------------------------------- !
-            call write_started_generating(settings%feedback)
-            ! ---------------------------------------------- !
-
-            ! Initialise the format
-            write(fmt_dbl,'("(",I0,A,")")') settings%nDims+settings%nDerived+1, DB_FMT
-
-            ! Open the live points file to sequentially add live points
-            if(settings%write_live) open(write_phys_unit,file=trim(phys_live_file(settings)), action='write')
-
-            ! Allocate the run time arrays, and set the default values for the variables
-            call initialise_run_time_info(settings,RTI)
-
-        end if
-
-        if (settings%nprior <= 0) then
-            nprior = settings%nlive
-        else
-            nprior = settings%nprior
-        end if
-
-        if(linear_mode(mpi_information)) then
-            !===================== LINEAR MODE =========================
-
-            live_point = settings%seed_point
-            do while(RTI%nlive(1)<nprior)
-                do i_repeat = 1,settings%nprior_repeat
-                    do i_dim=1,settings%nDims
-                        i_grade = grade(i_dim)
-                        nhat = 0d0
-                        nhat(i_dim) = 1d0
-
-                        time0 = time()
-                        live_point = slice_sample(loglikelihood,prior,settings%logzero,nhat,live_point,1d0,settings,nlikes(i_grade))
-                        time1 = time()
-                        times(i_grade) = times(i_grade) + time1 - time0
-                    end do
-                end do
-
-                call add_point(live_point,RTI%live,RTI%nlive,1) ! Add this point to the array
-                call write_generating_live_points(settings%feedback,RTI%nlive(1),nprior)
-                if(settings%write_live) then
-                    ! Write the live points to the live_points file
-                    write(write_phys_unit,fmt_dbl) live_point(settings%p0:settings%d1), live_point(settings%l0)
-                    flush(write_phys_unit) ! flush the unit to force write
-                end if
-
-            end do
-
-#ifdef MPI
-        else 
-            !===================== PARALLEL MODE =======================
-
-            if(is_root(mpi_information)) then
-                ! The root node just recieves data from all other processors
-
-                active_workers=mpi_information%nprocs-1 ! Set the number of active processors to the number of workers
-
-                do while(active_workers>0) 
-
-                    ! Recieve a point from any worker
-                    worker_id = catch_point(live_point,mpi_information)
-
-                    ! If its valid, and we need more points, add it to the array
-                    if(RTI%nlive(1)<nprior) then
-
-                        call add_point(live_point,RTI%live,RTI%nlive,1) ! Add this point to the array
-
-                        !-------------------------------------------------------------------------------!
-                        call write_generating_live_points(settings%feedback,RTI%nlive(1),nprior)
-                        !-------------------------------------------------------------------------------!
-
-                        if(settings%write_live) then
-                            ! Write the live points to the live_points file
-                            write(write_phys_unit,fmt_dbl) live_point(settings%p0:settings%d1), live_point(settings%l0)
-                            flush(write_phys_unit) ! flush the unit to force write
-                        end if
-
-                    end if
-
-
-                    if(RTI%nlive(1)<nprior) then
-                        call request_point(mpi_information,worker_id)  ! If we still need more points, send a signal to have another go
-                    else
-                        call no_more_points(mpi_information,worker_id) ! Otherwise, send a signal to stop
-                        active_workers=active_workers-1                ! decrease the active worker counter
-                    end if
-
-                end do
-
-
-
-
-            else
-
-                ! The workers simply generate and send points until they're told to stop by the administrator
-                live_point = settings%seed_point
-                do while(.true.)
-                    do i_repeat = 1,settings%nprior_repeat
-                        do i_dim=1,settings%nDims
-                            i_grade = grade(i_dim)
-                            nhat = 0d0
-                            nhat(i_dim) = 1d0
-
-                            time0 = time()
-                            live_point = slice_sample(loglikelihood,prior,settings%logzero,nhat,live_point,1d0,settings,nlikes(i_grade))
-                            time1 = time()
-                            times(i_grade) = times(i_grade) + time1 - time0
-                        end do
-                    end do
-        
-                    call throw_point(live_point,mpi_information)                                    ! Send it to the root node
-                    if(.not. more_points_needed(mpi_information)) exit                              ! If we've recieved a kill signal, then exit this loop
-
-                end do
-            end if
-#endif
-        end if !(nprocs case)
-
-#ifdef MPI
-        do i_grade=1,size(settings%grade_dims)
-            nlikes(i_grade) = sum_integers(nlikes(i_grade),mpi_information) ! Gather the likelihood calls onto one node
-            times(i_grade) = sum_doubles(times(i_grade),mpi_information) ! Sum up the total time taken
-        end do
-#endif
-
-
-        ! ----------------------------------------------- !
-        if(is_root(mpi_information)) call write_finished_generating(settings%feedback)  
-        ! ----------------------------------------------- !
-
-        if(is_root(mpi_information)) then
-            ! Find the average time taken
-            speed = times/nlikes
-
-            do i_grade = 1,size(settings%grade_dims)
-                write(stdout_unit,'("Speed ",I2," = ",E10.3, " seconds     ")') i_grade, speed(i_grade)
-            end do
-
-
-            ! Pass over the number of likelihood calls
-            RTI%nlike = nlikes
-
-            ! Set the local and global loglikelihood bounds
-            RTI%i(1)  = minpos(RTI%live(settings%l0,:,1)) ! Find the position of the minimum loglikelihood
-            RTI%logLp = RTI%live(settings%l0,RTI%i(1),1)  ! Store the value of the minimum loglikelihood 
-
-            ! Close the file
-            if(settings%write_live) close(write_phys_unit)
-
-            if(.not. allocated(RTI%num_repeats) ) allocate(RTI%num_repeats(size(settings%grade_dims)))
-            if (any(settings%grade_frac<=1)) then
-                RTI%num_repeats(1) = settings%num_repeats
-                RTI%num_repeats(2:) = nint(settings%grade_frac(2:)/(settings%grade_frac(1)+0d0)*RTI%num_repeats(1)*speed(1)/speed(2:))
-            else
-                RTI%num_repeats = int(settings%grade_frac)
-            end if
-
-            ! Set the posterior thinning factor
-            if(settings%boost_posterior<0d0) then
-                RTI%thin_posterior = 1d0
-            else
-                RTI%thin_posterior = (settings%boost_posterior+0d0)/(sum(RTI%num_repeats)+0d0)
-            end if
-
-            ! Calculate the minimum loglikelihood for future use
-            call find_min_loglikelihoods(settings,RTI)
-
-        end if
-
-
-
-
-
-    end subroutine GenerateLivePointsFromSeed
-
-
-
-
-
-
-
 end module generate_module
diff --git a/src/polychord/ini.f90 b/src/polychord/ini.f90
index ea60f382..55a1968d 100644
--- a/src/polychord/ini.f90
+++ b/src/polychord/ini.f90
@@ -79,8 +79,6 @@ subroutine read_params(file_name,settings,params,derived_params)
         settings%base_dir           = get_string(file_name,'base_dir','chains')
         settings%file_root          = get_string(file_name,'file_root','test')
         settings%seed               = get_integer(file_name,'seed', -1)
-
-        settings%generate_from_seed = get_logical(file_name,'generate_from_seed',.false.)
         settings%nprior_repeat      = get_integer(file_name,'nprior_repeat',-1)
         call get_doubles(file_name,'seed_point',settings%seed_point)
 
diff --git a/src/polychord/mpi_utils.F90 b/src/polychord/mpi_utils.F90
index 03d7315e..0c587bbf 100644
--- a/src/polychord/mpi_utils.F90
+++ b/src/polychord/mpi_utils.F90
@@ -607,32 +607,9 @@ end subroutine throw_seed
     ! whether or not to keep generating live points, or whether to stop
     !
     ! administrator         ----> worker
-    ! request_point        more_points_needed -> true
-    ! no_more_points       more_points_needed -> false
-    ! 
-
-    !> Request point
-    !!
-    !! This subroutine is used by the root node to request a new live point
-    subroutine request_point(mpi_information,worker_id)
-        implicit none
-        type(mpi_bundle), intent(in) :: mpi_information
-        integer, intent(in) :: worker_id         !> Worker to request a new point from
-
-
-        integer :: empty_buffer(0) ! empty buffer to send
-
-        call MPI_SEND(                   &
-            empty_buffer,                &! not sending anything
-            0,                           &! size of nothing
-            MPI_INTEGER,                 &! sending no integers
-            worker_id,                   &! process id to send to
-            tag_gen_request,             &! continuation tag
-            mpi_information%communicator,&! mpi handle
-            mpierror                     &! error flag
-            )
-
-    end subroutine request_point
+    ! no_more_points        keep_going -> false
+    ! request_live_point    keep_going -> true
+    ! live_point_needed     keep_going -> true
 
 
     !> No more points please
@@ -658,41 +635,6 @@ subroutine no_more_points(mpi_information,worker_id)
 
     end subroutine no_more_points
 
-    !> See if more points are needed
-    !!
-    !! This subroutine is used by the root node to request a new live point
-    function more_points_needed(mpi_information)
-        use abort_module
-        implicit none
-        type(mpi_bundle), intent(in) :: mpi_information
-
-        integer :: empty_buffer(0) ! empty buffer to send
-        integer, dimension(MPI_STATUS_SIZE) :: mpistatus  ! status identifier
-
-        logical :: more_points_needed !> Whether we need more points or not
-
-        call MPI_RECV(                   &!
-            empty_buffer,                &!
-            0,                           &!
-            MPI_INTEGER,                 &!
-            mpi_information%root,        &!
-            MPI_ANY_TAG,                 &!
-            mpi_information%communicator,&!
-            mpistatus,                   &!
-            mpierror                     &!
-            )
-
-        ! If we've recieved a kill signal, then exit this loop
-        if(mpistatus(MPI_TAG) == tag_gen_stop ) then
-            more_points_needed = .false.
-        else if(mpistatus(MPI_TAG) == tag_gen_request) then
-            more_points_needed = .true.
-        else
-            call halt_program('generate error: unrecognised tag')
-        end if
-
-    end function more_points_needed
-
     !> Request specific live points
     ! administrator                     ----> worker
     ! request_live_point(live_point)   point_needed -> true
diff --git a/src/polychord/nested_sampling.F90 b/src/polychord/nested_sampling.F90
index 0db480ae..276fe2e2 100644
--- a/src/polychord/nested_sampling.F90
+++ b/src/polychord/nested_sampling.F90
@@ -21,7 +21,7 @@ function NestedSampling(loglikelihood,prior, dumper, settings, mpi_communicator)
         use chordal_module,    only: SliceSampling
         use random_module,     only: random_integer,random_direction
         use cluster_module,    only: do_clustering
-        use generate_module,   only: GenerateSeed,GenerateLivePoints,GenerateLivePointsFromSeed
+        use generate_module,   only: GenerateSeed,GenerateLivePoints
         use maximise_module,   only: maximise
 #ifdef MPI
         use utils_module, only: normal_fb,stdout_unit
@@ -191,11 +191,7 @@ end subroutine dumper
             end if
 
             ! Intialise the run by setting all of the relevant run time info, and generating live points
-            if (settings%generate_from_seed) then
-                call GenerateLivePointsFromSeed(loglikelihood,prior,settings,RTI,mpi_information)
-            else
-                call GenerateLivePoints(loglikelihood,prior,settings,RTI,mpi_information)
-            end if
+            call GenerateLivePoints(loglikelihood,prior,settings,RTI,mpi_information)
 
             if(is_root(mpi_information)) then
                 if(settings%write_prior) call write_prior_file(settings,RTI) 
diff --git a/src/polychord/settings.f90 b/src/polychord/settings.f90
index d0318ab4..475029af 100644
--- a/src/polychord/settings.f90
+++ b/src/polychord/settings.f90
@@ -50,7 +50,6 @@ module settings_module
 
 
         real(dp), allocatable,dimension(:) :: seed_point
-        logical :: generate_from_seed = .false.
         integer :: nprior = -1
         integer :: nfail = -1
         integer :: nprior_repeat = -1