From 8f1555a7316be577d932f01f353bdfd59ebcd9cc Mon Sep 17 00:00:00 2001
From: Matthias Frey <mf248@st-andrews.ac.uk>
Date: Tue, 1 Feb 2022 15:15:51 +0000
Subject: [PATCH] add timer module + update Python script

---
 scripts/write_h5.py | 40 ++++++++++++++++++++++++++++++++++++----
 src/constants.f90   |  5 +++--
 src/makefile        |  5 +++--
 src/strat.f90       | 13 +++++++++++++
 4 files changed, 55 insertions(+), 8 deletions(-)

diff --git a/scripts/write_h5.py b/scripts/write_h5.py
index d16ca28..5cbdca7 100755
--- a/scripts/write_h5.py
+++ b/scripts/write_h5.py
@@ -1,10 +1,36 @@
 #!/usr/bin/env python
 
+import argparse
 import h5py
 import numpy as np
 import os
 from ps_config import nx, ny, ellx, ymin, ymax
 
+ev_dir = ''
+saveas = ''
+
+try:
+    parser = argparse.ArgumentParser(description="Generate H5 output file.")
+
+    required = parser.add_argument_group('required arguments')
+
+    parser.add_argument("--evolution-dir",
+                        type=str,
+                        required=True,
+                        help="evolution directory")
+
+    parser.add_argument("--saveas",
+                        type=str,
+                        required=True,
+                        help="name of file to be saved")
+
+    args = parser.parse_args()
+
+    ev_dir = args.evolution_dir
+    saveas = args.saveas
+except Exception as ex:
+    print(ex)
+
 print("Parameters from parameters.f90:")
 print("nx   = ", nx)
 print("ny   = ", ny)
@@ -14,7 +40,7 @@
 
 #-----------------------------------------------------------------
 # Open ene.asc file in one directory to get time between frames:
-in_file=open('evolution/ecomp.asc','r')
+in_file=open(os.path.join(ev_dir, 'ecomp.asc'),'r')
 time, ekin, epot, etot = np.loadtxt(in_file,dtype=float,unpack=True)
 in_file.close()
 nt = len(time)
@@ -26,9 +52,13 @@
 
 N = nx * (ny + 1)
 
-h5file = h5py.File('ps_fields.hdf5', 'w')
+h5file = h5py.File(saveas + '.hdf5', 'w')
+
+dt = h5py.string_dtype('ascii', 6)
 
-h5file.attrs['nsteps'] = nt
+h5file.attrs.create("output_type", r"fields", dtype=dt, shape=1)
+
+h5file.attrs['nsteps'] = [nt]
 
 box = h5file.create_group('box')
 box.attrs['extent'] = (ellx, ymax - ymin)
@@ -38,8 +68,10 @@
 for frame in range(nt):
     group = h5file.create_group('step#' + str(frame).zfill(10))
 
+    group.attrs['t'] = time[frame]
+
     for field in ['bb', 'zz']:
-        fname = os.path.join('evolution', field + '.r4')
+        fname = os.path.join(ev_dir, field + '.r4')
 
         in_file = open(fname,'r')
         raw_array = np.fromfile(in_file,dtype=np.float32)
diff --git a/src/constants.f90 b/src/constants.f90
index 0dc4db6..e0626ad 100644
--- a/src/constants.f90
+++ b/src/constants.f90
@@ -3,7 +3,7 @@ module constants
  !Include all modifiable parameters for use below:
 use parameters
 
-! Contains all the non-modifiable parameters as well as all 
+! Contains all the non-modifiable parameters as well as all
 ! quantities which never change throughout a simulation
 ! for the suite of ps f90 codes.
 
@@ -13,13 +13,14 @@ module constants
  !Grid dimensions used in write statements:
 integer,parameter:: ngridp=nx*(ny+1),nbytes=4*(ngridp+1)
 
- !Generic double precision numerical constants: 
+ !Generic double precision numerical constants:
 double precision,parameter:: zero=0.d0,one=1.d0,two=2.d0
 double precision,parameter:: three=3.d0,four=4.d0
 double precision,parameter:: f12=one/two,f14=one/four
 double precision,parameter:: f13=one/three,f23=two/three
 double precision,parameter:: pi=3.14159265358979d0,twopi=two*pi
 double precision,parameter:: small=1.d-12
+double precision,parameter:: hundred=100.0d0
 
  !Domain lengths and inverses:
 double precision,parameter:: xmax=ellx/two,xmin=-xmax
diff --git a/src/makefile b/src/makefile
index 8cabe10..1cb2d06 100644
--- a/src/makefile
+++ b/src/makefile
@@ -4,8 +4,9 @@ sourcedir = .
 installdir = ../bin
 
  # Set main source and object files:
-sources = $(sourcedir)/parameters.f90 $(sourcedir)/constants.f90 $(sourcedir)/spectral.f90 #Main f90 sources
-objects = parameters.o constants.o spectral.o #Main .o files
+sources = $(sourcedir)/parameters.f90 $(sourcedir)/constants.f90 $(sourcedir)/timer.f90 $(sourcedir)/spectral.f90
+#Main f90 sources
+objects = parameters.o constants.o timer.o spectral.o #Main .o files
 
  # Set location of fft library:
 fft_lib = stafft/stafft.f90 stafft/sta2dfft.f90
diff --git a/src/strat.f90 b/src/strat.f90
index bde6521..3a1e9cc 100644
--- a/src/strat.f90
+++ b/src/strat.f90
@@ -31,6 +31,7 @@ program strat
  !Import contants, parameters and common arrays:
 use constants
 use spectral
+use timer
 
 implicit none
 
@@ -53,11 +54,19 @@ program strat
  !Logical for use in saving data:
 logical:: gsave
 
+integer :: ps_timer, advance_timer
+
+call register_timer('ps', ps_timer)
+call register_timer('advance', advance_timer)
+
+call start_timer(ps_timer)
+
 !---------------------------------------------------------
  !Define fixed arrays and constants and read initial data:
 call initialise
 
 !>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
+call start_timer(advance_timer)
  !Start the time loop:
 do while (t < tsim)
 
@@ -65,6 +74,7 @@ program strat
   call advance
 
 enddo
+call stop_timer(advance_timer)
 !End of time loop
 !<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
@@ -78,6 +88,9 @@ program strat
  !Close all files:
 call finalise
 
+call stop_timer(ps_timer)
+
+call print_timer
 
  !Internal subroutine definitions (inherit global variables):
 !::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::