From a4220aee18a6ac9d39c5b5ea9466e74a806cbd98 Mon Sep 17 00:00:00 2001
From: Evgeny Blokhin <eb@tilde.pro>
Date: Sat, 11 Jan 2025 16:06:08 +0100
Subject: [PATCH] Extend examples

---
 examples/submit_any_engine_input.py | 36 +++++++++++++++++
 examples/submit_fullprof_input.py   | 61 +++++++++++++++++++++++++++++
 examples/submit_topas_input.py      | 22 ++++++++---
 3 files changed, 113 insertions(+), 6 deletions(-)
 create mode 100644 examples/submit_any_engine_input.py
 create mode 100644 examples/submit_fullprof_input.py

diff --git a/examples/submit_any_engine_input.py b/examples/submit_any_engine_input.py
new file mode 100644
index 0000000..07ef718
--- /dev/null
+++ b/examples/submit_any_engine_input.py
@@ -0,0 +1,36 @@
+#!/usr/bin/env python3
+
+import os
+import argparse
+
+from yascheduler import Yascheduler
+
+
+parser = argparse.ArgumentParser()
+parser.add_argument("-f", dest="file", action="store", type=str, required=True)
+parser.add_argument("-e", dest="engine", action="store", type=str, required=True)
+parser.add_argument("-l", dest="localrepo", action="store", type=bool, required=False, default=False)
+args = parser.parse_args()
+
+input_data = {}
+yac = Yascheduler()
+assert args.engine in yac.config.engines
+
+target = os.path.abspath(args.file)
+work_folder = os.path.dirname(target)
+with open(target, encoding="utf-8") as f:
+    MAIN_INPUT = f.read()
+
+if args.localrepo:
+    input_data["local_folder"] = None
+    print("**To save calc in a local repo**")
+else:
+    input_data["local_folder"] = work_folder
+    print("**To save calc in an input folder**")
+
+input_data[yac.config.engines[args.engine].input_files[0]] = MAIN_INPUT
+for inp in yac.config.engines[args.engine].input_files[1:]:
+    input_data[inp] = ""
+
+result = yac.queue_submit_task("test calc", input_data, args.engine)
+print(result)
diff --git a/examples/submit_fullprof_input.py b/examples/submit_fullprof_input.py
new file mode 100644
index 0000000..8f7cc5f
--- /dev/null
+++ b/examples/submit_fullprof_input.py
@@ -0,0 +1,61 @@
+#!/usr/bin/env python3
+"""Submit FP task"""
+
+from yascheduler import Yascheduler
+
+LABEL = "Al2O3 XRPD pattern"
+
+PATTERN_REQUEST = """COMM Corindon Al2O3
+! Files => DAT-file: corindon, PCR-file: corindonx
+!Job Npr Nph Nba Nex Nsc Nor Dum Iwg Ilo Ias Res Ste Nre Cry Uni Cor Opt Aut
+ 2 5 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0
+!
+!Ipr Ppl Ioc Mat Pcr Ls1 Ls2 Ls3 NLI Prf Ins Rpa Sym Hkl Fou Sho Ana
+ 0 0 1 0 1 0 0 0 0 2 0 0 0 0 0 0 1
+!
+! lambda1 Lambda2 Ratio Bkpos Wdt Cthm muR AsyLim Rpolarz ->Patt# 1
+1.540596 1.540596 0.50 65.00 20.00 0.7998 0.00 40.00 0.0000
+!
+!NCY Eps R_at R_an R_pr R_gl Thmin Step Thmax PSD Sent0
+ 1 0.01 0.65 0.65 0.35 0.65 10.0000 0.100000 175.0000 0.000 0.000
+!
+ 0 !Number of refined parameters
+!
+! Zero Code SyCos Code SySin Code Lambda Code MORE ->Patt# 1
+-0.090 21.00 0.0000 0.00 0.0000 0.00 0.0000 0.0000 0
+! Background coefficients/codes for Pattern# 1
+21.00 -5.66 -9.36 8.30 37.04 -24.55
+ 51.00 61.00 71.00 81.00 31.00 41.00
+!-------------------------------------------------------------------------------
+! Data for PHASE number: 1
+!-------------------------------------------------------------------------------
+Al2O3
+!
+!Nat Dis Ang Pr1 Pr2 Pr3 Jbt Irf Isy Str Furth ATZ Nvk Npr More
+ 2 0 0 0.0 0.0 1.0 0 0 0 0 0 611.760 0 5 0
+!
+R -3 c <--Space group symbol
+!Atom Typ X Y Z Biso Occ In Fin N_t Spc /Codes
+AL AL+3 0.00000 0.00000 0.35218 0.4000 0.33333 0 0 0 0
+ 0.00 0. 00 171.00 191.00 0.00
+O O-2 0.30610 0.00000 0.25000 0.5000 0.50000 0 0 0 0
+ 181.00 0.00 0.00 201.00 0.00
+!-------> Profile Parameters for Pattern # 1
+! Scale Shape1 Bov Str1 Str2 Str3 Strain-Model
+0.28556E-02 0.5000 0.00000 0.00000 0.00000 0.00000 0
+ 11.00000 161.000 0.000 0.000 0.000 0.000
+! U V W X Y GauSiz LorSiz Size-Model
+ 0.005865 0.025089 0.018587 0.000000 0.000000 0.000000 0.000000 0
+ 141.000 151.000 131.000 0.000 0.000 0.000 0.000
+! a b c alpha beta gamma #Cell Info
+ 4.75758 4.75758 12.9876 90.000 90.000 120.000
+ 111.000 111.000 121.000 0.000 0.000 111.000
+! Pref1 Pref2 Asy1 Asy2 Asy3 Asy4
+ 0.00000 0.00000 0.023 0.061 0.00000 0.00000
+ 0.00 0.00 91.00 101.00 0.00 0.00
+"""
+
+yac = Yascheduler()
+result = yac.queue_submit_task(LABEL, {"calc.pcr": PATTERN_REQUEST}, "fullprof")
+print(LABEL)
+print(result)
diff --git a/examples/submit_topas_input.py b/examples/submit_topas_input.py
index d6a5789..af4942f 100644
--- a/examples/submit_topas_input.py
+++ b/examples/submit_topas_input.py
@@ -3,13 +3,21 @@
 
 from yascheduler import Yascheduler
 
-LABEL = "SrTiO3 XRPD pattern"
+LABEL = "SrTiO3 XRPD dI"
 
 PATTERN_REQUEST = """
-iters 0
-yobs_eqn !x = 0; min 10 max 175 del 0.1
-
-Out_X_Ycalc( calc.xy )
+macro Out_Dif(file)
+{
+    out file phase_out file load out_record out_fmt out_eqn
+    {
+        " %11.5f"   = D_spacing;
+        " %11.5f\n" = I_after_scale_pks;
+    }
+}
+
+iters 1
+yobs_eqn = 0; min 0 max 80 del 0.01
+LP_Factor(0)
 
 lam
     ymin_on_ymax  0.0001
@@ -24,10 +32,12 @@
 site O   x  0.00000  y  0.00000  z  2.00000  occ O   1  beq  1
 site Sr  x  2.00000  y  2.00000  z  2.00000  occ Sr  1  beq  1
 site Ti  x  0.00000  y  0.00000  z  0.00000  occ Ti  1  beq  1
+
+Out_Dif( calc.xy )
 """
 
 
 yac = Yascheduler()
-result = yac.queue_submit_task(LABEL, {"calc.inp": PATTERN_REQUEST, "structure.inc": "", "input.xy: ""}, "topas")
+result = yac.queue_submit_task(LABEL, {"calc.inp": PATTERN_REQUEST, "structure.inc": ""}, "topas")
 print(LABEL)
 print(result)