Merge pull request #72 from lhcopt/release/v1.3.0

Release/v1.3.0

Author: sterbini

.gitignore

@@ -148,3 +148,11 @@ examples/run3_collision/temp/sliceho.res
 examples/run3_collision/temp/surveyaux.tfs
 examples/run3_collision/temp/twiss.tfs
 examples/run3_collision/last_twiss.0.gz
+miniconda
+pytrain
+sixtracktools
+xfields
+xline
+xobjects
+xpart
+xtrack

python_examples/clean_all

@@ -15,6 +15,6 @@ rm *.tfs
 rm -r xline 
 rm -r temp
 rm -r __pycache__ 
-
+rm -r xsuite_lines
 # Remove all links
 find -type l -exec rm {} \;

python_examples/hl_lhc_collisions_python/000_pymask.py

@@ -1,15 +1,33 @@
 import os
 import sys
 import json
-
+import yaml
 import numpy as np
 
-
 #####################################################
 # Read general configurations and setup envirnoment #
 #####################################################
 
-from config import configuration
+assert not(os.path.isfile('config.yaml')
+           and os.path.isfile('config.py')), (
+    "Please specify only a config file (yaml or py)")
+
+try:
+    with open('config.yaml','r') as fid:
+        configuration = yaml.safe_load(fid)
+except:
+    from config import configuration
+
+# Start tree_maker logging if log_file is present in config
+try:
+    import tree_maker
+    if 'log_file' not in configuration.keys():
+        tree_maker=None
+except:
+    tree_maker=None
+
+if tree_maker is not None:
+    tree_maker.tag_json.tag_it(configuration['log_file'], 'started')
 
 mode = configuration['mode']
 tol_beta = configuration['tol_beta']
@@ -27,8 +45,12 @@
 knob_settings = configuration['knob_settings']
 knob_names = configuration['knob_names']
 
-
 # Make links
+if links['tracking_tools'] == 'auto':
+    import pymask as pm
+    links['tracking_tools'] = str(
+            pm._pkg_root.parent.parent.absolute())
+
 for kk in links.keys():
     if os.path.exists(kk):
         os.remove(kk)
@@ -77,7 +99,8 @@
 mad.globals.par_verbose = int(configuration['verbose_mad_parts'])
 
 # Build sequence (alse creates link to optics_toolkit and calls it)
-ost.build_sequence(mad, beam=beam_to_configure)
+ost.build_sequence(mad, beam=beam_to_configure,
+                  configuration=configuration)
 
 # Set twiss formats for MAD-X parts (macro from opt. toolkit)
 mad.input('exec, twiss_opt;')
@@ -123,7 +146,7 @@
         ex={configuration['beam_norm_emit_x'] * 1e-6 / gamma_rel},
         ey={configuration['beam_norm_emit_y'] * 1e-6 / gamma_rel},
         mass={particle_mass},
-        charge={particle_charge},
+        charge={particle_charge};
     ''')
 
 
@@ -268,7 +291,7 @@
 
 if generate_b4_from_b2:
     mad_b4 = Madx(command_log="mad_b4.log")
-    ost.build_sequence(mad_b4, beam=4)
+    ost.build_sequence(mad_b4, beam=4,configuration=configuration)
 
     pm.configure_b4_from_b2(mad_b4, mad)
 
@@ -402,7 +425,7 @@
     if configuration['enable_knob_synthesis']:
         mad_track.input('exec, crossing_disable;')
         mad_track.input("call, file='modules/submodule_04e_s1_synthesize_knobs.madx';")
-        mad_track.input('exec, crossing_restore;')
+    mad_track.input('exec, crossing_restore;')
 
 
 ##################
@@ -559,3 +582,6 @@
 #############################
 # N.B. this erases the errors in the mad_track instance
 # pm.save_mad_sequence_and_error(mad_track, sequence_to_track, filename='final')
+
+if tree_maker is not None:
+    tree_maker.tag_json.tag_it(configuration['log_file'], 'completed')

python_examples/hl_lhc_collisions_python/checks_and_doc/install_miniconda.sh

@@ -0,0 +1,18 @@
+wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh         
+bash Miniconda3-latest-Linux-x86_64.sh -b  -p ./miniconda -f                       
+source miniconda/bin/activate                                                      
+pip install ipython jupyterlab numpy scipy pandas awkward matplotlib               
+pip install pyarrow pyyaml pytest                                                 
+pip install cpymad                                                                 
+pip install xsuite                                                                 
+git clone [email protected]:lhcopt/lhcerrors.git                                      
+git clone [email protected]:lhcopt/lhctoolkit.git                                     
+git clone [email protected]:lhcopt/lhcmask.git                                        
+cd lhcmask                                                                         
+git checkout release/v1.3.0                                                        
+pip install -e .                                                                   
+cd ../                                                                             
+git clone https://github.com/PyCOMPLETE/FillingPatterns.git                        
+pip install ./FillingPatterns                                                      
+python -m pip install sixtracktools                                                
+python -m pip install NAFFlib 

python_examples/hl_lhc_collisions_python/checks_and_doc/t005_check_crabs.py

@@ -140,7 +140,7 @@ def prepare_line(path, input_type):
     ddd = json.load(fid)
 partco = xp.Particles.from_dict(ddd['particle_on_madx_co'])
 z_slices = s_rel * 2.0
-partco = xp.build_particles(particle_ref=partco, zeta=z_slices)
+partco = xp.build_particles(particle_on_co=partco, mode='shift', zeta=z_slices)
 
 
 list_co = ltest.slow_track_elem_by_elem(partco)
@@ -221,7 +221,8 @@ def prepare_line(path, input_type):
 part = xp.Particles.from_dict(ddd['particle_on_madx_co'])
 
 z_test = np.array([0, z_crab_track])
-part = xp.build_particles(particle_ref=part,
+part = xp.build_particles(particle_on_co=part,
+        mode='shift',
         zeta = z_test,
         x = 0*z_test + np.array([0, x_twiss[0]]),
         y = 0*z_test + np.array([0, y_twiss[0]]),

python_examples/hl_lhc_collisions_python/checks_and_doc/t007_check_orbit_and_lin_normal_form.py

@@ -21,7 +21,7 @@
     tracker.track(particles)
 
 for nn in 'x px y py zeta delta'.split():
-    assert np.abs(getattr(particles, nn) - getattr(partCO, nn)) < 1e-11
+    assert np.abs(getattr(particles, nn) - getattr(partCO, nn)) < 2e-11
 
 WW = np.array(line_dict['WW_finite_diffs'])
 WWinv = np.array(line_dict['WWInv_finite_diffs'])
@@ -37,7 +37,7 @@
 x_norm = ampl_sigmas * np.sqrt(geom_emit_x) * np.cos(theta)
 px_norm = ampl_sigmas * np.sqrt(geom_emit_x) * np.sin(theta)
 
-particles_matched  = xp.build_particles(particle_ref=partCO,
+particles_matched  = xp.build_particles(particle_on_co=partCO,
                                         x_norm=x_norm, px_norm=px_norm,
                                         R_matrix=np.array(line_dict['RR_finite_diffs']))
 particles_test = particles_matched.copy()

python_examples/hl_lhc_collisions_python/checks_and_doc/t008_check_against_sixtrack.py

@@ -31,14 +31,15 @@
 
 tracker = xt.Tracker(line=line)
 
-particles = xp.build_particles(particle_ref=partCO,
+particles = xp.build_particles(particle_on_co=partCO,
+        mode='shift',
         x=np.array(displace_x),
         y=np.array(displace_y))
 
 tracker.track(particles, turn_by_turn_monitor=True, num_turns=num_turns)
 
 print('Xtrack')
-print(tracker.record_last_track.x)
+print(tracker.record_last_track.x.transpose())
 print('Sixtrack')
 print(x_tbt_sixtrack)
 

python_examples/hl_lhc_collisions_python/checks_and_doc/tests.md

@@ -16,9 +16,9 @@ We setup the python version:
 cd ../../python_examples/hl_lhc_collisions_python
 
 ```
-In config.py we select:
-```python
-mode : 'b1_with_bb_legacy_macros'
+In config.yaml we select:
+```yaml
+mode : b1_with_bb_legacy_macros
 ```
 We run the python version:
 ```
@@ -36,9 +36,9 @@ diff fc.34 ../../examples/hl_lhc_collision/fc.34
 
 
 ## Test 2 - b1 with new bb tools
-In config.py we select:
-```python
-'mode' : 'b1_with_bb',
+In config.yaml we select:
+```yaml
+mode : b1_with_bb
 ```
 
 We exeute the python version:
@@ -121,10 +121,12 @@ We setup the python version:
 cd ../../python_examples/hl_lhc_collisions_python
 
 ```
-In config.py we select:
-```python
-'mode' : 'b4_without_bb',
-force_leveling : {'on_sep8': -0.03425547139366354, 'on_sep2': 0.14471680504084292}
+In config.yaml we select:
+```yaml
+mode: b4_without_bb,
+force_leveling:
+  on_sep8: -0.03425547139366354
+  on_sep2: 0.14471680504084292
 ```
 (the separations are forced in order to be consitent with the mad-x test case for which the same values are impored, as the legacy leveling macro does not work in this case).
 
@@ -155,10 +157,12 @@ We setup the python version:
 cd ../../python_examples/hl_lhc_collisions_python
 
 ```
-In config.py we select:
-```python
-'mode' : 'b4_from_b2_without_bb',
-'force_leveling' : {'on_sep8': -0.03425547139366354, 'on_sep2': 0.14471680504084292}
+In config.yaml we select:
+```yaml
+mode: b4_from_b2_without_bb
+force_leveling: 
+  on_sep8: -0.03425547139366354
+  on_sep2: 0.14471680504084292
 ```
 (the separations are forced in order to be consitent with the mad-x test case for which the same values are impored, as the legacy leveling macro does not work in this case).
 
@@ -183,10 +187,9 @@ We setup the python version:
 cd ../../python_examples/hl_lhc_collisions_python
 
 ```
-In config.py we select:
+In config.yaml we select:
 ```python
-'mode' : 'b4_from_b2_with_bb',
-
+mode: b4_from_b2_with_bb,
 ```
 We run the python version:
 ```
@@ -222,6 +225,41 @@ phi_weak = Phi
 phi_c_weak = Phi_c
 ```
 
+## Test 7 and 8 - Check the matching and the tracking
+
+Select on config.yaml
+
+```yaml
+beam: b1_without_bb
+```
+and run 
+
+```bash 
+python t003_fc_to_fort.py
+python t007_check_orbit_and_lin_normal_form.py
+python t008_check_against_sixtrack.py
+```
+
+then repeat for 
+
+```yaml
+beam: b1_with_bb
+```
+
+and
+
+```yaml
+beam: b4_from_b2_without_bb
+```
+
+and
+
+```yaml
+beam: b4_from_b2_with_bb
+```
+
+
+
 ## To check a mad test againt its reference
 
 ```bash