Merge pull request #77 from lhcopt/Release/v1.3.1

Release/v1.3.1

Author: sterbini

pymask/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "v1.3.0"
+__version__ = "v1.3.1"
 
 from .beambeam import *
 from .madpoint import *

pymask/pymasktools.py

@@ -3,6 +3,7 @@
 import json
 
 import numpy as np
+import pandas as pd
 
 import xtrack as xt
 import xpart as xp
@@ -375,7 +376,8 @@ def get_optics_and_orbit_at_start_ring(mad, seq_name, with_bb_forces=False,
         px = twiss_table.px[0],
         y = twiss_table.y[0],
         py = twiss_table.py[0],
-        psigma = twiss_table.pt[0]/mad_beam.beta,
+        ptau = twiss_table.pt[0],
+        zeta = twiss_table.t[0] * mad_beam.beta
     )
     particle_on_madx_co.zeta = (twiss_table.t[0]
                                 *particle_on_madx_co.beta0
@@ -544,3 +546,59 @@ def _restore_beam_beam(line):
                 del(ee._temp_Ddelta_sub)
             else:
                 raise ValueError('What?!')
+
+
+
+def seqedit(mad,seq_name,editing,madInput = True):
+    """Wrapper for MADX seqedit function
+
+    -> editing: dict or pd.DataFrame,
+        "mode" needs to be specified for each element {install, remove, replace, skip}
+        other columns need to be specified depending on the chosen mode, based on the parameters from the MADX user guide.
+    -> madInput: bool,
+        used to skip the mad.input() call and simply return the string
+    """
+    
+    # Converting to pd.DataFrame
+    if type(editing) is dict:
+        editing = pd.DataFrame(editing)
+    
+    # SORTING prior to the installation
+    if 'at' in list(editing.columns):
+        editing.sort_values('at',inplace=True)
+    
+    
+    # ELEMENTS
+    def installStr(row):
+        return f'{row["mode"]},element = {row["element"]},class={row["class"]},at = {row["at"]},from = {row["from"]};'
+
+    def removeStr(row):
+        return f'{row["mode"]},element = {row["element"]};' 
+    
+    def replaceStr(row):
+        return f'{row["mode"]},element = {row["element"]},by = {row["by"]};' 
+    
+    def skipStr(row):
+        return ''
+
+    entryStr = {'install':installStr,'remove':removeStr,'replace':replaceStr,'skip':skipStr}
+    elementsEntry = '\n'.join(filter(None, [entryStr[row['mode']](row) for _,row in editing.iterrows()]))
+    
+    
+    # Generating MADX call
+    output = f'''
+        use, sequence = {seq_name};
+        SEQEDIT, SEQUENCE={seq_name};
+            FLATTEN;
+            {elementsEntry}
+            FLATTEN;
+        ENDEDIT;
+
+        use, sequence = {seq_name};
+    '''
+
+    
+    # Sending input to mad and returning it as a string
+    if madInput:
+        mad.input(output)
+    return output

python_examples/hl_lhc_collisions_python/checks_and_doc/helpers.py

@@ -154,7 +154,7 @@ def track_particle_sixtrack(
         px_tbt[:, i_part] = sixdump_part.px
         y_tbt[:, i_part] = sixdump_part.y
         py_tbt[:, i_part] = sixdump_part.py
-        zeta_tbt[:, i_part] = sixdump_part.zeta
+        zeta_tbt[:, i_part] = sixdump_part.tau * sixdump_part.beta0
         delta_tbt[:, i_part] = sixdump_part.delta
 
     extra = {}

python_examples/hl_lhc_collisions_python/checks_and_doc/install_miniconda.sh

@@ -7,12 +7,16 @@ 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                                        
+git clone [email protected]:lhcopt/lhcmask.git   
+git clone [email protected]:lhcopt/beambeam_macros.git
+cd beambeam_macros
+gfortran headonslice.f -o  headonslice
+cd ..
 cd lhcmask                                                                         
-git checkout release/v1.3.0                                                        
+git checkout release/v1.3.1                                                        
 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 -m pip install sixtracktools            
+python -m pip install NAFFlib

python_examples/hl_lhc_collisions_python/checks_and_doc/t005_check_crabs.py

@@ -21,26 +21,26 @@
 phi_weak = Phi
 phi_c_weak = Phi_c
 
-# # B1 ip1
-# beam_track = 'b1'
-# ip_choice = 1
-# plane = 'x'
-# phi_weak = Phi
-# phi_c_weak = Phi_c
-
-# # B4 ip5
-# beam_track = 'b4'
-# ip_choice = 5
-# plane = 'y'
-# phi_weak = Phi
-# phi_c_weak = Phi_c
-
-# # B4 ip1
-# beam_track = 'b4'
-# ip_choice = 1
-# plane = 'x'
-# phi_weak = -Phi
-# phi_c_weak = -Phi_c
+# B1 ip1
+beam_track = 'b1'
+ip_choice = 1
+plane = 'x'
+phi_weak = Phi
+phi_c_weak = Phi_c
+
+# B4 ip5
+beam_track = 'b4'
+ip_choice = 5
+plane = 'y'
+phi_weak = Phi
+phi_c_weak = Phi_c
+
+# B4 ip1
+beam_track = 'b4'
+ip_choice = 1
+plane = 'x'
+phi_weak = -Phi
+phi_c_weak = -Phi_c
 
 phi_strong = -phi_weak
 phi_c_strong = -phi_c_weak
@@ -60,7 +60,7 @@ def prepare_line(path, input_type):
     elif input_type == 'sixtrack':
         print('Build xsuite from sixtrack input:')
         sixinput_test = sixtracktools.sixinput.SixInput(path)
-        ltest = xt.Line.from_sixinput(sixinput_test)
+        ltest = sixinput_test.generate_xtrack_line()
         print('Done')
     else:
         raise ValueError('What?!')

python_examples/hl_lhc_collisions_python/config.yaml

@@ -1,6 +1,6 @@
 # Links to be made for tools and scripts
 links:
-  tracking_tools: /afs/cern.ch/eng/tracking-tools
+  tracking_tools: auto
   modules: tracking_tools/modules
   tools: tracking_tools/tools
   beambeam_macros: tracking_tools/beambeam_macros

python_examples/ions_python/checks_and_doc/helpers.py

@@ -154,7 +154,7 @@ def track_particle_sixtrack(
         px_tbt[:, i_part] = sixdump_part.px
         y_tbt[:, i_part] = sixdump_part.y
         py_tbt[:, i_part] = sixdump_part.py
-        zeta_tbt[:, i_part] = sixdump_part.zeta
+        zeta_tbt[:, i_part] = sixdump_part.tau * sixdump_part.beta0
         delta_tbt[:, i_part] = sixdump_part.delta
 
     extra = {}

python_examples/run3_collisions_python/checks_and_doc/helpers.py

@@ -154,7 +154,7 @@ def track_particle_sixtrack(
         px_tbt[:, i_part] = sixdump_part.px
         y_tbt[:, i_part] = sixdump_part.y
         py_tbt[:, i_part] = sixdump_part.py
-        zeta_tbt[:, i_part] = sixdump_part.zeta
+        zeta_tbt[:, i_part] = sixdump_part.tau * sixdump_part.beta0
         delta_tbt[:, i_part] = sixdump_part.delta
 
     extra = {}

python_examples/run3_collisions_python/checks_and_doc/t008_check_against_sixtrack.py

@@ -44,8 +44,8 @@
 print(x_tbt_sixtrack)
 
 assert np.allclose(tracker.record_last_track.x[0, :], x_tbt_sixtrack[:,0],
-       rtol=1e-15, atol=9e-11)
+       rtol=1e-14, atol=9e-10)
 assert np.allclose(tracker.record_last_track.y[0, :], y_tbt_sixtrack[:,0],
-       rtol=1e-15, atol=15e-11)
+       rtol=1e-14, atol=9e-10)
 assert np.allclose(tracker.record_last_track.delta[0, :], delta_tbt_sixtrack[:,0],
-       rtol=1e-15, atol=5e-11)
+       rtol=1e-14, atol=5e-10)