This is an old revision of the document!
Extracting the intensity contribution from a certain phase from a batch data set
Intensity contribution from individual phase can be saved out from GUI interface “right-click → save if displayed…”.
However, there were multiple questions asked in the forum concerning how to extract phase contribution through Launch Mode .inp file setup, and even do this for in-situ data set.
The solution below has been enlightened by the Alan Coelho's 2-step refinement & Matthew Rowles's Sequential Refinement method.
TOPAS V6 allows a keyword num_runs which instructs the programme to run an .inp file multiple times, which means above 2-step solution can be devised in one .inp file with “num_runs 2” and several #if switches:
num_runs 2
#if (Run_Number == 1)
iters 0
#endif
#if Run_Number == 0;
system_before_save_OUT { copy INP_File##.inp INP_File##.backup } 'Backup this .inp file in the first run
#endif
out_file = Concat(String(INP_File), ".INP"); ' This allow the refinement result to be accepted.
#if Run_Number == 1;
system_after_save_OUT { copy INP_File##.backup INP_File##.inp } 'Restore this .inp file to its initial status from the backup in the final run
#endif
xdd "somepattern.raw"
#if (Run_Number == 0)
bkg @ 713.3525387 332.4034599 -218.0099371
One_on_X(@, 9993.352223)
#endif
LP_Factor( 0)
Specimen_Displacement(samp_disp, -0.05080112471)
Mixture_LAC_1_on_cm( 0)
mixture_MAC 0
mixture_density_g_on_cm3 1.6605402e+22
Rp 300
Rs 300
lpsd_th2_angular_range_degrees 2.29
lpsd_equitorial_divergence_degrees 0.5
axial_conv
filament_length 12
sample_length 20
receiving_slit_length 20
primary_soller_angle 5
secondary_soller_angle 5
axial_n_beta 30
CuKa(0.0001)
#if (Run_Number == 1)
xdd_out Output_phase_contribution.xy load out_record out_fmt out_eqn
{
" %11.6f " = X + 2 samp_disp Cos(X Deg_on_2)/Rp Rad; ' Correct sample displacement from an internal standard, hkl_Al in this case
" %11.6f\n " = Ycalc;
}
#endif
#if (Run_Number == 0)
xo_Is ' Amorphous Hump
xo @ 14.70505682
peak_type spv
spv_h1 @ 0.9845624876
spv_h2 @ 1.396576759
spv_l1 0.0040801296_LIMIT_MIN_0
spv_l2 0.9958599408_LIMIT_MAX_1
I 97.34548273
hkl_Is
hkl_m_d_th2 1 1 1 8 2.33311367 38.5568314 I @ 74.14699402
hkl_m_d_th2 2 0 0 6 2.02053571 44.8203506 I @ 96.76241314
LVol_FWHM_CS_G_L( 1, 113.2882082, 0.89, 158.3779042,,,@, 177.9527013_LIMIT_MAX_115.908746)
Stephens_cubic(@, 0.2634600653_LIMIT_MIN_0,@, -2072.424113,@, -5379.345555)
r_bragg 1.213209076
phase_MAC 0
phase_name "hkl_Al" ' Internal Standard
MVW( 0, 65.99173092, 0)
space_group Fm-3m
Cubic(!a_000040787 4.049) 'Fixed to the lattice parameter from a PDF card.
hkl_Is
hkl_m_d_th2 1 0 0 6 3.72346902 23.8787327 I @ 0.0001220703125_LIMIT_MIN_1e-15
hkl_m_d_th2 0 0 1 2 3.66351223 24.2754326 I @ 4.043069301
...
e0_from_Strain( 0.0004851245559,@, 0.2223647167_LIMIT_MIN_0.0001,,)
r_bragg 0.1279653452
phase_MAC 0
phase_name "hkl_LiC6" ' Some other irrelevant phases
MVW( 0, 58.64925299, 0)
space_group P6/mmm
Hexagonal(a_010834148 4.299491625,c_010834148 3.66351217)
#endif
hkl_Is
hkl_m_d_th2 0 0 2 2 5.54676771 15.9653101 I @ 2.664253279
hkl_m_d_th2 0 0 4 2 2.77338386 32.2515259 I @ 10.48756371
...
LVol_FWHM_CS_G_L( 1, 173.7971979, 0.89, 242.97,,,, 273_LIMIT_MIN_200 min =200;)
e0_from_Strain( 0.001701696021,, 0.78,,)
r_bragg 0.2228689481
phase_MAC 0
phase_name "hkl_Na0.53MnO2" ' This is the phase of interest, which you want its intensity contributions saved out
MVW( 0, 78.20697387, 0)
space_group P63/mmc
Hexagonal(a_040201752 2.853135761,c_040201752 11.09353545)
It can be seen that, in the first run (Run_Number = 0), the #if switches allows a normal Pawley refinement which refines the sample displacement according to an internal standard (hkl_Al in this case).
In the second run (Run_Number = 1), the #if switches only turned on the phase of interest with “iters 0” and get the intensity saved out.
To apply this method for a batch of data set (e.g. in-situ data set), which contains, say 100 patterns, a .inp file with “num_run = 2 * 100;” can be set as below:
The below setup has an restriction that, the file names of the dataset must contain an increasing run number: e.g. *_1.raw, *_2.raw, ***_3.raw, ….. A simple windows/DOS batch rename can achieve this.
num_runs =2*100; 'This set the Reserved Keywords "Run_Number" goes from 0 to 199
#if (Mod(Run_Number,2) == 1) ' Normal Pawley refinement when Run_Number is an even number; Save the phase intensity when Run_Number is an odd number
iters 0
#endif
#if Run_Number == 0;
system_before_save_OUT { copy INP_File##.inp INP_File##.backup }
#endif
out_file = Concat(String(INP_File), ".INP"); 'This accepts the refinement result, especially the sample displacement
#if Run_Number == 2*100-1;
system_after_save_OUT { copy INP_File##.backup INP_File##.inp }
#endif
#prm filenum = Round((Run_Number+1)/2); 'This calculates the run number of the file, NOTE Round(0.5) evaluates to 0 in TOPAS V5, but evaluates to 1 in TOPAS V6!
xdd Somepattern_#out filenum##.raw 'This allow TOPAS to find the corresponding pattern
#if (Mod(Run_Number,2) == 0)
bkg @ 713.3525387 332.4034599 -218.0099371
One_on_X(@, 9993.352223)
#else bkg 100 ' A arbitrary bkg 100 is added to the phase contribution in case some plotting software don't like 0 intensity.
#endif
LP_Factor( 0)
Specimen_Displacement(samp_disp, -0.05080112471)
Mixture_LAC_1_on_cm( 0)
mixture_MAC 0
mixture_density_g_on_cm3 1.6605402e+22
Rp 300
Rs 300
lpsd_th2_angular_range_degrees 2.29
lpsd_equitorial_divergence_degrees 0.5
axial_conv
filament_length 12
sample_length 20
receiving_slit_length 20
primary_soller_angle 5
secondary_soller_angle 5
axial_n_beta 30
CuKa(0.0001)
#if (Mod(Run_Number,2) == 1) ' When Run_Number is an odd number, save the phase contribution to a file with the run number of its raw data
xdd_out OUTPUT_NMO_#out filenum##.xy load out_record out_fmt out_eqn
{
" %11.6f " = X + 2 samp_disp Cos(X Deg_on_2)/Rp Rad; ' Correct sample displacement of the phase
" %11.6f\n " = Ycalc;
}
#endif
#if (Mod(Run_Number,2) == 0)
xo_Is 'Amorphous hump
xo @ 14.70505682
peak_type spv
spv_h1 @ 0.9845624876
spv_h2 @ 1.396576759
spv_l1 0.0040801296_LIMIT_MIN_0
spv_l2 0.9958599408_LIMIT_MAX_1
I 97.34548273
hkl_Is
hkl_m_d_th2 1 1 1 8 2.33311367 38.5568314 I @ 74.14699402
hkl_m_d_th2 2 0 0 6 2.02053571 44.8203506 I @ 96.76241314
LVol_FWHM_CS_G_L( 1, 113.2882082, 0.89, 158.3779042,,,@, 177.9527013_LIMIT_MAX_115.908746)
Stephens_cubic(@, 0.2634600653_LIMIT_MIN_0,@, -2072.424113,@, -5379.345555)
r_bragg 1.213209076
phase_MAC 0
phase_name "hkl_Al" 'Internal Standard with fixed lattice parameter
MVW( 0, 65.99173092, 0)
space_group Fm-3m
Cubic(!a_000040787 4.049)
hkl_Is
hkl_m_d_th2 1 0 0 6 3.72346902 23.8787327 I @ 0.0001220703125_LIMIT_MIN_1e-15
hkl_m_d_th2 0 0 1 2 3.66351223 24.2754326 I @ 4.043069301
...
LVol_FWHM_CS_G_L( 1, 689.7614989, 0.89, 964.2925977,,,@, 1083.474829_LIMIT_MIN_0.3)
e0_from_Strain( 0.0004851245559,@, 0.2223647167_LIMIT_MIN_0.0001,,)
r_bragg 0.1279653452
phase_MAC 0
phase_name "hkl_LiC6" 'Other irrelevant phases
MVW( 0, 58.64925299, 0)
space_group P6/mmm
Hexagonal(a_010834148 4.299491625,c_010834148 3.66351217)
#endif
hkl_Is
hkl_m_d_th2 0 0 2 2 5.54676771 15.9653101 I @ 2.664253279
hkl_m_d_th2 0 0 4 2 2.77338386 32.2515259 I @ 10.48756371
...
LVol_FWHM_CS_G_L( 1, 173.7971979, 0.89, 242.97,,,, 273_LIMIT_MIN_200 min =200;)
e0_from_Strain( 0.001701696021,, 0.78,,)
r_bragg 0.2228689481
phase_MAC 0
phase_name "hkl_Na0.53MnO2" ' The phase of interest, the intensity of which needs be saved out
MVW( 0, 78.20697387, 0)
space_group P63/mmc
Hexagonal(a_040201752 2.853135761,c_040201752 11.09353545)
