Trace: • manual_part_3
Table of Contents
11 Chargeflipping
The chargeflipping method of Oszlányi & Süto (2004) has been implemented using the keywords shown in Table 11‑2. Also included is the use of the tangent formula (Hauptman & Karle, 1956) within the iterative chargeflipping process. Equations appearing in chargeflipping keywords can be functions of the items shown in Table 11‑1. At the end of a charge flipping process a file with the same name as that given by cf_hkl_file is created but with a *.FC extension. Almost all of the chargeflipping keywords can be equations allowing for great flexibility in regards to changing resolution etc… on the fly. Table 11‑3 lists chargeflipping examples found in the CF directory.
Table 11‑1. Items that can be used in chargeflipping equations  
Get(Aij) Get(alpha_sum) Get(density) Get(cycles_since_last_best) Get(d_squared_inverse) Get(initial_phase) Get(iters_since_last_best) Get(F000) Get(max_density) Get(max_density_at_cycle_iter_0) Get(num_reflections_above_d_min) Get(phase_difference) Get(r_factor_1), Get(r_factor_2) Get(threshold)  These are updated internally each chargeflipping iteration or cycle or when needed. 
Reserved parameter names Cycle_Iter, Cycle, Iter, D_spacing  
Macros  
Ramp, Ramp_Clamp, Cycle_Ramp,Tangent, Restart_CF, Pick, Pick_Best  See TOPAS.INC for details. 
Out_for_cf(file) : Outputs the A matrix from a Pawley refinement for use in charge flipping; uses cf_in_A_matrix. See example CFCIMEPAWLEY.INP. 

Table 11‑2. Keywords that can be used in chargeflipping. 
11.1 Chargeflipping usage
CF works particularlly well on data at good resolution (<1Å resolution). For data at poor resolution or for difficult structures then inclusion of the tangent formula can facilitate solution and sharpen electron densities, see example CF1A7Y.INP. Powder diffraction data usually fall under the poor resolution/data quality category and as such additional symmetry restraints using symmetry_obey_0_to_1 can sharpen electron densities. Example CFALVO4.INP demonstrates the use of the tangent formula on powder data.
The choice and amount of perturbation necessary for finding a solution are important considerations. Not enough perturbation leads to the system being trapped within a local parameter space; too much perturbation may lead to a solution not being found and in addition contrast in Rfactors prior to and at convergence are diminished leading to difficult to identify solutions. Many of the examples in the CF directory uses the Ramp macro to gradually vary control parameters, here are some examples:
fraction_density_to_flip = Ramp(0.85, 0.8, 100);
fraction_reflections_weak = Ramp(0.5, 0, 100);
flip_regime_2 = Ramp(1, 0, 200);
flip_regime_3 = Ramp(0.25, 0.5, 200);
symmetry_obey_0_to_1 = Ramp(0.5, 1, 100);
tangent_scale_difference_by = Ramp(0, 1, 100);
Choosing control parameters in this manner gradually decreases perturbation allowing for solutions to be found and identified. This is similar to a simulated annealing process where temperatures start at high values and then progressively lowered.
11.1.1 Perturbations
Perturbations can be categorized as being of either phase, structure factor intensity or electron density perturbations as shown in Table 11‑2. There are two built in flipping regimes, flip_regime_2 and flip_regime_3, and one user defined regime flip_equation. Only one can be used and they all modify the electron density. In the absence of a flipping regime the following is used:
_{}  (11‑1) 
where d corresponds to the electron density threshold.
Using the tangent formula on either difficult structures or on data at poor resolution often leads to uranium atom solutions. Uranium atom solutions can be avoided by modifying the electron density using a flipping regime that dampens high electron densities or by using pick_atoms.
Using a large number of triplets per E_{h} value (a value for tangent_max_triplets_per_h greater than 100) reduces perturbation, increases occurrences of uranium atom solutions and increases the chances of finding a solution after an initial phase randomization. A large number of triplets would typically be used for poor resolution data; correspondingly a flipping regime that avoids uranium atom solutions should be chosen.
Perturbations mostly increase randomness in the system with the exceptions of the tangent formula, scale_density_below_threshold and histogram_match_scale_fwhm.
11.1.2 The Ewald sphere, weak reflections and CF termination
By default CF uses the minimum observed d spacing to define the Ewald sphere; alternatively min_d can be used. The Ewald sphere can be increased using extend_calculated_sphere_to; this inserts missing reflections and gives them the status of “weak” reflections. Weak reflections are also inserted for missing reflections within the Ewald sphere. Weak reflection phases and structure factors can be modified using scale_weak_reflections and add_to_phases_of_weak_reflections.
Reflections that have zero intensities according to the space group are not included in CF; correspondingly the number of observed reflections removed are reported. Structure factor intensities within a family of reflections are determined by averaging the observed structure factors intensities. This averaging is also performed on calculated intensities each CF iteration for weak reflections.
Changing the space group is possible; changing the space group to a higher symmetry from that as implied in the input hkl file often makes sense. Changing the space group to a lower symmetry implies less symmetry and is useful for checking whether a significantly better Rfactor is realized.
Typically a fraction of observed reflections are given the status of “weak” using fraction_reflections_weak. When a solution is found and CF terminates a *.FC file is saved; this file comprises structures factors that produced the best Rfactor. A new CF process can be initiated with phase information saved in the *.FC file using the Restart_CF macro. To further complete the structure the new CF process may for example reduce perturbations in order to sharpen the electron density.
11.1.3 Powder data considerations
For powder data it is usually best to maximize the number of constraints due to poor data quality; it is also best to use *.A files as generated by a Pawley refinement and to then use cf_in_A_matrix. No weak observed reflections within the observed Ewald sphere should be assigned by setting fraction_reflections_weak to zero. Instead weak reflections can be included by extending the Ewald sphere with something like:
extend_calculated_sphere_to 1
add_to_phases_of_weak_reflections = 90 Ramp(1, 0, 100);
If the Ewald sphere is extended such that the weak reflections are many then some of these weak reflections could well be of high intensity. Subsequently offsetting high intensity weak reflections by a constant could lead to too much perturbation and thus the following may be preferential:
extend_calculated_sphere_to 1
add_to_phases_of_weak_reflections = Rand(180,180) Ramp(1, 0, 100);
In a Pawley refinement the calculated intensities at the low dspcaing edge of are often in error to a large extent; it is therefore best to remove these reflections using delete_observed_reflections, for example example:
delete_observed_reflections = D_spacing < 1.134;
A typical first try INP file template for powders is as follows:
macro Nr { 100 }
charge_flipping
cf_in_A_matrix PAWLEY_FILE.A
space_group $
a # b # c al # be # ga #
delete_observed_reflections = D_spacing < #;
extend_calculated_sphere_to #
add_to_phases_of_weak_reflections = 90 Ramp(1, 0, Nr);
flip_regime_2 = Ramp(1, 0, Nr);
symmetry_obey_0_to_1 = Ramp(0.5, 1, Nr);
Tangent(.3, 30)
min_grid_spacing .3
load f_atom_type f_atom_quantity { … }
11.1.4 The algorithm of Oszlányi & Süto (2005) and F000
Normalized structure factors enhances the chances of finding a solution (Oszlányi & Süto, 2006) and are realized by inclusion of f_atom_type’s and when correct_for_temperature_effects is nonzero. Example CF1A7YGABOR.INP implements the algorithm of Oszlányi & Süto (2005) with normalized structure factors. In the original algorithm the amount of charge flipped is a function of the maximum electron density; this can be realized using:
user_threshold = 0.2 Get(max_density_at_cycle_iter_0);
Get(max_density_at_cycle_iter_0) is a different value at the start of each CF process as phases are chosen randomly. An alternative means of defining the threshold is:
fraction_density_to_flip 0.83
The CF process is sensitive to the threshold value. A value of 0.83 for fraction_density_to_flip is optimum for 1a7y and produces a solution in ~1000 iterations. A solution is not found however at 0.75 or 0.85. To overcome this sensitivity the fraction_density_to_flip parameter could be ramped as a function of iteration from a high value to a low value, or,
fraction_density_to_flip = Ramp(0.85, 0.8, 100);
Implementation of such a ramp solves 1a7y in ~2000 iterations.
F000 is allowed to float when scale_F000 is set to 1. In the Oszlányi & Süto (2005) algorithm a floating F000 produces the best results for some structures but not for others (see section 11.2.3).
When the electron density is perturbed then a floating F000 often produces unfavourable oscillations in Rfactors. In general the electron density is best left unperturbed when scale_F000 is nonzero.
Example CF1A7YGABOR.INP does not seem to solve at a lower resolution, try for example:
delete_observed_reflections = D_spacing < 1.1;
On the other hand when scale_F000 is zero then electron density perturbations are possible; CF_1A7Y.INP solves 1a7y at 1.1 Angstrom (ie. include “delete_observed_reflections = D_spacing < 1.1”); CF_1A7Y.INP uses flip_regime_2 and the tangent formula.
11.2 Chargeflipping Investigations / Tutorials
The effects of CF keywords can be investigated by inclusion/exclusion of keywords or by changing equations. This section lists some investigative examples and highlights the use of keywords necessary to solve particular examples found in the CF directory.
11.2.1 Preventing uranium atom solutions using pick_atoms
Example CF1A7YOMIT.INP uses pick_atoms to modify the peaks of the highest intensity atoms as follows:
pick_atoms *
choose_to 5
omit = Rand(1, 1.1);
This example additionally uses the tangent formula and 1a7y solves in ~100 iterations and with a large contrast in Rfactors before and at converegnce. Another means to modify the peaks are:
pick_atoms *
choose_to 5
insert = Rand(.1, 1);
The insert case is slightly slower than the omit case as the 5 atoms are first omitted before insertion. Each case however solves 1a7y in a similar number of iterations.
Example CF1A7YNOTANGENT.INP is similar but without the tangent formula, 1a7y in this case solves in ~1000 iterations.
11.2.2 The tangent formula on powder data
In CFALVO4.INP comment out the Tangent line as follows:
‘ Tangent(.5, 50)
Run CFALVO4.INP and turn on Octahedra viewing in the OpenGL window. Visual inspection of picked atoms should show electron densities that are not recognizable as correct solutions.
Include the Tangent line and rerun; after a minute or two and at the bottom of the Ramps visual inspection of picked atoms should show a well defined solution.
Thus use of the tangent formula assists in solving CFALVO4.INP.
11.2.3 Pseudo symmetry – 441 atom oxide
CF works particularly well on pseudo symmetric structures (Oszlányi et el., 2006). Example CFPN02.INP is an oxide structure that contains 441 atom in the asymmetric unit (Lister et el., 2004); run CF to convergence. Pick atoms and turn on Octahedra viewing; all polyhedra should be well formed. Thus CF works extremely fast and trivializes the solving of such structures. The contents of the INP file is as follows:
charge_flipping
cf_hkl_file 020pn.hkl
space_group Pn
a 24.1332
b 19.5793
c 25.1091
be 99.962
fraction_reflections_weak 0.4
symmetry_obey_0_to_1 .3
Tangent(.25, 30)
load f_atom_type f_atom_quantity
{
MO = 42 2;
P = (126  42) 2;
O = (441  126) 2;
}
The tangent formula is used to assist symmetry_obey_0_to_1 and to assist in finding the solution faster; it is not necessary for this example however. The Oszlányi & Süto (2005) algorithm can be used by replaceing symmetry_obey_0_to_1 and the Tangent line with the following:
scale_F000 1
fraction_reflections_weak .4
add_to_phases_of_weak_reflections 90
user_threshold = 0.15 Get(max_density_at_cycle_iter_0);
Slow convergence is then observed and the reason is the use of F000. This is opposite to the case of 1a7y in CF1A7YGABOR.INP where F000 is necessary. Setting scale_F000 to zero greatly increases the rate of convergence.
11.2.4 Origin finding and symmetry_obey_0_to_1
When symmetry_obey_0_to_1 is defined origin finding is performed each iteration of charge flipping. Symmetry elements of the space group are used in finding an origin. On finding an origin the electron density is shifted to a position that best matches the symmetry of the space group. Additionally a restraint is placed on the electron density pixels forcing symmetry to be obeyed.
Run CFAE14.INP to convergence; notice the P1 symmetry. Remove symmetry_obey_0_to_1 and run to convergence; the origin should now be arbitrary.
11.2.5 symmetry_obey_0_to_1 on poor resolution data
Run CFAE5.INP until a solution is found; terminate CF, this saves the phase information to the file AE5.FC.
Copy AE5.FC to AE5SAVE.FC.
Place the following lines into the file CFAE5POOR.INP
set_initial_phases_to ae5save.fc
randomize_initial_phases_by 0
This simply starts CF with optimum phase values. Also include the following line:
symmetry_obey_0_to_1 .75
Run CFAE5POOR.INP; the atom positions after picking should visually produce the correct result. Comment out symmetry_obey_0_to_1 and rerun CFAE5POOR.INP. Rfactors should diverge and picked atoms should show a nonsolution. Thus symmetry_obey_0_to_1 assists in solving CFAE5POOR.INP.
Include symmetry_obey_0_to_1 and remove set_initial_phases_to and randomize_initial_phases_by and then rerun CFAE5POOR.INP. A solution should be obtained in a few minutes. Note that in this example the default flipping regime leads to regular occurrences of uranium atom solutions; this can be trivially ascertained by viewing the electron density. To reduce the occurrences of uranium atom solutions the following flipping regime is used:
flip_regime_3 0.5
11.2.6 Sharpening clouds  extend_calculated_sphere_to
Example CFAE9POOR.INP demonstrates the limit to which the present CF implementation can operate. Single crystal data is purposely chosen to isolate resolution effects and not intensity errors. The tangent formula is critical where without it the CF process is extremely perturbed and unstable. “flip_regime_3 .5” is used due to occurrences of uranium atom solutions.
There are no ramps, instead the CF process is restarted when the Rfactor fails to decrease for 100 consecutive iterations, or,
break_cycle_if_true = Get(iters_since_last_best) > 100;
randomize_phases_on_new_cycle_by = Rand(180, 180);
Half of the observed reflections are considered weak and additionally missing reflections up to 1 Angstrom are included and considered weak using:
fraction_reflections_weak 0.5
extend_calculated_sphere_to 1
The intensities of weak reflections are left untouched and instead a Pi/2 phase shift is randomly applied to ~30% of weak reflections as follows:
add_to_phases_of_weak_reflections = If(Rand(0, 1) < .3, 90, 0);
A symmetry_obey_0_to_1 of 0.7 is used not merely to find an origin but rather to prevent the electron density from straying.
Run CFAE9POOR.INP and a solution should be clearly recognizable after a few minutes. Change/remove keywords and rerun to view effects. Examples CFCIMEPOOR.INP and CFAE5POOR.INP are similar.
11.2.7 A difficult powder, CFSUCROSE.INP
CFSUCROSE.INP without scale_density_below_threshold=0 exhibits large oscillations in Rfactors resulting in difficult to identify solutions; this can be prevented by increasing the amount of charge flipped and including scale_density_below_threshold=0, for example
fraction_density_to_flip 0.83
scale_density_below_threshold 0
When scale_density_below_threshold=0 is used the percentage of charge that is less than the threshold before the application of scale_density_below_threshold is reported; the difference between this reported value and (1fraction_density_to_flip) gives the amount of flipped pixels that survived scale_density_below_threshold. At fraction_density_to_flip of 0.83 approximately 23% of pixels survives scale_density_below_threshold=0 which in effect means that only 23% of pixels are actually flipped out of the original 83%.
picked_atoms is used as a perturbation where 30% of atoms are omitted using:
pick_atoms *
activate = Cycle_Iter == 0;
insert = If(Rand(0, 1) > 0.3, 10, 0);
Note that atoms are inserted at an intensity that is 10 times the average intensity. This increases the weight of inserted atoms relative to electron density noise. It also initially gives more weight to weak reflections.
Use of scale_density_below_threshold often results in CF requiring more interations to solution; a solution however is preferable to no solution.
11.2.8 Increasing contrast in Rfactors
The act of flipping introduces an appreciable amount of unwanted high frequencies in the structure factors. This effect can be reduced by dampening high frequencies using apply_exp_scale which is ON by default. apply_exp_scale changes Rfactors and not phases, directions taken by CF are unchanged.
Run CF1A7Y.INP until convergence. The difference in Rfactors before and at convergence should be ~0.39 (ie. 0.81 and 0.42). Turn OFF apply_exp_scale by including the following line:
apply_exp_scale 0
Rerun CF1A7Y.INP until convergence. The difference in Rfactors before and at convergence should now be ~0.29 (ie. 0.81 and 0.52). Thus apply_exp_scale increases contrast in Rfactors. Note that most of the increase seems to be realized from dspacings less than 1 Angstrom.
11.3 Chargeflipping Examples
Table 11‑3. Examples found in the CF directory, Number of atoms corresponds to the number of nonhydrogen atoms within the asymmetric unit.  
Single crystal data  Number of atoms in asymmetric unit  Space group 
cf1a7y.inp cf1a7ygabor.inp cf1a7yomit.inp cf1a7ynotangent.inp  314  P1 
cfae14.inp  43  P1 
cfae5.inp cfae5poor.inp  23  C2/c 
cfae9.inp cfae9poor.inp  53  P1 
cfgebaa.inp  17  P4_{1}2_{1}2 
cfpn02.inp  441  Pn 
cfylidm.inp  17  P2_{1}2_{1}2_{1} 
Powder data  
cfalvo4.inp, cfalvo4pawley.inp  18  P1 
cfcimepawley.inp cfcime.inp, cfcimehisto.inp cfcimepoor.inp, cfcimepoorhisto.inp  17  P2_{1}/a 
cfsucrose.inp, cfsucrosepawley.inp  23  P2_{1} 
11.4 Keywords in detail
[add_to_cloud_N !E]
[add_to_cloud_when !E]
The current cloud is added to the GUI cloud creating a running average cloud for display purposes. add_to_cloud_N corresponds to the number of most recent clouds to include in the running average. add_to_cloud_when determines when the current cloud is to be included in the running average; here’s an example:
add_to_cloud_N 10
add_to_cloud_when = Mod(Cycle_Iter, 2);
Averaged clouds eliminate noise and is effective if the cloud remains stationery which is generally the case. Note that add_to_phases_of_weak_reflections can produce translations of the cloud and should not be included when averaging clouds.
[add_to_phases_of_weak_reflections !E]
Allows for modification to phases of weak reflections. For example, to add p/2 to the phases of weak reflections then the following could be used:
add_to_phases_of_weak_reflections 90
When add_to_phases_of_weak_reflections is defined then the intensities of weak reflections are not set to zero; instead they are left untouched meaning that their intensities are set to the values as determined by the inverse Fourier transform. See also scale_weak_reflections.
[apply_exp_scale !E]
Determines a and b each CF iteration such that the following is a minimum:
Rfactor = ∑ a Exp(b / D_spacing^2) Fc – Fo 
where Fc and Fo are the calculated and observed moduli respectively. Use of apply_exp_scale corrects Rfactors in case of an incorrect temperature factor correction as applied when normalizing structure factors. Use of apply_exp_scale typically increases the difference between Rfactors prior to and at convergence. apply_exp_scale is used by default, setting it to zero prevents its use.
[cf_hkl_file $file]
Defines the input hkl file.
[cf_in_A_matrix $file [scale_Aij !E] ]
Data input is from a file created using out_A_matrix from a previous Pawley refinement. The correlations in $file are used to partition intensities during each iteration of chargeflipping. This partitioning is applied to structure factors as used by CF and as used by the tangent formula.
scale_Aij can be used to modify the A matrix offdiagonal coefficients, here are some examples:
scale_Aij = Get(Aij);
scale_Aij = Get(Aij)^2; ‘ the default
scale_Aij = 0; ‘ Equivalent to using a Pawley generated hkl file
CF on powder data can also be initiated using standard hkl files.
[break_cycle_if_true !E]
Interrupts charge flipping to execute randomize_phases_on_new_cycle_by. Cycle_Iter is set to zero and Cycle is incremented.
[correct_for_atomic_scattering_factors !E]
Structure factors are normalized when nonzero and when f_atom_type’s are defined. By default structure factors are normalized.
[correct_for_temperature_effects !E]
Attempts to remove isotropic temperature effects from the structure factors. correct_for_temperature_effects is ON by default, setting it to zero will prevent the correction. Normalized structure factors are realized when correct_for_temperature_effects is ON and the unit cell contents is defined using f_atom_type and f_atom_quantity.
[delete_observed_reflections !E]
Reflections are deleted before entering CF according to delete_observed_reflections; it can be a function of D_spacing, for example:
delete_observed_reflections = D_spacing < 1.1;
Once deleted, observed reflections cannot be reinstated by changing min_d.
[extend_calculated_sphere_to !E]
Used to sharpen electron density clouds by filling in missing reflections; added reflections are given the status of “weak”. extend_calculated_sphere_to can be used in conjunction with scale_weak_reflections and add_to_phases_of_weak_reflections to modify “weak” reflection magnitudes and phases respectively (see section 11.2.6); here’s an example:
extend_calculated_sphere_to 1
add_to_phases_of_weak_reflections = If(Rand(0, 1) < .3, 90, 0);
[f_atom_type $type f_atom_quantity !E]…
Defines atom types and number of atoms within the unit cell; used by the tangent formula in determining E_{h} values and by the OpenGL display for picking atoms. For the tangent formula then realtive quantities are important.
[find_origin !E]
If defined and nonzero then origin finding is turned ON. symmetry_obey_0_to_1 defines find_origin by default. symmetry_obey_0_to_1 can be used without find_origin by defining and setting find_origin to zero.
[flip_equation !E]
Allwows for a user defined flip; here’s an example:
flip_equation =
If(Get(density) < Get(threshold), Get(density), Get(density));
[flip_regime_2 !E]
The elctron density is modified according to Eq. (11‑1) and then further modified using:
_{}flip_regime_2 is typically ramped from 1 to 0.
[flip_regime_3 !E]
The elctron density is modified according to Eq. (11‑1) and then further modified using:
_{}A value of 0.5 for flip_regime_3 introduces little perturbation whilst reducing the occurance of uranium atom solutions. It is recommended that flip_regime_3 be used in cases where flip_regime_2 produces uranium atom solutions. An additional perturbation, such as “add_to_phases_of_weak_reflections=90;” may be necessary.
[fraction_density_to_flip !E]
The amount of charge flipped is fractionally based. A value of 0.6, for example, sets the threshold d such that the sign of the lowest 60% of charge is changed. Get(threshold) can be used to retrieve d.
[fraction_reflections_weak !E]
Defines the fraction of observed reflections to flag as “weak”. When scale_weak_reflections, add_to_phases_of_weak_reflections and extend_calculated_sphere_to are all not defined then intensities of weak reflections are set to zero effectively removing them from the charge flipping process. Otherwise intensities of weak reflections are not set to zero; instead they are left untouched prior to scale_weak_reflections and add_to_phases_of_weak_reflections and space group family averaging.
[histogram_match_scale_fwhm !E]
[hm_size_limit_in_fwhm !E]
[hm_covalent_fwhm !E]
An implementation of Histogram Matching (Baerlocher et al., 2007) where the distribution of pixels within the unit cell is restrained to one that mathes Gaussian atoms with intensities corresponding to the atoms defined by f_atom_type‘s. The Histogram matching operation is performed when histogram_match_scale_fwhm evaluates to a nonzero value. Subsequently the full width at half maximum (FWHM) of the Gaussians (obtained from the file ATOM_RADIUS.DEF) is scaled by histogram_match_scale_fwhm. hm_size_limit_in_fwhm corresponds to the extent to which the Gaussians are calculated in units of FWHM. Covalent radii is used if hm_covalent_fwhm evaluates to a nonzero value otherwise ionic radii is used. An example use is as follows:
histogram_match_scale_fwhm = If(Mod(Cycle_Iter, 3), 0, 1);
hm_size_limit_in_fwhm 1
hm_covalent_fwhm 1
Reported on is the fraction of pixels modified; values of 1 for both histogram_match_scale_fwhm and hm_size_limit_in_fwhm seem optimal where typically ~15 to 20% of pixels are modified. Use of histogram matching should produce Rfactors at convergence that are equal to or than less Rfactors produced when not using histogram matching. Histogram matching sharpens the electron density cloud for data at poor resolution (see examples CFCIMEHISTO.INP and CFCIMEPOORHISTO.INP).
[min_d !E]
Determines in Angstroms the resolution of observed reflections to work with; only observed reflections with a dspacing above min_d are considered. min_d is evaluated each CF iteration. Get(num_observed_reflections_above_d_min) is updated when a change in min_d is detected. See also extend_calculated_sphere_to and delete_observed_reflections.
[min_grid_spacing !E]
If defined then the grid spacing used is set to the smaller of min_d/2 and min_grid_spacing; useful for obtaining many grid points for graphical purposes.
[neutron_data]
Signals that the input data is of neutron type. Used in the picking of atoms and additionally E_{h} values are not corrected from any defined f_atom_type and f_atom_quantity keywords.
[pick_atoms $atoms]…
[activate !E]
[choose_from !E]
[choose_to !E]
[choose_randomly !E]
[omit !E]
[displace !E]
[insert !E]
pick_atoms modifies the electron density based on picked atoms. $atom corresponds to the atom types to be operated on; it can contain the wild card character ‘*’ and the negation character ‘!’, see section 7.6 for details. The operations of pick_atoms are invoked when activate evaluates to a nonzero value; for example,
pick_atoms “O C”
activate = Mod(Cycle_Iter, 20) == 0;
The picking routine will attempts to locate the atom types found in $atom based on the intensities of picked atoms and the scattering power of the atoms defined in f_atom_type. For example,
load f_atom_type f_atom_quantity { Ca 2 O 10 C 12 }
pick_atoms “O C”
Here 2 Ca atoms are first picked and then 10 O atoms and then 12 C atoms. The picked atoms operated on will be the O and C atoms with the Ca atoms ignored.
choose_from and choose_to can be used to limit the number of atoms operated on. Note, that picked atoms within a particular pick_atoms are sorted in decreasing intensity order. For example, to not operate on the first thee O atoms and the last 2 C atoms then the following could be used:
choose_from 4
choose_to 20
choose_randomly further reduces the atoms operated on and is exected after choose_from and choose_to.
omit removes operated on atoms from the electron density. Atoms can be partially removed by setting omit to values less than 1. Values greater than 1 can also be used, the effect is to change the sign of the electron density. omit operating on a few of the highest intensity atoms is an extremely effective means of preventing the occurance of uranium atom solutions, see CF1A7YOMIT.INP; for example:
pick_atoms *
choose_to 5
omit = Rand(1, 1.1);
Omitting atoms randomly is a technique referred to as “random omit maps“ in ShelXD, (Schneider and Sheldrick, 2002).
insert inserts operated on atoms; a value of 1 inserts the atoms with an intensity that is equal to the average of the picked atoms. Values of less than 1 descreases the intensity of the inserted atoms. When insert is defined then omit is internally defined if it does not already exist. Thus, atoms are removed before insertion by default.
displace (in Angstroms) displaces atom positions from their picked positions; it is evaluated before insert. For example, to randomly displace atoms by 0.3 Angstroms then the following could be used:
displace = Rand(0.4, 0.6);
insert 1
There can be more than one occurance of pick_atoms, for example to limit uranium atom solutions then the follow can be used:
pick_atoms *
choose_to 5
insert = Rand(.1, 1);
To further randomly remove ~33% of atoms then the following could additionally be used:
break_cycle_if_true = Get(iters_since_last_best) > 10;
pick_atoms *
activate = Cycle_Iter == 0;
insert = If(Rand(0, 1) > 0.33, 10, 0);
Note that in this example atoms are inserted at ten times the average picked intensity; this simply gives more weight to picked atoms relative to electron density noise. Additionaly weak reflections are also given more weighting.
[pick_atoms_when !E]
Atoms are picked in the OpenGL display when pick_atoms_when evaluates to a nonzero value; here’s an example:
pick_atoms_when = Mod(Cycle_Iter + 1, 10) == 0;
Note that picking can be manually initiated from the Cloud dialog of the OpenGL display. A text description of picked atoms can be obtained by opening the “Temporary output” text window of the OpenGL window.
[randomize_initial_phases_by !E]
Initializes phases. To start a process with already saved phase information then the following could be used:
set_initial_phases_to aleady_saved.fc
randomize_initial_phases_by 0 ' this has a default of Rand(180,180)
[randomize_phases_on_new_cycle_by !E]
randomize_phases_on_new_cycle_by = Rand(180, 180); ‘ an example
[scale_density_below_threshold !E]
Electron density pixels that are less than the threshold value are scaled by scale_density_below_threshold. Values for scale_density_below_threshold thata re less than 1 tends to sharpen the electron density and to reduce large oscillations in Rfactors; the latter occurs for bad data, see example CFSUCROSE.INP. A value of zero for scale_density_below_threshold results in “low density elimination“ simlar to that of Shiono & Woolfson (1992).
[scale_E !E]
Normalized structure factors (E_{h} values) are a function of correct_for_temperature_effects and unit cell contents. scale_E allows for an additional scaling of E_{h} values.
[scale_F !E]
CF works with normalized structure factors by default. scale_F is an additional scaling of structure factors. The defualt scale_F broadens electron density peaks to avoid pixilation effects and is given by:
scale_F = Exp(0.2 Get(d_squared_inverse));
[scale_F000 !E]
Scale should be set to 1 for compliance with the algorithm of Oszlányi & Süto (2004). When scale_F000 is non_zero then modifcations to the electron density produces unfavourable effects.
[scale_weak_reflections !E]
By default weak reflection structure factors are set to zero; however when either scale_weak_reflections or add_to_phases_of_weak_reflections is defined then weak reflections structure factors are instead modified accordingly, for example:
scale_weak_reflections = Rand(0.2, 0.4);
scale_weak_reflections or add_to_phases_of_weak_reflections can be a function of D_spacing.
[set_initial_phases_to $file]
[modify_initial_phases !E]
Sets initial phases to those appearing in $file. Typically $file corresponds to a *.FC file saved in a previous chargeflipping process. modify_initial_phases is executed each iteration of CF; it can be used to restrain the phases of $file. For example,
modify_initial_phases =
Get(initial_phase) + Min(Abs(Get(phase_difference)), 45);
where phase_difference corresponds to the difference between the current phase and the initial phase; it has a value between ±90º. modify_initial_phases can be used to constrain phases to those as determined by HRTEM (Baerlocher et al., 2007).
[space_group $]
If defined then the cf_hkl_file is assumed to comprise merged hkls corresponding to the defined space group; otherwise the cf_hkl_file is assumed to be of space group type P1.
[symmetry_obey_0_to_1 !E]
If a space group is defined then symmetry is adhered to according to symmetry_obey_0_to_1. symmetry_obey_0_to_1 can be through of as a real space electron density restraint; its value should range between 0 and 1. If 1 then symmetry is obeyed 100%. symmetry_obey_0_to_1 is implemented follows:
For a particular set of equivalent grid points as determined by the equivalent positions of the space group an average density r_{avg} is obtained. The electron densities on the grid points are then adjusted as follows:
r_{new} = r (1  symmetry_obey_0_to_1) + symmetry_obey_0_to_1 r_{avg}
The text output 'symmetry error' as displayed when symmetry_obey_0_to_1 is used is defined as follows:
'symmetry error' = _{}
where the summation is over all of the electron density grid points.
symmetry_obey_0_to_1 defines find_origin by default. find_origin is applied before symmetry_obey_0_to_1. find_origin shifts the electron density such that an approximate error in 'symmetry error' is minimized; thus find_origin assists in the symmetry_obey_0_to_1 restraint.
[tangent_num_h_read !E]
[tangent_num_k_read !E]
[tangent_num_h_keep !E]
[tangent_max_triplets_per_h !E]
[tangent_min_triplets_per_h !E]
[tangent_scale_difference_by !E]
tangent_num_h_read and tangent_num_k_read defines the number of highest h and highest k reflections to read in determining triplets.
tangent_num_h_keep defines the number of highest h reflections to include for tangent formula updating.
tangent_max_triplets_per_h and tangent_min_triplets_per_h defines the maximum and minium number of triplets per reflection h. Reflections with less that tangent_min_triplets_per_h are not included for tangent formula updating.
tangent_scale_difference_by corresponds to S in the following:
_{} _{} _{} _{} _{}, _{}  (1) 
[user_threshold !E]
By default Get(threshold) is determined using fraction_density_to_flip. When defined then user_threshold overrides fraction_density_to_flip. Electron density pixels are normalized to have a maximum value of 1, thus typical values for user_threshold range between 0 and 0.1.
[use_Fc]
Sets initial phases to those saved in a previous *.FC file. The FC file used corresponds to the same name as the data file, defined using cf_hkl_file or cf_in_A_matrix, but with a FC extension. use_Fc is similar to set_initial_phases_to except that the file used is implied.
[verbose #]
A value of 1 outputs text in a verbose manner. A value of 0 outputs text only when a Rfactor less that a previous value is encountered within a particular Cyle.
[view_cloud !E]
Informs a detected GUI to display the electron density. Here are some examples:
view_cloud 1 ' Update cloud every chargeflipping iteration
view_cloud = Mod(Cycle_Iter, 10) == 0;
12 Indexing
The following algorithm is based on the iterative method of Coelho (2003). Unlike lp_serach it requires the extraction of dspacings. The INDEXING directory contains example INP files, for example:
index_zero_error
try_space_groups “2 75”
load index_d {
8.912
7.126
4.296
…
}
Individual space groups can be tried or for simplicity all of the Bravais lattices can be tried by placing them in the INP file using the standard macros as follows:
Bravais_Cubic_sgs
Bravais_Trigonal_Hexagonal_sgs
Bravais_Tetragonal_sgs
Bravais_Orthorhombic_sgs
Bravais_Monoclinic_sgs
Bravais_Triclinic_sgs
On termination of Indexing a *.NDX file is created with a name corresponding to the name of the INP file and placed in the same directory as the INP file. The *.NDX file contains solutions found as well as a detailed summary of the best 20 solutions. Here’s an example of an NDX file:
' Indexing method  Alan Coelho (2003), J. Appl. Cryst. 36, 8695
' Time: 2.015 seconds
'Sg Status UNI Vol Gof Zero Lps…
Indexing_Solutions_With_Zero_Error_2 {
0) P42/nmc 3 0 1187.321 38.82 0.0000 11.1924 …
1) P42/nmc 3 0 1187.057 38.64 0.0000 11.1896 …
2) P42/nmc 3 0 1187.458 38.61 0.0000 11.1914 …
…
}
/*
======================================================================
0) P1 0 985.652 30.80 0.0111 7.0877 …
h k l dc do dodc 2Thc 2Tho 2Tho2Thc
0 0 1 15.857 15.830 0.027 5.569 5.578 0.009
0 1 0 8.765 8.750 0.015 10.084 10.101 0.017
0 0 2 7.928 7.910 0.018 11.151 11.177 0.026
0 1 1 7.788 7.780 0.008 11.352 11.364 0.012
0 1 1 7.559 7.560 0.001 11.698 11.696 0.002
…
*/
12.1 Reprocessing solutions  DET files
Details of solutions can be obtained at a later stage by including solution lines found in the NDX file into the INP file. For example, supposing details of solutions 50 and 51 were sought then the following (see example INDEXING\EX10.INP) could be used:
index_lam 1.540596
index_zero_error
try_space_groups 2
Indexing_Solutions_With_Zero_Error_2 {
50) P1 1 0 2064.788 9.74 0.0000 …
51) P1 3 0 3128.349 9.61 0.0115 …
}
load index_d {
15.83 good
8.75
7.91
…
}
After running this INP file a *.DET file is created containing details of the supplied solutions.
12.2 Keywords and data structures
The data structures for indexing are as follows:
Tindexing
[index_min_lp !E2] [index_max_lp !E]
[index_max_number_of_solutions #3000]
[index_I E1 [good]]
[x_angle_scaler #0.1]
[x_scaler #]
Values for most keywords are automatically determined or have default values (appearing as numbers above) adequate for difficult indexing problems. In the following example from UPPW (service provided by Armel Le Bail to the SDPD mailing list at http://sdpd.univlemans.fr/uppw/) only a few keywords are necessary. Also note the use of the dummy keyword; this allows for the exclusion of 2q and I values without having to edit the columns of data.
seed
index_lam 0.79776
index_zero_error
index_max_Nc_on_No 6
try_space_groups 3
load index_th2 dummy dummy index_I dummy {
' d (A) 2Theta Height Area FWHM
1.724 26.50645 2758.3 23303.7 0.0450
2.646 17.27733 150393.8 747063.6 0.0250
3.235 14.13204 98668.8 493153.7 0.0250
3.417 13.37776 11102.6 53185.0 0.0250
5.190 8.80955 782.7 3910.9 0.0250
…
}
12.3 Keywords in detail
[index_lam !E1.540596]
Defines the wavelength in Å.
[index_min_lp !E2.5] [index_max_lp !E]
Defines the minimum and maximum allowed lattice parameters. Typically the maximum is determined automatically.
[index_max_Nc_on_No !E5]
Determines the maximum ratio of the number of calculated to observed lines. The value of 6 allows for up to 83% of missing lines.
[index_max_number_of_solutions #1000]
The number of best solutions to keep.
[index_max_th2_error !E0.05]
Used for determining impurity lines (unindexed lines UNI in *.NDX). Large values, 1 for example, forces the consideration of more observed input lines. For example if it is know that there are none or maybe just one impurity line then a large value for index_max_th2_error will speed up the indexing procedure.
[index_max_zero_error !E0.2]
Excludes solutions with zero errors greater than index_max_zero_error.
[index_th2 !E  index_d !E]…
[index_I E1 [good]]
index_th2 or index_d defines a reflection entry in 2q degrees or dspacing in Å.
index_I is typically set to the area under the peak; it is used to weight the reflection.
good signals that the corresponding dspacing is not an impurity line. A single use of good on a large dspacing decreases the number of possible solutions and hence speeds up the indexing process (see examples INDEXING\EX10.INP).
[index_x0 !E]
Defines X_{hh} in the reciprocal lattice equation:
_{}In a triclinic lattice the highest dspacing can probably be indexed as 100 or 200 etc. Thus
index_x0 = 1/(d_{max})^2;
speeds up the indexing process (if, in this case, the first line can be indexed as 100) and additionally the chances of finding the correct solution is enhanced. Example EX13.INP demonstrates this. Note that if the data is in 2Th degrees then the following can be used:
index_x0 = (2 Sin(2Th_{min} Pi/360) / wavelength))^2;
The two macros Index_x0_from_d and Index_x0_from_th2 simplify the use of index_x0.
[index_zero_error]
Includes a zero error.
[seed]
Seeds the random number generator.
[try_space_groups $]…
[x_angle_scaler #0.1]
[x_scaler #]
Defines the space groups to be searched. The macros Bravais_Cubic_sgs etc… (see TOPAS.INC) defines lowest symmetry Bravais space groups. It is almost always sufficient to use only these. Higher symmetry space groups for the Bravais lattices corresponding to the 10 best solutions is subsequently searched. Here are some examples of using try_space_groups.
Search  Use 
Primitive monoclinic  try_space_groups 3 
The two monoclinic Bravais lattices of lowest symmetry.  Bravais_Monoclinic_sgs 
Ccentered monoclinic of lowest symmetry.  try_space_groups 5 
All orthorhombic space groups individually.  Unique_Orthorhombic_sgs 
Below is a list showing which space groups have identical hkls in regards to powder data.
x_scaler is a scaling factor used for determining the number of steps to search in parameter space. x_scaler needs to be less than 1. Increasing x_scaler searches parameter space in finer detail. Default values are as follows:
Cubic 0.99
Hexagonal/Trigonal 0.95
Tetragonal 0.95
Orthorhombic 0.89
Monoclinic 0.85
Triclinic 0.72
x_angle_scaler is a scaling factor for determining the number of angular steps for monoclinic and triclinic space groups. Small values, 0.05 for example, increases the number of angular steps. The dult value of 0.1 is usually sufficient.
12.4 Identifying dominant zones
Here are two example output lines from an NDX file.
0) P42/nmc 3 0 1187.124 38.82 0.0000 11.1904 11.1904 9.4799 90.000 90.000 90.000 ' === 24 19
6) P421c 3 0 1187.124 35.67 0.0000 11.1904 11.1904 9.4799 90.000 90.000 90.000 ' === 24 19
Ø The 1^{st} column corresponds to the rank of the solution.
Ø The 2^{nd} corresponds to the space group.
Ø The 3^{rd} corresponds to the Status of the solution with meaning of the number as follows:
Status 1:  Weighting applied as defined in Coelho (2003)  
Status 2:  Zero error attempt applied  
Status 3:  Zero error attempt successful and impurity lines removal attempt successful  
Status 4:  Impurity line(s) removed 
Ø The 4^{th} column corresponds to the number of unindexed lines.
Ø The 5^{th} column corresponds to the volume of the lattice.
Ø The 6^{th} corresponds to the goodness of fit value.
Ø The 7^{th} corresponds to the zero error if index_zero_error is included.
Ø Columns 8 to 13 contains the lattice parameters.
The last 2 columns contain the number of nonzero h^{2} + k^{2} + h k and l^{2} values used in the indexed lines. These represent the hkl coefficient for X0 and X1 respectively for Trigonal/Hexagonal systems. When one of these numbers are zero then the corresponding lattice parameters is not represented and the number is therefore displayed as the negative number of –999. This facility is particularly useful for identifying dominant zones. For example, if the smallest lattice parameter is 3Å and the smallest dspacings is 4Å then it is impossible to determine the small lattice parameter. In these cases values of –999 will be obtained.
The following table gives the hkl coefficients corresponding to the X_{nn} reciprocal lattice parameters for the 7 crystal systems.
X0  X1  X2  X3  X4  X5  
Cubic  h^{2}+k^{2}+l^{2}  
Hexagonal Trigonal  h^{2}+k^{2}+h k  l^{2}  
Tetragonal  h^{2}+k^{2}  l^{2}  
Orhtorhombic  h^{2}  k^{2}  l^{2}  
Monoclinic  h^{2}  k^{2}  l^{2}  h l  
Triclinic  h^{2}  k^{2}  l^{2}  h k  h l  k l 
12.5 %%***%% Probable causes of Failure %%***%%
The most probable cause of failure is the inclusion of too many dspacings. If it is assumed that the smallest lattice parameter is greater than 3Å then it is problematic to include dspacings with values less than about 2.5Å when there are already 30 to 40 reflections with d values greater than 2.5Å. Some of the problems caused by very low dspacings are:
Ø The number of calculated lines increases dramatically and thus index_max_Nc_on_No will need to be increased.
Ø The low dspacings are probably inaccurate due to peak overlap at the high angles they are observed at.
A situation where it is necessary to include low dspacings is when there are only a few dspacings available as in higher symmetry lattices.
12.6 Unique space group hkls in Powder diffraction
Space group numbers with identical hkls  Space group symbols with identical hkls 
Triclinic  
1 2  P1 P1 
Monoclinic  
9 15  Cc C2/c 
5 8 12  C2 Cm C2/m 
14  P21/c 
7 13  Pc P2/c 
4 11  P21 P21/m 
3 6 10  P2 Pm P2/m 
Orthorhombic  
70  Fddd 
43  Fdd2 
22 42 69  F222 Fmm2 Fmmm 
68  Ccca 
73  Ibca 
37 66  Ccc2 Cccm 
45 72  Iba2 Ibam 
41 64  Aba2 Cmca 
46 74  Ima2 Imma 
36 40 63  Cmc21 Ama2 Cmcm 
39 67  Abm2 Cmma 
20  C2221 
23 24 44 71  I222 I212121 Imm2 Immm 
21 35 38 65  C222 Cmm2 Amm2 Cmmm 
52  Pnna 
56  Pccn 
60  Pbcn 
61  Pbca 
48  Pnnn 
54  Pcca 
50  Pban 
33 62  Pna21 Pnma 
34 58  Pnn2 Pnnm 
32 55  Pba2 Pbam 
30 53  Pnc2 Pmna 
29 57  Pca21 Pbcm 
27 49  Pcc2 Pccm 
31 59  Pmn21 Pmmn 
26 28 51  Pmc21 Pma2 Pmma 
19  P212121 
18  P21212 
17  P2221 
16 25 47  P222 Pmm2 Pmmm 
Tetragonal  
142  I41/acd 
110  I41cd 
141  I41/amd 
109 122  I41md I42d 
108 120 140  I4cm I4c2 I4/mcm 
88  I41/a 
80 98  I41 I4122 
79 82 87 97 107 119 121 139  I4 I4 I4/m I422 I4mm I4m2 I42m I4/mmm 
130  P4/ncc 
126  P4/nnc 
133  P42/nbc 
103 124  P4cc P 4/mcc 
104 128  P4nc P 4/mnc 
106 135  P42bc P 42/mbc 
137  P42/nmc 
138  P42/ncm 
134  P42/nnm 
125  P4/nbm 
114  P421c 
105 112 131  P42mc P42c P42/mmc 
102 118 136  P42nm P4n2 P42/mnm 
101 116 132  P42cm P4c2 P42/mcm 
100 117 127  P4bm P4b2 P4/mbm 
86  P42/n 
85 129  P4/n P4/nmm 
92 96  P41212 P43212 
94  P42212 
76 78 91 95  P41 P43 P4122 P4322 
77 84 93  P42 P 42/m P4222 
90 113  P4212 P421m 
75 81 83 89 99 111 115 123  P4 P4 P4/m P422 P4mm P42m P4m2 P4/mmm 
Trigonal & Hexagonal  
161 167  R3c R3c 
146 148 155 160 166  R3 R3 R32 R3m R3m 
184 192  P6cc P6/mcc 
159 163 186 190 194  P31c P31c P63mc P62c P63/mmc 
158 165 185 188 193  P3c1 P3c1 P63cm P6c2 P63/mcm 
169 170 178 179  P61 P65 P6122 P6522 
144 145 151 152 153 154 171 172 180 181  P31 P32 P3112 P3121 P3212 P3221 P62 P64 P6222 P6422 
173 176 182  P63 P63/m P6322 
143 147 149 150 156 157 162 164 168 174 175 177 183 187 189 191  P3 P3 P312 P321 P3m1 P31m P31m P3m1 P6 P6 P6/m P622 P6mm P6m2 P62m P6/mmm 
Cubic  
228  Fd3c 
219 226  F43c Fm3c 
203 227  Fd3 Fd3m 
210  F4132 
196 202 209 216 225  F23 Fm3 F432 F43m Fm3m 
230  Ia3d 
220  I43d 
206  Ia3 
214  I4132 
197 199 204 211 217 229  I23 I213 Im3 I432 I43m Im3m 
222  Pn3n 
218 223  P43n Pm3n 
201 224  Pn3 Pn3m 
205  Pa3 
212 213  P4332 P4132 
198 208  P213 P4232 
195 200 207 215 221  P23 Pm3 P432 P43m Pm3m 
12.7 Equations in Indexing  Background
a, b and c lattice vectors can be converted to Cartesian coordinates with a collinear with the Cartesian x axis and b coplanar with the Cartesian xy plane as follows:
a = a_{x} i b = b_{x} i + b_{y} j c = c_{x} i + c_{y} j + c_{z} k  (12‑1) 
where
a_{x} = a
b_{x} = b cos(g), b_{y} = b sin(g)
c_{x} = c cos(b), c_{y} = c (cos(a) – cos(b) cos(g)) / sin(g), c_{z}^{2} = c^{2}  (c_{x})^{2}– (c_{y})^{2}
a, b, c are the lattice parameters and a, b, g the lattice angles. The reciprocal lattice vectors A, B, and C calculated from the lattice vectors of Eq. (12‑1) become:
A= A_{x} i + A_{y} j + A_{z}k
B = B_{y} j + B_{z} k
C = C_{z}
The equation relating a particular dspacing d_{hkl} to a particular hkl in terms of the reciprocal lattice parameters is:
_{}  (12‑2) 
where
_{}_{}_{}_{}_{}_{}
13 Batch mode operation – TC.EXE
The command line program tc.exe provides for batch mode operation. Running tc.exe without arguments displays help information. Running an INP file is as follows:
tc pbso4
Macros can be passed to the command line. One use for this is to pass a file name to an INP file as follows:
1) Create a TEMPLATE.INP file with the required refinement details, this should look something like the following:
xdd FILE
etc…
2) TEMPLATE.INP is fed to tc.exe by command line and the word FILE (within TEMPLATE.INP) is expanded to whatever the macro on the command line is. For example,
tc …\file_directory\TEMPLATE.INP “macro FILE { file.xy }”
The macro called FILE is described on the command line within quotation marks. On running tc.exe the word 'FILE' occurring in TEMPATE.INP is expanded to 'file.xy'. Note that more than one macro can be described on the command line.
To process a whole directory of data files, say *.XY file for example, then:
1) From the file directory execute the DOS command:
dir *.xy > …\main_ta_directory\XY.BAT
The XY.BAT file will then reside in the main TA directory.
2) Edit …\main_ta_directory\XY.BAT to look like the following:
tc …\file_directory\template “macro FILE { file1.xy }”
copy …\file_directory\template.out …\file_directory\file1.out
tc …\file_directory\template.inp “macro FILE { file2.xy }”
copy …\file_directory\template.out …\file_directory\file2.out
etc….
After each run of tc.exe a TEMPLATE.OUT file is created containing refined results. This file is copied to another file “file1.out”, “file2.out” etc… in order to save it from being overwritten.
After running XY.BAT a number of *.OUT files is created one for each *.XY file.
In summary TC.EXE receives TEMPLATE.INP to process. Words occurring in TEMPLATE.INP are expanded depending on the macros described on the command line.
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